Publications

2016

Testing and Validation of Computational Methods for Mass Spectrometry.
Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A.
Journal of proteome research Volume 15 (2016) p.809-814

2016 update of the PRIDE database and its related tools.
Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.
Nucleic acids research Volume 44 (2016) p.D447-56

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.
Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y.
Bioinformatics (Oxford, England) Volume 32 (2016) p.821-827

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
Nucleic acids research Volume 44 (2016) p.W320-7

Gramene 2016: comparative plant genomics and pathway resources.
Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.
Nucleic acids research Volume 44 (2016) p.D1133-40

The Reactome pathway Knowledgebase.
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.
Nucleic acids research Volume 44 (2016) p.D481-7

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.
Molecular & cellular proteomics : MCP Volume 15 (2016) p.305-317

Improved definition of the mouse transcriptome via targeted RNA sequencing.
Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ.
Genome research Volume 26 (2016) p.705-716

Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.
Truszkowski J, Goldman N.
Systematic biology Volume 65 (2016) p.328-333

Association between DNA Methylation in Whole Blood and Measures of Glucose Metabolism: KORA F4 Study.
Kriebel J, Herder C, Rathmann W, Wahl S, Kunze S, Molnos S, Volkova N, Schramm K, Carstensen-Kirberg M, Waldenberger M, Gieger C, Peters A, Illig T, Prokisch H, Roden M, Grallert H.
PloS one Volume 11 (2016) p.e0152314

Sudden Cardiac Arrest and Rare Genetic Variants in the Community.
Milano A, Blom MT, Lodder EM, van Hoeijen DA, Barc J, Koopmann TT, Bardai A, Beekman L, Lichtner P, van den Berg MP, Wilde AA, Bezzina CR, Tan HL.
Circulation. Cardiovascular genetics Volume 9 (2016) p.147-153

Identification of a germline F692L drug resistance variant in cis with Flt3-ITD in knock-in mice.
Dovey OM, Chen B, Mupo A, Friedrich M, Grove CS, Cooper JL, Lee B, Varela I, Huang Y, Vassiliou GS.
Haematologica Volume (2016) p.

The FAIR Guiding Principles for scientific data management and stewardship.
Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.
Scientific data Volume 3 (2016) p.160018

The ORFeome Collaboration: a genome-scale human ORF-clone resource.
ORFeome Collaboration.
Nature methods Volume 13 (2016) p.191-192

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins.
McMahon AC, Rahman R, Jin H, Shen JL, Fieldsend A, Luo W, Rosbash M.
Cell Volume 165 (2016) p.742-753

Promiscuous or discriminating: Has the favored mRNA target of Fragile X Mental Retardation Protein been overlooked?
McMahon AC, Rosbash M.
Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.7009-7011

A high-content platform to characterise human induced pluripotent stem cell lines.
Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A, Stegle O, Kielty CM, HipSci Consortium, Durbin R, Watt FM, Danovi D.
Methods (San Diego, Calif.) Volume 96 (2016) p.85-96

Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Rakitsch B, Stegle O.
Genome biology Volume 17 (2016) p.33

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T.
PLoS computational biology Volume 12 (2016) p.e1004943

Ten Simple Rules for Selecting a Bio-ontology.
Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C.
PLoS computational biology Volume 12 (2016) p.e1004743

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.
Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M.
Cell reports Volume 14 (2016) p.648-661

GWAS for executive function and processing speed suggests involvement of the CADM2 gene.
Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann RS, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia SL, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp RG, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Generation Scotland, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen AJ, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH.
Molecular psychiatry Volume 21 (2016) p.189-197

ProbOnto: ontology and knowledge base of probability distributions.
Swat MJ, Grenon P, Wimalaratne S.
Bioinformatics (Oxford, England) Volume (2016) p.

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH.
Nature genetics Volume 48 (2016) p.427-437

Web-based volume slicer for 3D electron-microscopy data from EMDB.
Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A.
Journal of structural biology Volume 194 (2016) p.164-170

EMDataBank unified data resource for 3DEM.
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W.
Nucleic acids research Volume 44 (2016) p.D396-403

EMPIAR: a public archive for raw electron microscopy image data.
Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A.
Nature methods Volume 13 (2016) p.387-388

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N.
Nucleic acids research Volume 44 (2016) p.e77

Divergence in gene expression within and between two closely related flycatcher species.
Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H.
Molecular ecology Volume 25 (2016) p.2015-2028

Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution.
Fernández-Sampedro MA, Invergo BM, Ramon E, Bertranpetit J, Garriga P.
Scientific reports Volume 6 (2016) p.21570

SureChEMBL: a large-scale, chemically annotated patent document database.
Papadatos G, Davies M, Dedman N, Chambers J, Gaulton A, Siddle J, Koks R, Irvine SA, Pettersson J, Goncharoff N, Hersey A, Overington JP.
Nucleic acids research Volume 44 (2016) p.D1220-8

Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.
Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR.
Drug safety Volume 39 (2016) p.697-707

Focus on Extracellular Vesicles: Physiological Role and Signalling Properties of Extracellular Membrane Vesicles.
Iraci N, Leonardi T, Gessler F, Vega B, Pluchino S.
International journal of molecular sciences Volume 17 (2016) p.171

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.
Foulger RE, Denny P, Hardy J, Martin MJ, Sawford T, Lovering RC.
Neuroinformatics Volume 14 (2016) p.297-304

UniProt Tools.
Pundir S, Martin MJ, O'Donovan C, UniProt Consortium.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 53 (2016) p.1.29.1-1.29.15

The UniProtKB guide to the human proteome.
Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.
Nature methods Volume 13 (2016) p.425-430

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.
Nucleic acids research Volume 44 (2016) p.D746-52

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.
Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K.
Nucleic acids research Volume 44 (2016) p.D620-3

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.
Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T.
Oncotarget Volume 7 (2016) p.6693-6710

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.
BMC bioinformatics Volume 17 (2016) p.155

The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.
Chiapparino A, Maeda K, Turei D, Saez-Rodriguez J, Gavin AC.
Progress in lipid research Volume 61 (2016) p.30-39

Crowdsourcing biomedical research: leveraging communities as innovation engines.
Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G.
Nature reviews. Genetics Volume 17 (2016) p.470-486

A review of the new HGNC gene family resource.
Gray KA, Seal RL, Tweedie S, Wright MW, Bruford EA.
Human genomics Volume 10 (2016) p.6

Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.
Nature methods Volume 13 (2016) p.310-318

A multiple-phenotype imputation method for genetic studies.
Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J.
Nature genetics Volume 48 (2016) p.466-472

PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.
Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FS.
Nucleic acids research Volume 44 (2016) p.D663-8

FlyBase portals to human disease research using Drosophila models.
Millburn GH, Crosby MA, Gramates LS, Tweedie S, FlyBase Consortium.
Disease models & mechanisms Volume 9 (2016) p.245-252

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ.
Nucleic acids research Volume 44 (2016) p.D385-95

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.
Nature communications Volume 7 (2016) p.11778

Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics.
Harper AL, McKinney LV, Nielsen LR, Havlickova L, Li Y, Trick M, Fraser F, Wang L, Fellgett A, Sollars ES, Janacek SH, Downie JA, Buggs RJ, Kjær ED, Bancroft I.
Scientific reports Volume 6 (2016) p.19335

RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H.
Leukemia Volume (2016) p.

Genomic Classification and Prognosis in Acute Myeloid Leukemia.
Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O'Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Döhner K, Schlenk RF, Döhner H, Campbell PJ.
The New England journal of medicine Volume 374 (2016) p.2209-2221

Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.
Pancsa R, Varadi M, Tompa P, Vranken WF.
Nucleic acids research Volume 44 (2016) p.D429-34

The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome.
Satou Y, Miyazato P, Ishihara K, Yaguchi H, Melamed A, Miura M, Fukuda A, Nosaka K, Watanabe T, Rowan AG, Nakao M, Bangham CR.
Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.3054-3059

ncRNA orthologies in the vertebrate lineage.
Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.
Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R.
Biophysical journal Volume 110 (2016) p.372-381

Rapid dissemination of human T-lymphotropic virus type 1 during primary infection in transplant recipients.
Cook LB, Melamed A, Demontis MA, Laydon DJ, Fox JM, Tosswill JH, de Freitas D, Price AD, Medcalf JF, Martin F, Neuberger JM, Bangham CR, Taylor GP.
Retrovirology Volume 13 (2016) p.3

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood SA, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W.
Nature methods Volume 13 (2016) p.229-232

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.
Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP.
Genome biology Volume 17 (2016) p.45

Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting.
Kalman LV, Agúndez J, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Caudle K, Coulthard SA, Daly AK, Tredici AD, den Dunnen JT, Drozda K, Everts RE, Flockhart D, Freimuth RR, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale RF, van Schaik R, Whirl-Carrillo M, Yeo K, Zanger UM.
Clinical pharmacology and therapeutics Volume 99 (2016) p.172-185

WormBase 2016: expanding to enable helminth genomic research.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C, Harris TW, Kishore R, Lee R, Lomax J, Li Y, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Schindelman G, Stanley E, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW.
Nucleic acids research Volume 44 (2016) p.D774-80

Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR.
Oncotarget Volume 7 (2016) p.15648-15661

A Landscape of Pharmacogenomic Interactions in Cancer.
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LF, Saez-Rodriguez J, McDermott U, Garnett MJ.
Cell Volume (2016) p.

Multilevel models improve precision and speed of IC50 estimates.
Vis DJ, Bombardelli L, Lightfoot H, Iorio F, Garnett MJ, Wessels LF.
Pharmacogenomics Volume 17 (2016) p.691-700

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.
Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T.
Drug discovery today Volume 21 (2016) p.1063-1075

Metadata management for high content screening in OMERO.
Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR.
Methods (San Diego, Calif.) Volume 96 (2016) p.27-32

Consent Codes: Upholding Standard Data Use Conditions.
Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, Fiume M, Sherry ST.
PLoS genetics Volume 12 (2016) p.e1005772

Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC.
RNA (New York, N.Y.) Volume 22 (2016) p.667-676

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A.
Cell reports Volume 14 (2016) p.1246-1257

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.
Structure (London, England : 1993) Volume 24 (2016) p.502-508

The pig X and Y Chromosomes: structure, sequence, and evolution.
Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, Gilbert J, Austin-Guest S, Beal K, Carvalho-Silva D, Cheng W, Gordon D, Grafham D, Hardy M, Harley J, Hauser H, Howden P, Howe K, Lachani K, Ellis PJ, Kelly D, Kerry G, Kerwin J, Ng BL, Threadgold G, Wileman T, Wood JM, Yang F, Harrow J, Affara NA, Tyler-Smith C.
Genome research Volume 26 (2016) p.130-139

Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis.
Castillo-Quan JI, Li L, Kinghorn KJ, Ivanov DK, Tain LS, Slack C, Kerr F, Nespital T, Thornton J, Hardy J, Bjedov I, Partridge L.
Cell reports Volume 15 (2016) p.638-650

The genetic regulatory signature of type 2 diabetes in human skeletal muscle.
Scott LJ, Erdos MR, Huyghe JR, Welch RP, Beck AT, Wolford BN, Chines PS, Didion JP, Narisu N, Stringham HM, Taylor DL, Jackson AU, Vadlamudi S, Bonnycastle LL, Kinnunen L, Saramies J, Sundvall J, Albanus RD, Kiseleva A, Hensley J, Crawford GE, Jiang H, Wen X, Watanabe RM, Lakka TA, Mohlke KL, Laakso M, Tuomilehto J, Koistinen HA, Boehnke M, Collins FS, Parker SC.
Nature communications Volume 7 (2016) p.11764

The Ensembl Variant Effect Predictor.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.
Genome biology Volume 17 (2016) p.122

Ensembl regulation resources.
Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, Brent S, Amode R, Parker A, Trevanion S, Birney E, Dunham I, Flicek P.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering.
Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V.
Royal Society open science Volume 3 (2016) p.150484

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.
Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study, Wright CF.
Human molecular genetics Volume 25 (2016) p.927-935

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.
Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA.
Journal of molecular biology Volume 428 (2016) p.253-267

Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Finn R.
Nucleic acids research Volume 44 (2016) p.D343-50

The Dfam database of repetitive DNA families.
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ.
Nucleic acids research Volume 44 (2016) p.D81-9

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.
Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB.
PLoS computational biology Volume 12 (2016) p.e1004862

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.
Proteins Volume (2016) p.

The EMBL-EBI channel.
McEntyre J, Birney E.
F1000Research Volume 5 (2016) p.52

Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.
Kenyan Bacteraemia Study Group, Wellcome Trust Case Control Consortium 2 (WTCCC2), Rautanen A, Pirinen M, Mills TC, Rockett KA, Strange A, Ndungu AW, Naranbhai V, Gilchrist JJ, Bellenguez C, Freeman C, Band G, Bumpstead SJ, Edkins S, Giannoulatou E, Gray E, Dronov S, Hunt SE, Langford C, Pearson RD, Su Z, Vukcevic D, Macharia AW, Uyoga S, Ndila C, Mturi N, Njuguna P, Mohammed S, Berkley JA, Mwangi I, Mwarumba S, Kitsao BS, Lowe BS, Morpeth SC, Khandwalla I, Kilifi Bacteraemia Surveillance Group, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Deloukas P, Peltonen L, Williams TN, Scott JA, Chapman SJ, Donnelly P, Hill AV, Spencer CC.
American journal of human genetics Volume 98 (2016) p.1092-1100

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ Jr, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R.
Genome biology Volume 17 (2016) p.32

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.
Nature Volume 534 (2016) p.47-54

The topography of mutational processes in breast cancer genomes.
Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S.
Nature communications Volume 7 (2016) p.11383

Epigenome-wide Association Studies and the Interpretation of Disease -Omics.
Birney E, Smith GD, Greally JM.
PLoS genetics Volume 12 (2016) p.e1006105

Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803.
Hollingshead S, Kopečná J, Armstrong DR, Bučinská L, Jackson PJ, Chen GE, Dickman MJ, Williamson MP, Sobotka R, Hunter CN.
Frontiers in plant science Volume 7 (2016) p.292

Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.
Jupp S, Burdett T, Welter D, Sarntivijai S, Parkinson H, Malone J.
Journal of biomedical semantics Volume 7 (2016) p.17

libChEBI: an API for accessing the ChEBI database.
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P.
Journal of cheminformatics Volume 8 (2016) p.11

ChEBI in 2016: Improved services and an expanding collection of metabolites.
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C.
Nucleic acids research Volume 44 (2016) p.D1214-9

Data standards can boost metabolomics research, and if there is a will, there is a way.
Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S.
Metabolomics : Official journal of the Metabolomic Society Volume 12 (2016) p.14

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.
Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS.
Journal of proteome research Volume 15 (2016) p.360-373

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.
Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann SA, Swint-Kruse L.
Journal of molecular biology Volume 428 (2016) p.671-678

The European Bioinformatics Institute in 2016: Data growth and integration.
Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R.
Nucleic acids research Volume 44 (2016) p.D20-6

The Time Is Right to Focus on Model Organism Metabolomes.
Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR.
Metabolites Volume 6 (2016) p.

MetaboLights: An Open-Access Database Repository for Metabolomics Data.
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 53 (2016) p.14.13.1-14.13.18

Extending gene ontology in the context of extracellular RNA and vesicle communication.
Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC.
Journal of biomedical semantics Volume 7 (2016) p.19

Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.
Wagih O, Sugiyama N, Ishihama Y, Beltrao P.
Molecular & cellular proteomics : MCP Volume 15 (2016) p.236-245

Effects of Pin1 Loss in Hdh(Q111) Knock-in Mice.
Agostoni E, Michelazzi S, Maurutto M, Carnemolla A, Ciani Y, Vatta P, Roncaglia P, Zucchelli S, Leanza G, Mantovani F, Gustincich S, Santoro C, Piazza S, Del Sal G, Persichetti F.
Frontiers in cellular neuroscience Volume 10 (2016) p.110

The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.
PloS one Volume 11 (2016) p.e0154556

Reporting phenotypes in mouse models when considering body size as a potential confounder.
Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK, Karp NA.
Journal of biomedical semantics Volume 7 (2016) p.2

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J.
Journal of biomedical semantics Volume 7 (2016) p.8

Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells.
Rattay K, Meyer HV, Herrmann C, Brors B, Kyewski B.
Journal of autoimmunity Volume 67 (2016) p.65-75

MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.
Bioinformatics (Oxford, England) Volume 32 (2016) p.1905-1906

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.
Bolser D, Staines DM, Pritchard E, Kersey P.
Methods in molecular biology (Clifton, N.J.) Volume 1374 (2016) p.115-140

The Ensembl gene annotation system.
Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SM.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Tools and data services registry: a community effort to document bioinformatics resources.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.
Nucleic acids research Volume 44 (2016) p.D38-47

GENOMICS. A federated ecosystem for sharing genomic, clinical data.
Global Alliance for Genomics and Health.
Science (New York, N.Y.) Volume 352 (2016) p.1278-1280

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C.
Nature genetics Volume 48 (2016) p.593-599

PhytoPath: an integrative resource for plant pathogen genomics.
Pedro H, Maheswari U, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ.
Nucleic acids research Volume 44 (2016) p.D688-93

Biocuration of functional annotation at the European nucleotide archive.
Gibson R, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Pallreddy S, Pakseresht N, Rajan J, Rosselló M, Silvester N, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 44 (2016) p.D58-66

Value, but high costs in post-deposition data curation.
ten Hoopen P, Amid C, Buttigieg PL, Pafilis E, Bravakos P, Cerdeño-Tárraga AM, Gibson R, Kahlke T, Legaki A, Narayana Murthy K, Papastefanou G, Pereira E, Rossello M, Luisa Toribio A, Cochrane G.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Consolidating and Exploring Antibiotic Resistance Gene Data Resources.
Xavier BB, Das AJ, Cochrane G, De Ganck S, Kumar-Singh S, Aarestrup FM, Goossens H, Malhotra-Kumar S.
Journal of clinical microbiology Volume 54 (2016) p.851-859

The International Nucleotide Sequence Database Collaboration.
Cochrane G, Karsch-Mizrachi I, Takagi T, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 44 (2016) p.D48-50

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.
Rensch T, Villar D, Horvath J, Odom DT, Flicek P.
Genome biology Volume 17 (2016) p.139

The Evolutionary Fates of a Large Segmental Duplication in Mouse.
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, Pardo-Manuel de Villena F.
Genetics Volume (2016) p.

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.
Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC, Lagomorph Genomics Consortium.
The Journal of heredity Volume 107 (2016) p.295-308

Logical Modeling and Dynamical Analysis of Cellular Networks.
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.
Frontiers in genetics Volume 7 (2016) p.94

Ensembl Genomes 2016: more genomes, more complexity.
Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM.
Nucleic acids research Volume 44 (2016) p.D574-80

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Lun AT, Bach K, Marioni JC.
Genome biology Volume 17 (2016) p.75

Classification of low quality cells from single-cell RNA-seq data.
Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA.
Genome biology Volume 17 (2016) p.29

HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S.
Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.
Sangrador-Vegas A, Mitchell AL, Chang HY, Yong SY, Finn RD.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.
Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD.
Nucleic acids research Volume 44 (2016) p.D604-9

Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M.
Open biology Volume 6 (2016) p.

Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Vallejos CA, Richardson S, Marioni JC.
Genome biology Volume 17 (2016) p.70

Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins.
Huerta V, Ramos Y, Yero A, Pupo D, Martín D, Toledo P, Fleitas N, Gallien S, Martín AM, Márquez GJ, Pérez-Riverol Y, Sarría M, Guirola O, González LJ, Domon B, Chinea G.
Journal of proteomics Volume 131 (2016) p.205-213

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.
Nature communications Volume 7 (2016) p.10415

Ensembl 2016.
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P.
Nucleic acids research Volume 44 (2016) p.D710-6

UniProt-DAAC: Domain Architecture Alignment and Classification, a New Method for Automatic Functional Annotation in UniProtKB.
Doğan T, MacDougall A, Saidi R, Bateman A, O'Donovan C, Martin MJ.
Bioinformatics (Oxford, England) Volume (2016) p.

EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data.
Mitchell A, Bucchini F, Cochrane G, Denise H, ten Hoopen P, Fraser M, Pesseat S, Potter S, Scheremetjew M, Sterk P, Finn RD.
Nucleic acids research Volume 44 (2016) p.D595-603

The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A.
Nucleic acids research Volume 44 (2016) p.D279-85

Exploring the chemistry and evolution of the isomerases.
Martínez Cuesta S, Rahman SA, Thornton JM.
Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.1796-1801

Ten Simple Rules for Taking Advantage of Git and GitHub.
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.
PLoS computational biology Volume 12 (2016) p.e1004947

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Goolam M, Scialdone A, Graham SJ, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M.
Cell Volume 165 (2016) p.61-74

Exploring the potential of public proteomics data.
Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H.
Proteomics Volume 16 (2016) p.214-225

Resolving early mesoderm diversification through single-cell expression profiling.
Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B.
Nature Volume 535 (2016) p.289-293

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT.
PLoS genetics Volume 12 (2016) p.e1006024

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N.
F1000Research Volume 5 (2016) p.

Making sense of big data in health research: Towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.
Genome medicine Volume 8 (2016) p.71

2015

Gene Ontology Consortium: going forward.
Gene Ontology Consortium.
Nucleic acids research Volume 43 (2015) p.D1049-56

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E.
Journal of biomedical semantics Volume 6 (2015) p.10

Strong-field plasmonic photoemission in the mid-IR at <1 GW/cm² intensity.
Teichmann SM, Rácz P, Ciappina MF, Pérez-Hernández JA, Thai A, Fekete J, Elezzabi AY, Veisz L, Biegert J, Dombi P.
Scientific reports Volume 5 (2015) p.7584

UniProt: a hub for protein information.
UniProt Consortium.
Nucleic acids research Volume 43 (2015) p.D204-12

An atlas of mouse CD4(+) T cell transcriptomes.
Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA.
Biology direct Volume 10 (2015) p.14

Enhancer evolution across 20 mammalian species.
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT.
Cell Volume 160 (2015) p.554-566

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C.
BMC bioinformatics Volume 16 (2015) p.56

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.
Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P.
Genome biology Volume 16 (2015) p.178

Precision medicine: Look to the mice.
Lloyd KC, Meehan T, Beaudet A, Murray S, Svenson K, McKerlie C, West D, Morse I, Parkinson H, Brown S, Mallon AM, Moore M.
Science (New York, N.Y.) Volume 349 (2015) p.390

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM.
Nucleic acids research Volume 43 (2015) p.D1071-8

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.
Kafkas Ş, Kim JH, Pi X, McEntyre JR.
Journal of biomedical semantics Volume 6 (2015) p.1

Updates in Rhea--a manually curated resource of biochemical reactions.
Morgat A, Axelsen KB, Lombardot T, Alcántara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A.
Nucleic acids research Volume 43 (2015) p.D459-64

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN.
American journal of human genetics Volume 97 (2015) p.111-124

SpeckTackle: JavaScript charts for spectroscopy.
Beisken S, Conesa P, Haug K, Salek RM, Steinbeck C.
Journal of cheminformatics Volume 7 (2015) p.17

Spatiotemporal isolation of attosecond soft X-ray pulses in the water window.
Silva F, Teichmann SM, Cousin SL, Hemmer M, Biegert J.
Nature communications Volume 6 (2015) p.6611

Searching and Navigating UniProt Databases.
Pundir S, Magrane M, Martin MJ, O'Donovan C, UniProt Consortium.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 50 (2015) p.1.27.1-10

Key challenges for the creation and maintenance of specialist protein resources.
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.
Proteins Volume 83 (2015) p.1005-1013

The GOA database: gene Ontology annotation updates for 2015.
Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C.
Nucleic acids research Volume 43 (2015) p.D1057-63

The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD.
Nucleic acids research Volume 43 (2015) p.D213-21

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.
Ten Hoopen P, Pesant S, Kottmann R, Kopf A, Bicak M, Claus S, Deneudt K, Borremans C, Thijsse P, Dekeyzer S, Schaap DM, Bowler C, Glöckner FO, Cochrane G.
Standards in genomic sciences Volume 10 (2015) p.20

Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.
Nucleic acids research Volume 43 (2015) p.D130-7

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.
Raposo AA, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DL, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS.
Cell reports Volume (2015) p.

HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.
Nucleic acids research Volume 43 (2015) p.W30-8

The IPD and IMGT/HLA database: allele variant databases.
Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG.
Nucleic acids research Volume 43 (2015) p.D423-31

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.
Database : the journal of biological databases and curation Volume 2015 (2015) p.bav063

Epigenome data release: a participant-centered approach to privacy protection.
Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T.
Genome biology Volume 16 (2015) p.142

The ocean sampling day consortium.
Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO.
GigaScience Volume 4 (2015) p.27

RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium.
Nucleic acids research Volume 43 (2015) p.D123-9

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.
Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D, Teichmann SA, Betz AG.
PLoS genetics Volume 11 (2015) p.e1005251

Structure, dynamics, assembly, and evolution of protein complexes.
Marsh JA, Teichmann SA.
Annual review of biochemistry Volume 84 (2015) p.551-575

Structural and evolutionary versatility in protein complexes with uneven stoichiometry.
Marsh JA, Rees HA, Ahnert SE, Teichmann SA.
Nature communications Volume 6 (2015) p.6394

Principles of assembly reveal a periodic table of protein complexes.
Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA.
Science (New York, N.Y.) Volume 350 (2015) p.aaa2245

A mouse informatics platform for phenotypic and translational discovery.
Ring N, Meehan TF, Blake A, Brown J, Chen CK, Conte N, Di Fenza A, Fiegel T, Horner N, Jacobsen JO, Karp N, Lawson T, Mason JC, Matthews P, Morgan H, Relac M, Santos L, Smedley D, Sneddon D, Pengelly A, Tudose I, Warren JW, Westerberg H, Yaikhom G, Parkinson H, Mallon AM.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 26 (2015) p.413-421

European Adder bites in dogs in southern Germany. A retrospective study over a 6.5-year period.
Turković V, Teichmann S, Dörfelt R.
Tierarztliche Praxis. Ausgabe K, Kleintiere/Heimtiere Volume 43 (2015) p.221-230

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ.
Journal of integrative bioinformatics Volume 12 (2015) p.266

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.
Journal of integrative bioinformatics Volume 12 (2015) p.270

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.
Journal of integrative bioinformatics Volume 12 (2015) p.271

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.
Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Hummel M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenze D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nagel I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, ICGC MMML-Seq project, BLUEPRINT project, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B.
Nature genetics Volume 47 (2015) p.1316-1325

Biology, wet and dry.
Teichmann S, Pain E.
Science (New York, N.Y.) Volume 349 (2015) p.662

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P.
PLoS computational biology Volume 11 (2015) p.e1004362

Development of data representation standards by the human proteome organization proteomics standards initiative.
Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.
Journal of the American Medical Informatics Association : JAMIA Volume 22 (2015) p.495-506

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2903-2905

BioModels: Content, Features, Functionality, and Use.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.
CPT: pharmacometrics & systems pharmacology Volume 4 (2015) p.e3

BioModels: ten-year anniversary.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C.
Nucleic acids research Volume 43 (2015) p.D542-8

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.
Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI.
Nature genetics Volume 47 (2015) p.746-756

Genenames.org: the HGNC resources in 2015.
Gray KA, Yates B, Seal RL, Wright MW, Bruford EA.
Nucleic acids research Volume 43 (2015) p.D1079-85

The history of the CATH structural classification of protein domains.
Sillitoe I, Dawson N, Thornton J, Orengo C.
Biochimie Volume 119 (2015) p.209-217

The cardiovascular gene annotation initiative: Impact on data analysis
Lovering RC, Rodriguez-Lopez M, Campbell NH, Huntley RP, Sawford T, O’Donovan C, Orchard S, Hermjakob H, Martin M, Mayr M, Humphries SE, Talmud PJ.
Atherosclerosis Volume 241 (2015) p.e37

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.
Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS.
Metabolomics : Official journal of the Metabolomic Society Volume 11 (2015) p.872-894

Palmitoylation and palmitoyl-transferases in Plasmodium parasites.
Hodson N, Invergo B, Rayner JC, Choudhary JS.
Biochemical Society transactions Volume 43 (2015) p.240-245

Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins.
Invergo BM, Montanucci L, Bertranpetit J.
Proceedings. Biological sciences / The Royal Society Volume 282 (2015) p.20152215

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.
Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Russiñol N, Queirós AC, Beekman R, Rodríguez-Madoz JR, San José-Enériz E, Fang F, Gutiérrez NC, García-Verdugo JM, Robson MI, Schirmer EC, Guruceaga E, Martens JH, Gut M, Calasanz MJ, Flicek P, Siebert R, Campo E, Miguel JF, Melnick A, Stunnenberg HG, Gut IG, Prosper F, Martín-Subero JI.
Genome research Volume 25 (2015) p.478-487

A public repository for mass spectrometry imaging data.
Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA.
Analytical and bioanalytical chemistry Volume 407 (2015) p.2027-2033

Identification of artesunate as a specific activator of ferroptosis in pancreatic cancer cells.
Eling N, Reuter L, Hazin J, Hamacher-Brady A, Brady NR.
Oncoscience Volume 2 (2015) p.517-532

Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters.
Li P, Seneviratne CJ, Alpi E, Vizcaino JA, Jin L.
Antimicrobial agents and chemotherapy Volume 59 (2015) p.6101-6112

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N.
Nucleic acids research Volume 43 (2015) p.W15-23

Identifying novel sequence variants of RNA 3D motifs.
Zirbel CL, Roll J, Sweeney BA, Petrov AI, Pirrung M, Leontis NB.
Nucleic acids research Volume 43 (2015) p.7504-7520

Emerging Drug Target In Pancreatic Cancer: Placing Sirtuin 1 on the Canvas.
Giry-Laterriere M, Pinho AV, Eling N, Chantrill L, Rooman I.
Current cancer drug targets Volume 15 (2015) p.463-468

Expression data analysis with Reactome.
Jupe S, Fabregat A, Hermjakob H.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 49 (2015) p.8.20.1-9

Proteomics data visualisation.
Vizcaíno JA, Barsnes H, Hermjakob H.
Proteomics Volume 15 (2015) p.1339-1340

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS.
Journal of proteome research Volume 14 (2015) p.3415-3431

Collaborative computational project for electron cryo-microscopy.
Wood C, Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M.
Acta crystallographica. Section D, Biological crystallography Volume 71 (2015) p.123-126

A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.
Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H.
Proteomics Volume 15 (2015) p.1390-1404

Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P.
Plant & cell physiology Volume 56 (2015) p.e3

Predicting malignancy from mammography findings and image-guided core biopsies.
Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.
International journal of data mining and bioinformatics Volume 11 (2015) p.257-276

Efficient set tests for the genetic analysis of correlated traits.
Casale FP, Rakitsch B, Lippert C, Stegle O.
Nature methods Volume 12 (2015) p.755-758

Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
Brage S, Westgate K, Franks PW, Stegle O, Wright A, Ekelund U, Wareham NJ.
PloS one Volume 10 (2015) p.e0137206

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.342-346

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.44-55

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage.
Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D.
PLoS genetics Volume 11 (2015) p.e1004920

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.
Reimand J, Wagih O, Bader GD.
PLoS genetics Volume 11 (2015) p.e1004919

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Wagih O, Reimand J, Bader GD.
Nature methods Volume 12 (2015) p.531-533

INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.
INFRAFRONTIER Consortium.
Nucleic acids research Volume 43 (2015) p.D1171-5

Operon and non-operon gene clusters in the C. elegans genome.
Blumenthal T, Davis P, Garrido-Lecca A.
WormBook : the online review of C. elegans biology Volume (2015) p.1-20

Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism.
Patel S, Roncaglia P, Lovering RC.
BMC bioinformatics Volume 16 (2015) p.186

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.
Metabolomics : Official journal of the Metabolomic Society Volume 11 (2015) p.1587-1597

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.
Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW, GOBLET Consortium.
PLoS computational biology Volume 11 (2015) p.e1004143

Europe: Lifelong learning for all in biomedicine.
Brooksbank C, Johnson C.
Nature Volume 524 (2015) p.415

Avianbase: a community resource for bird genomics.
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Genome biology Volume 16 (2015) p.21

The genome of the vervet (Chlorocebus aethiops sabaeus).
Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GW, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB.
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A random forest approach to capture genetic effects in the presence of population structure.
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Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.
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Extending reference assembly models.
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Third Report on Chicken Genes and Chromosomes 2015.
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The Importance of Biological Databases in Biological Discovery.
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Biological psychiatry Volume 77 (2015) p.749-763

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
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eLife Volume 4 (2015) p.e05255

The Classification and Evolution of Enzyme Function.
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Biophysical journal Volume 109 (2015) p.1082-1086

Applying the ARRIVE Guidelines to an In Vivo Database.
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PLoS biology Volume 13 (2015) p.e1002151

Domain atrophy creates rare cases of functional partial protein domains.
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Genome biology Volume 16 (2015) p.88

Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
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The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
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MinION Analysis and Reference Consortium: Phase 1 data release and analysis.
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CATH: comprehensive structural and functional annotations for genome sequences.
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Using human genetics to make new medicines.
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Nature reviews. Genetics Volume 16 (2015) p.561-562

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
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Bioinformatics (Oxford, England) Volume 31 (2015) p.1274-1278

Increased brain activation during working memory processing after pediatric mild traumatic brain injury (mTBI).
Westfall DR, West JD, Bailey JN, Arnold TW, Kersey PA, Saykin AJ, McDonald BC.
Journal of pediatric rehabilitation medicine Volume 8 (2015) p.297-308

Towards recommendations for metadata and data handling in plant phenotyping.
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Journal of experimental botany Volume 66 (2015) p.5417-5427

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, Rayner NW, Robertson N, Scott RA, Prokopenko I, Scott LJ, Green T, Sparso T, Thuillier D, Yengo L, Grallert H, Wahl S, Frånberg M, Strawbridge RJ, Kestler H, Chheda H, Eisele L, Gustafsson S, Steinthorsdottir V, Thorleifsson G, Qi L, Karssen LC, van Leeuwen EM, Willems SM, Li M, Chen H, Fuchsberger C, Kwan P, Ma C, Linderman M, Lu Y, Thomsen SK, Rundle JK, Beer NL, van de Bunt M, Chalisey A, Kang HM, Voight BF, Abecasis GR, Almgren P, Baldassarre D, Balkau B, Benediktsson R, Blüher M, Boeing H, Bonnycastle LL, Bottinger EP, Burtt NP, Carey J, Charpentier G, Chines PS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Doney AS, Dorkhan M, Edkins S, Eriksson JG, Esko T, Eury E, Fadista J, Flannick J, Fontanillas P, Fox C, Franks PW, Gertow K, Gieger C, Gigante B, Gottesman O, Grant GB, Grarup N, Groves CJ, Hassinen M, Have CT, Herder C, Holmen OL, Hreidarsson AB, Humphries SE, Hunter DJ, Jackson AU, Jonsson A, Jørgensen ME, Jørgensen T, Kao WH, Kerrison ND, Kinnunen L, Klopp N, Kong A, Kovacs P, Kraft P, Kravic J, Langford C, Leander K, Liang L, Lichtner P, Lindgren CM, Lindholm E, Linneberg A, Liu CT, Lobbens S, Luan J, Lyssenko V, Männistö S, McLeod O, Meyer J, Mihailov E, Mirza G, Mühleisen TW, Müller-Nurasyid M, Navarro C, Nöthen MM, Oskolkov NN, Owen KR, Palli D, Pechlivanis S, Peltonen L, Perry JR, Platou CG, Roden M, Ruderfer D, Rybin D, van der Schouw YT, Sennblad B, Sigurðsson G, Stančáková A, Steinbach G, Storm P, Strauch K, Stringham HM, Sun Q, Thorand B, Tikkanen E, Tonjes A, Trakalo J, Tremoli E, Tuomi T, Wennauer R, Wiltshire S, Wood AR, Zeggini E, Dunham I, Birney E, Pasquali L, Ferrer J, Loos RJ, Dupuis J, Florez JC, Boerwinkle E, Pankow JS, van Duijn C, Sijbrands E, Meigs JB, Hu FB, Thorsteinsdottir U, Stefansson K, Lakka TA, Rauramaa R, Stumvoll M, Pedersen NL, Lind L, Keinanen-Kiukaanniemi SM, Korpi-Hyövälti E, Saaristo TE, Saltevo J, Kuusisto J, Laakso M, Metspalu A, Erbel R, Jöcke KH, Moebus S, Ripatti S, Salomaa V, Ingelsson E, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Koistinen H, Tuomilehto J, Hveem K, Njølstad I, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, de Faire U, Hamsten A, Illig T, Peters A, Cauchi S, Sladek R, Froguel P, Hansen T, Pedersen O, Morris AD, Palmer CN, Kathiresan S, Melander O, Nilsson PM, Groop LC, Barroso I, Langenberg C, Wareham NJ, O'Callaghan CA, Gloyn AL, Altshuler D, Boehnke M, Teslovich TM, McCarthy MI, Morris AP, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.
Nature genetics Volume 47 (2015) p.1415-1425

Nomenclature of Toso, Fas apoptosis inhibitory molecule 3, and IgM FcR.
Kubagawa H, Carroll MC, Jacob CO, Lang KS, Lee KH, Mak T, McAndrews M, Morse HC 3rd, Nolan GP, Ohno H, Richter GH, Seal R, Wang JY, Wiestner A, Coligan JE.
Journal of immunology (Baltimore, Md. : 1950) Volume 194 (2015) p.4055-4057

Progress in Medicine: Experts Take Stock.
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PLoS medicine Volume 12 (2015) p.e1001933

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.
Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N.
PLoS computational biology Volume 11 (2015) p.e1004546

Human genomics: The end of the start for population sequencing.
Birney E, Soranzo N.
Nature Volume 526 (2015) p.52-53

Improving the Sequence Ontology terminology for genomic variant annotation.
Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K.
Journal of biomedical semantics Volume 6 (2015) p.32

DREAMTools: a Python package for scoring collaborative challenges.
Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.
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Computational and analytical challenges in single-cell transcriptomics.
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Nature reviews. Genetics Volume 16 (2015) p.133-145

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA.
Cell stem cell Volume 17 (2015) p.471-485

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S.
PLoS computational biology Volume 11 (2015) p.e1004333

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
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Nature communications Volume 6 (2015) p.8687

Prediction of human population responses to toxic compounds by a collaborative competition.
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Nature biotechnology Volume 33 (2015) p.933-940

Analysis of the tryptic search space in UniProt databases.
Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Ríos D, O'Donovan C, Vizcaíno JA, Martin MJ.
Proteomics Volume 15 (2015) p.48-57

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
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Science (New York, N.Y.) Volume 347 (2015) p.1258522

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.
Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira PG, Asher CL, Jurkowski TP, Segonds-Pichon A, Bachman M, González-Navarrete I, Minoche AE, Krueger F, Lowy E, Marcet-Houben M, Rodriguez-Ales JL, Nascimento FS, Balasubramanian S, Gabaldon T, Tarver JE, Andrews S, Himmelbauer H, Hughes WO, Guigó R, Reik W, Sumner S.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.13970-13975

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D.
Nucleic acids research Volume 43 (2015) p.D707-13

App for the calculation of blood lactate markers.
Newell J, Korir P, Moore B, Pedlar C.
Journal of sports sciences Volume 33 (2015) p.568-569

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.
Hostaš J, Jakubec D, Laskowski RA, Gnanasekaran R, Řezáč J, Vondrášek J, Hobza P.
Journal of chemical theory and computation Volume 11 (2015) p.4086-4092

The UK10K project identifies rare variants in health and disease.
UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CM, Timpson NJ, Durbin R, Soranzo N.
Nature Volume 526 (2015) p.82-90

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF, UK10K Consortium, Gambaro G, Richards JB, Durbin R, Timpson NJ, Marchini J, Soranzo N.
Nature communications Volume 6 (2015) p.8111

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.
Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB.
Frontiers in genetics Volume 6 (2015) p.197

Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion.
Schwarz RF, Branicky R, Grundy LJ, Schafer WR, Brown AE.
PLoS computational biology Volume 11 (2015) p.e1004322

Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.
Schwarz RF, Ng CK, Cooke SL, Newman S, Temple J, Piskorz AM, Gale D, Sayal K, Murtaza M, Baldwin PJ, Rosenfeld N, Earl HM, Sala E, Jimenez-Linan M, Parkinson CA, Markowetz F, Brenton JD.
PLoS medicine Volume 12 (2015) p.e1001789

Whole-genome sequence-based analysis of thyroid function.
Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Davey Smith G, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG, UK0K Consortium.
Nature communications Volume 6 (2015) p.5681

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.
Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK.
Bioinformatics (Oxford, England) Volume 31 (2015) p.140-142

A contribution to the rational design of Ru(CO)3Cl2L complexes for in vivo delivery of CO.
Seixas JD, Santos MF, Mukhopadhyay A, Coelho AC, Reis PM, Veiros LF, Marques AR, Penacho N, Gonçalves AM, Romão MJ, Bernardes GJ, Santos-Silva T, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 44 (2015) p.5058-5075

PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.
Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA.
PloS one Volume 10 (2015) p.e0131274

Behavioural and molecular endophenotypes in psychotic disorders reveal heritable abnormalities in glutamatergic neurotransmission.
Scoriels L, Salek RM, Goodby E, Grainger D, Dean AM, West JA, Griffin JL, Suckling J, Nathan PJ, Lennox BR, Murray GK, Bullmore ET, Jones PB.
Translational psychiatry Volume 5 (2015) p.e540

Getting the right answers: understanding metabolomics challenges.
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Expert review of molecular diagnostics Volume 15 (2015) p.97-109

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.
Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.
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Data integration in biological research: an overview.
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Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited.
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Towards the computational design of protein post-translational regulation.
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Bioorganic & medicinal chemistry Volume 23 (2015) p.2877-2882

Expression change in Angiopoietin-1 underlies change in relative brain size in fish.
Chen YC, Harrison PW, Kotrschal A, Kolm N, Mank JE, Panula P.
Proceedings. Biological sciences / The Royal Society Volume 282 (2015) p.

Differential genetic interactions of yeast stress response MAPK pathways.
Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ.
Molecular systems biology Volume 11 (2015) p.800

BetaCavityWeb: a webserver for molecular voids and channels.
Kim JK, Cho Y, Lee M, Laskowski RA, Ryu SE, Sugihara K, Kim DS.
Nucleic acids research Volume 43 (2015) p.W413-8

Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK, Geeleher P, Seoighe C.
BMC bioinformatics Volume 16 (2015) p.286

Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution.
Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE.
Molecular ecology Volume 24 (2015) p.1218-1235

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.
Dean R, Harrison PW, Wright AE, Zimmer F, Mank JE.
Molecular biology and evolution Volume 32 (2015) p.2646-2656

Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation.
Wright AE, Zimmer F, Harrison PW, Mank JE.
Genetics Volume 201 (2015) p.587-598

Origin of the response to adrenal and sex steroids: Roles of promiscuity and co-evolution of enzymes and steroid receptors.
Baker ME, Nelson DR, Studer RA.
The Journal of steroid biochemistry and molecular biology Volume 151 (2015) p.12-24

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.
Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D.
PloS one Volume 10 (2015) p.e0130600

Sexual selection drives evolution and rapid turnover of male gene expression.
Harrison PW, Wright AE, Zimmer F, Dean R, Montgomery SH, Pointer MA, Mank JE.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.4393-4398

BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model.
Perna D, Karreth FA, Rust AG, Perez-Mancera PA, Rashid M, Iorio F, Alifrangis C, Arends MJ, Bosenberg MW, Bollag G, Tuveson DA, Adams DJ.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E536-45

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM.
PloS one Volume 10 (2015) p.e0139446

Inflammaging and cancer: a challenge for the Mediterranean diet.
Ostan R, Lanzarini C, Pini E, Scurti M, Vianello D, Bertarelli C, Fabbri C, Izzi M, Palmas G, Biondi F, Martucci M, Bellavista E, Salvioli S, Capri M, Franceschi C, Santoro A.
Nutrients Volume 7 (2015) p.2589-2621

Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC.
Journal of cheminformatics Volume 7 (2015) p.31

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia.
De Fanti S, Barbieri C, Sarno S, Sevini F, Vianello D, Tamm E, Metspalu E, van Oven M, Hübner A, Sazzini M, Franceschi C, Pettener D, Luiselli D.
PloS one Volume 10 (2015) p.e0144391

The ensembl regulatory build.
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR.
Genome biology Volume 16 (2015) p.56

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW.
Scientific reports Volume 5 (2015) p.11487

Verifying the fully "Laplacianised" posterior Naive Bayesian approach and more.
Mussa HY, Marcus D, Mitchell JB, Glen RC.
Journal of cheminformatics Volume 7 (2015) p.27

Genome3D: exploiting structure to help users understand their sequences.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.
Nucleic acids research Volume 43 (2015) p.D382-6

Kinase-two-hybrid: towards the conditional interactome.
Ochoa D, Beltrao P.
Molecular systems biology Volume 11 (2015) p.798

The Ensembl REST API: Ensembl Data for Any Language.
Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GR, Ruffier M, Taylor K, Vullo A, Flicek P.
Bioinformatics (Oxford, England) Volume 31 (2015) p.143-145

Detection of significant protein coevolution.
Ochoa D, Juan D, Valencia A, Pazos F.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2166-2173

Ensembl 2015.
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P.
Nucleic acids research Volume 43 (2015) p.D662-9

Bacteria and the evolution of honest signals. The case of ornamental throat feathers in spotless starlings
Ruiz‐Rodríguez M, Tomás G, Martín‐Gálvez D, Ruiz‐Castellano C, Soler JJ, McGraw K.
Functional ecology. Volume 29 (2015) p.701-709

Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B.
Journal of computational biology : a journal of computational molecular cell biology Volume 22 (2015) p.387-401

The BioMart community portal: an innovative alternative to large, centralized data repositories.
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.
Nucleic acids research Volume 43 (2015) p.W589-98

Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F.
Methods (San Diego, Calif.) Volume 85 (2015) p.54-61

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.
Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B.
Genome research Volume 25 (2015) p.41-56

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL.
BMC genomics Volume 16 (2015) p.982

Shared resources, shared costs--leveraging biocuration resources.
Orchard S, Hermjakob H.
Database : the journal of biological databases and curation Volume 2015 (2015) p.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O.
Nature biotechnology Volume 33 (2015) p.155-160

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.
Lowe R, Slodkowicz G, Goldman N, Rakyan VK.
Epigenetics Volume 10 (2015) p.274-281

The relationship between target-class and the physicochemical properties of antibacterial drugs.
Mugumbate G, Overington JP.
Bioorganic & medicinal chemistry Volume 23 (2015) p.5218-5224

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.
Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW.
Scientific reports Volume 5 (2015) p.18178

PomBase 2015: updates to the fission yeast database.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V.
Nucleic acids research Volume 43 (2015) p.D656-61

RSAT 2015: Regulatory Sequence Analysis Tools.
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.
Nucleic acids research Volume 43 (2015) p.W50-6

Synthesis and structure-activity-relationship studies of thiazolidinediones as antiplasmodial inhibitors of the Plasmodium falciparum cysteine protease falcipain-2.
Sharma RK, Younis Y, Mugumbate G, Njoroge M, Gut J, Rosenthal PJ, Chibale K.
European journal of medicinal chemistry Volume 90 (2015) p.507-518

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.
Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C.
Cancer research Volume 75 (2015) p.194-202

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.
Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J.
BMC microbiology Volume 15 (2015) p.146

Update of the human and mouse Fanconi anemia genes.
Dong H, Nebert DW, Bruford EA, Thompson DC, Joenje H, Vasiliou V.
Human genomics Volume 9 (2015) p.32

The technology and biology of single-cell RNA sequencing.
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA.
Molecular cell Volume 58 (2015) p.610-620

Eyeing the Cyr61/CTGF/NOV (CCN) group of genes in development and diseases: highlights of their structural likenesses and functional dissimilarities.
Krupska I, Bruford EA, Chaqour B.
Human genomics Volume 9 (2015) p.24

Devising a Consensus Framework for Validation of Novel Human Coding Loci.
Bruford EA, Lane L, Harrow J.
Journal of proteome research Volume 14 (2015) p.4945-4948

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC.
Nature biotechnology Volume 33 (2015) p.503-509

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR.
Genome biology Volume 16 (2015) p.201

Section level search functionality in Europe PMC.
Kafkas Ş, Pi X, Marinos N, Talo' F, Morrison A, McEntyre JR.
Journal of biomedical semantics Volume 6 (2015) p.7

Prospective derivation of a living organoid biobank of colorectal cancer patients.
van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.
Cell Volume 161 (2015) p.933-945

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.
Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP.
Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.904-920

Pharmacogenomic agreement between two cancer cell line data sets.
Cancer Cell Line Encyclopedia Consortium, Genomics of Drug Sensitivity in Cancer Consortium.
Nature Volume 528 (2015) p.84-87

Unravelling druggable signalling networks that control F508del-CFTR proteostasis.
Hegde RN, Parashuraman S, Iorio F, Ciciriello F, Capuani F, Carissimo A, Carrella D, Belcastro V, Subramanian A, Bounti L, Persico M, Carlile G, Galietta L, Thomas DY, Di Bernardo D, Luini A.
eLife Volume 4 (2015) p.

Blood transcriptomics of drug-naive sporadic Parkinson's disease patients.
Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S.
BMC genomics Volume 16 (2015) p.876

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.
Structure (London, England : 1993) Volume 23 (2015) p.1156-1167

Longevity GWAS Using the Drosophila Genetic Reference Panel.
Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM.
The journals of gerontology. Series A, Biological sciences and medical sciences Volume 70 (2015) p.1470-1478

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.
Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P.
Genome research Volume 25 (2015) p.167-178

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.
Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.5437-5442

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.
Hrabě de Angelis M, Nicholson G, Selloum M, White JK, Morgan H, Ramirez-Solis R, Sorg T, Wells S, Fuchs H, Fray M, Adams DJ, Adams NC, Adler T, Aguilar-Pimentel A, Ali-Hadji D, Amann G, André P, Atkins S, Auburtin A, Ayadi A, Becker J, Becker L, Bedu E, Bekeredjian R, Birling MC, Blake A, Bottomley J, Bowl MR, Brault V, Busch DH, Bussell JN, Calzada-Wack J, Cater H, Champy MF, Charles P, Chevalier C, Chiani F, Codner GF, Combe R, Cox R, Dalloneau E, Dierich A, Di Fenza A, Doe B, Duchon A, Eickelberg O, Esapa CT, Fertak LE, Feigel T, Emelyanova I, Estabel J, Favor J, Flenniken A, Gambadoro A, Garrett L, Gates H, Gerdin AK, Gkoutos G, Greenaway S, Glasl L, Goetz P, Da Cruz IG, Götz A, Graw J, Guimond A, Hans W, Hicks G, Hölter SM, Höfler H, Hancock JM, Hoehndorf R, Hough T, Houghton R, Hurt A, Ivandic B, Jacobs H, Jacquot S, Jones N, Karp NA, Katus HA, Kitchen S, Klein-Rodewald T, Klingenspor M, Klopstock T, Lalanne V, Leblanc S, Lengger C, le Marchand E, Ludwig T, Lux A, McKerlie C, Maier H, Mandel JL, Marschall S, Mark M, Melvin DG, Meziane H, Micklich K, Mittelhauser C, Monassier L, Moulaert D, Muller S, Naton B, Neff F, Nolan PM, Nutter LM, Ollert M, Pavlovic G, Pellegata NS, Peter E, Petit-Demoulière B, Pickard A, Podrini C, Potter P, Pouilly L, Puk O, Richardson D, Rousseau S, Quintanilla-Fend L, Quwailid MM, Racz I, Rathkolb B, Riet F, Rossant J, Roux M, Rozman J, Ryder E, Salisbury J, Santos L, Schäble KH, Schiller E, Schrewe A, Schulz H, Steinkamp R, Simon M, Stewart M, Stöger C, Stöger T, Sun M, Sunter D, Teboul L, Tilly I, Tocchini-Valentini GP, Tost M, Treise I, Vasseur L, Velot E, Vogt-Weisenhorn D, Wagner C, Walling A, Wattenhofer-Donze M, Weber B, Wendling O, Westerberg H, Willershäuser M, Wolf E, Wolter A, Wood J, Wurst W, Yildirim AÖ, Zeh R, Zimmer A, Zimprich A, EUMODIC Consortium, Holmes C, Steel KP, Herault Y, Gailus-Durner V, Mallon AM, Brown SD.
Nature genetics Volume 47 (2015) p.969-978

Principles and application of LIMS in mouse clinics.
Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 26 (2015) p.467-481

Finding our way through phenotypes.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.
PLoS biology Volume 13 (2015) p.e1002033

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC, WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY.
Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.
Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G.
Nature genetics Volume 47 (2015) p.717-726

SurvCurv database and online survival analysis platform update.
Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3878-3880

NMR Exchange Format: a unified and open standard for representation of NMR restraint data.
Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW.
Nature structural & molecular biology Volume 22 (2015) p.433-434

Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery.
Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, Castro-Pichel J, Martínez-Jiménez F, Papadatos G, Kumar V, Colmenarejo G, Mugumbate G, Hurle M, Barroso V, Young RJ, Martinez-Hoyos M, González del Río R, Bates RH, Lopez-Roman EM, Mendoza-Losana A, Brown JR, Alvarez-Ruiz E, Marti-Renom MA, Overington JP, Cammack N, Ballell L, Barros-Aguire D.
PloS one Volume 10 (2015) p.e0142293

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation.
Mugumbate G, Abrahams KA, Cox JA, Papadatos G, van Westen G, Lelièvre J, Calus ST, Loman NJ, Ballell L, Barros D, Overington JP, Besra GS.
PloS one Volume 10 (2015) p.e0121492

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M.
Genome research Volume 25 (2015) p.504-513

Genetic Interaction Scoring Procedure for Bacterial Species.
Wagih O, Parts L.
Advances in experimental medicine and biology Volume 883 (2015) p.169-185

Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M.
Data in brief Volume 4 (2015) p.468-473

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.
Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, METABRIC Group, Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C.
Molecular oncology Volume 9 (2015) p.115-127

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.
BMC systems biology Volume 9 (2015) p.8

Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M.
Journal of proteomics Volume 126 (2015) p.163-171

Reply to '"Mycobacterium indicus pranii" is a strain of Mycobacterium intracellulare': "M. indicus pranii" is a distinct strain, not derived from M. intracellulare, and is an organism at an evolutionary transition point between a fast grower and slow grower.
Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE.
mBio Volume 6 (2015) p.

Cooperative development of logical modelling standards and tools with CoLoMoTo.
Naldi A, Monteiro PT, Müssel C, Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1154-1159

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.
Kotelnikova E, Bernardo-Faura M, Silberberg G, Kiani NA, Messinis D, Melas IN, Artigas L, Schwartz E, Mazo I, Masso M, Alexopoulos LG, Mas JM, Olsson T, Tegner J, Martin R, Zamora A, Paul F, Saez-Rodriguez J, Villoslada P.
Multiple sclerosis (Houndmills, Basingstoke, England) Volume 21 (2015) p.138-146

Linking gene expression to phenotypes via pathway information.
Papatheodorou I, Oellrich A, Smedley D.
Journal of biomedical semantics Volume 6 (2015) p.17

ADME SARfari: comparative genomics of drug metabolizing systems.
Davies M, Dedman N, Hersey A, Papadatos G, Hall MD, Cucurull-Sanchez L, Jeffrey P, Hasan S, Eddershaw PJ, Overington JP.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1695-1697

TNNI3K in cardiovascular disease and prospects for therapy.
Milano A, Lodder EM, Bezzina CR.
Journal of molecular and cellular cardiology Volume 82 (2015) p.167-173

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.
Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS.
Nucleic acids research Volume 43 (2015) p.W104-8

Content discovery and retrieval services at the European Nucleotide Archive.
Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 43 (2015) p.D23-9

A single-cell model of PIP3 dynamics using chemical dimerization.
MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J.
Bioorganic & medicinal chemistry Volume 23 (2015) p.2868-2876

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.
Whelan S, Allen JE, Blackburne BP, Talavera D.
Systematic biology Volume 64 (2015) p.42-55

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.
Laird MR, Langille MG, Brinkman FS.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3348-3349

Fine mapping of bone structure and strength QTLs in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T.
Bone Volume 81 (2015) p.417-426

Computational proteomics: Integrating mass spectral data into a biological context.
Carvalho PC, Padron G, Calvete JJ, Perez-Riverol Y.
Journal of proteomics Volume 129 (2015) p.1-2

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.
Chiang Z, Vastermark A, Punta M, Coggill PC, Mistry J, Finn RD, Saier MH Jr.
Briefings in bioinformatics Volume 16 (2015) p.865-872

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium.
Bioinformatics (Oxford, England) Volume 31 (2015) p.926-932

Molecular disease presentation in diabetic nephropathy.
Heinzel A, Mühlberger I, Stelzer G, Lancet D, Oberbauer R, Martin M, Perco P.
Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association Volume 30 Suppl 4 (2015) p.iv17-25

Preface. Bacterial pangenomics.
Mengoni A, Fondi M, Galardini M.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.v-vi

Mapping contigs using CONTIGuator.
Galardini M, Mengoni A, Bazzicalupo M.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.163-176

From pangenome to panphenome and back.
Galardini M, Mengoni A, Mocali S.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.257-270

Extracellular vesicles and their synthetic analogues in aging and age-associated brain diseases.
Smith JA, Leonardi T, Huang B, Iraci N, Vega B, Pluchino S.
Biogerontology Volume 16 (2015) p.147-185

Acellular approaches for regenerative medicine: on the verge of clinical trials with extracellular membrane vesicles?
Fuster-Matanzo A, Gessler F, Leonardi T, Iraci N, Pluchino S.
Stem cell research & therapy Volume 6 (2015) p.227

Known Allergen Structures Predict Schistosoma mansoni IgE-Binding Antigens in Human Infection.
Farnell EJ, Tyagi N, Ryan S, Chalmers IW, Pinot de Moira A, Jones FM, Wawrzyniak J, Fitzsimmons CM, Tukahebwa EM, Furnham N, Maizels RM, Dunne DW.
Frontiers in immunology Volume 6 (2015) p.26

A new system for profiling drug-induced calcium signal perturbation in human embryonic stem cell-derived cardiomyocytes.
Lewis KJ, Silvester NC, Barberini-Jammaers S, Mason SA, Marsh SA, Lipka M, George CH.
Journal of biomolecular screening Volume 20 (2015) p.330-340

Applying extracellular vesicles based therapeutics in clinical trials - an ISEV position paper.
Lener T, Gimona M, Aigner L, Börger V, Buzas E, Camussi G, Chaput N, Chatterjee D, Court FA, Del Portillo HA, O'Driscoll L, Fais S, Falcon-Perez JM, Felderhoff-Mueser U, Fraile L, Gho YS, Görgens A, Gupta RC, Hendrix A, Hermann DM, Hill AF, Hochberg F, Horn PA, de Kleijn D, Kordelas L, Kramer BW, Krämer-Albers EM, Laner-Plamberger S, Laitinen S, Leonardi T, Lorenowicz MJ, Lim SK, Lötvall J, Maguire CA, Marcilla A, Nazarenko I, Ochiya T, Patel T, Pedersen S, Pocsfalvi G, Pluchino S, Quesenberry P, Reischl IG, Rivera FJ, Sanzenbacher R, Schallmoser K, Slaper-Cortenbach I, Strunk D, Tonn T, Vader P, van Balkom BW, Wauben M, Andaloussi SE, Théry C, Rohde E, Giebel B.
Journal of extracellular vesicles Volume 4 (2015) p.30087

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A.
PLoS computational biology Volume 11 (2015) p.e1004478

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.
Bacci G, Ceccherini MT, Bani A, Bazzicalupo M, Castaldini M, Galardini M, Giovannetti L, Mocali S, Pastorelli R, Pantani OL, Arfaioli P, Pietramellara G, Viti C, Nannipieri P, Mengoni A.
Antonie van Leeuwenhoek Volume 107 (2015) p.785-797

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J.
Nature communications Volume 6 (2015) p.8033

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.
Science (New York, N.Y.) Volume 348 (2015) p.666-669

Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.
Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.
Nature biotechnology Volume 33 (2015) p.1109

The BioStudies database.
McEntyre J, Sarkans U, Brazma A.
Molecular systems biology Volume 11 (2015) p.847

Where Next for Genetics and Genomics?
Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M, McVean G.
PLoS biology Volume 13 (2015) p.e1002216

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O.
Skeletal muscle Volume 5 (2015) p.35

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.
BMC genomics Volume 16 Suppl 8 (2015) p.S2

Cellular phenotype database: a repository for systems microscopy data.
Kirsanova C, Brazma A, Rustici G, Sarkans U.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2736-2740

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.
Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E99-100

Europe PMC: a full-text literature database for the life sciences and platform for innovation.
Europe PMC Consortium.
Nucleic acids research Volume 43 (2015) p.D1042-8

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziołowski C, Klamt S.
BMC bioinformatics Volume 16 (2015) p.345

The Protein Ensemble Database.
Varadi M, Tompa P.
Advances in experimental medicine and biology Volume 870 (2015) p.335-349

Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ.
Science (New York, N.Y.) Volume 348 (2015) p.880-886

Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes.
Gerstung M, Pellagatti A, Malcovati L, Giagounidis A, Porta MG, Jädersten M, Dolatshad H, Verma A, Cross NC, Vyas P, Killick S, Hellström-Lindberg E, Cazzola M, Papaemmanuil E, Campbell PJ, Boultwood J.
Nature communications Volume 6 (2015) p.5901

The EMBL-EBI bioinformatics web and programmatic tools framework.
Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R.
Nucleic acids research Volume 43 (2015) p.W580-4

Dynamics of Lgr6⁺ Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis.
Füllgrabe A, Joost S, Are A, Jacob T, Sivan U, Haegebarth A, Linnarsson S, Simons BD, Clevers H, Toftgård R, Kasper M.
Stem cell reports Volume 5 (2015) p.843-855

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.
Ju YS, Tubio JM, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group, ICGC Breast Cancer Working Group, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MT, van't Veer LJ, Tan BK, Aparicio S, Span PN, Martens JW, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR.
Genome research Volume 25 (2015) p.814-824

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers.
Shlien A, Campbell BB, de Borja R, Alexandrov LB, Merico D, Wedge D, Van Loo P, Tarpey PS, Coupland P, Behjati S, Pollett A, Lipman T, Heidari A, Deshmukh S, Avitzur N, Meier B, Gerstung M, Hong Y, Merino DM, Ramakrishna M, Remke M, Arnold R, Panigrahi GB, Thakkar NP, Hodel KP, Henninger EE, Göksenin AY, Bakry D, Charames GS, Druker H, Lerner-Ellis J, Mistry M, Dvir R, Grant R, Elhasid R, Farah R, Taylor GP, Nathan PC, Alexander S, Ben-Shachar S, Ling SC, Gallinger S, Constantini S, Dirks P, Huang A, Scherer SW, Grundy RG, Durno C, Aronson M, Gartner A, Meyn MS, Taylor MD, Pursell ZF, Pearson CE, Malkin D, Futreal PA, Stratton MR, Bouffet E, Hawkins C, Campbell PJ, Tabori U, Biallelic Mismatch Repair Deficiency Consortium.
Nature genetics Volume 47 (2015) p.257-262

Subclonal diversification of primary breast cancer revealed by multiregion sequencing.
Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, Aas T, Alexandrov LB, Larsimont D, Davies H, Li Y, Ju YS, Ramakrishna M, Haugland HK, Lilleng PK, Nik-Zainal S, McLaren S, Butler A, Martin S, Glodzik D, Menzies A, Raine K, Hinton J, Jones D, Mudie LJ, Jiang B, Vincent D, Greene-Colozzi A, Adnet PY, Fatima A, Maetens M, Ignatiadis M, Stratton MR, Sotiriou C, Richardson AL, Lønning PE, Wedge DC, Campbell PJ.
Nature medicine Volume 21 (2015) p.751-759

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Henriques D, Rocha M, Saez-Rodriguez J, Banga JR.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2999-3007

Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and Legal Requirements.
Sariyar M, Schluender I, Smee C, Suhr S.
Biopreservation and biobanking Volume 13 (2015) p.263-270

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.
Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, Gannon V, Allison LJ, Hanson MF, Dallman T, Ashton P, Franz E, van Hoek AH, French NP, George T, Biggs PJ, Forbes KJ.
Scientific reports Volume 5 (2015) p.14145

Computational approaches for inferring the functions of intrinsically disordered proteins.
Varadi M, Vranken W, Guharoy M, Tompa P.
Frontiers in molecular biosciences Volume 2 (2015) p.45

Empirical inference of circuitry and plasticity in a kinase signaling network.
Wilkes EH, Terfve C, Gribben JG, Saez-Rodriguez J, Cutillas PR.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.7719-7724

Modeling Signaling Networks to Advance New Cancer Therapies.
Saez-Rodriguez J, MacNamara A, Cook S.
Annual review of biomedical engineering Volume 17 (2015) p.143-163

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.
Varadi M, Zsolyomi F, Guharoy M, Tompa P.
PloS one Volume 10 (2015) p.e0139731

Cancer evolution: mathematical models and computational inference.
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.
Systematic biology Volume 64 (2015) p.e1-25

DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder.
Varadi M, Guharoy M, Zsolyomi F, Tompa P.
BMC bioinformatics Volume 16 (2015) p.153

A global reference for human genetic variation.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.
Nature Volume 526 (2015) p.68-74

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.
Squizzato S, Park YM, Buso N, Gur T, Cowley A, Li W, Uludag M, Pundir S, Cham JA, McWilliam H, Lopez R.
Nucleic acids research Volume 43 (2015) p.W585-8

The 3D organization of chromatin explains evolutionary fragile genomic regions.
Berthelot C, Muffato M, Abecassis J, Roest Crollius H.
Cell reports Volume 10 (2015) p.1913-1924

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C.
Systematic biology Volume 64 (2015) p.778-791

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T, Quest for Orthologs Species Tree Working Group.
Genome biology and evolution Volume 7 (2015) p.1988-1999

The complex portal--an encyclopaedia of macromolecular complexes.
Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.
Nucleic acids research Volume 43 (2015) p.D479-84

The European Genome-phenome Archive of human data consented for biomedical research.
Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P.
Nature genetics Volume 47 (2015) p.692-695

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.
Louis A, Nguyen NT, Muffato M, Roest Crollius H.
Nucleic acids research Volume 43 (2015) p.D682-9

What you need to know to make the most of big data in biology.
Thornton J.
Lancet (London, England) Volume 385 Suppl 1 (2015) p.S5-6

A large-scale crop protection bioassay data set.
Gaulton A, Kale N, van Westen GJ, Bellis LJ, Bento AP, Davies M, Hersey A, Papadatos G, Forster M, Wege P, Overington JP.
Scientific data Volume 2 (2015) p.150032

flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1337-1339

Transcriptional profiling of chronic clinical hepatic schistosomiasis japonica indicates reduced metabolism and immune responses.
Gobert GN, Burke ML, McManus DP, Ellis MK, Chuah C, Ramm GA, Wang Y, Li Y.
Parasitology Volume 142 (2015) p.1453-1468

Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.
Senger S, Bartek L, Papadatos G, Gaulton A.
Journal of cheminformatics Volume 7 (2015) p.49

Integrative approaches for signalling and metabolic networks.
Hatzimanikatis V, Saez-Rodriguez J.
Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.844-845

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.
Kruger FA, Gaulton A, Nowotka M, Overington JP.
Bioinformatics (Oxford, England) Volume 31 (2015) p.776-778

Activity, assay and target data curation and quality in the ChEMBL database.
Papadatos G, Gaulton A, Hersey A, Overington JP.
Journal of computer-aided molecular design Volume 29 (2015) p.885-896

Chemical databases: curation or integration by user-defined equivalence?
Hersey A, Chambers J, Bellis L, Patrícia Bento A, Gaulton A, Overington JP.
Drug discovery today. Technologies Volume 14 (2015) p.17-24

Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.
Meex RC, Hoy AJ, Morris A, Brown RD, Lo JC, Burke M, Goode RJ, Kingwell BA, Kraakman MJ, Febbraio MA, Greve JW, Rensen SS, Molloy MP, Lancaster GI, Bruce CR, Watt MJ.
Cell metabolism Volume 22 (2015) p.1078-1089

ChEMBL web services: streamlining access to drug discovery data and utilities.
Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP.
Nucleic acids research Volume 43 (2015) p.W612-20

diXa: a data infrastructure for chemical safety assessment.
Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JC.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1505-1507

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.
PloS one Volume 10 (2015) p.e0137367

Chimira: analysis of small RNA sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3365-3367

Solid tumors of childhood display specific serum microRNA profiles.
Murray MJ, Raby KL, Saini HK, Bailey S, Wool SV, Tunnacliffe JM, Enright AJ, Nicholson JC, Coleman N.
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology Volume 24 (2015) p.350-360

High-density P300 enhancers control cell state transitions.
Witte S, Bradley A, Enright AJ, Muljo SA.
BMC genomics Volume 16 (2015) p.903

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.
GigaScience Volume 4 (2015) p.38

SPARQL-enabled identifier conversion with Identifiers.org.
Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1875-1877

Erratum: A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N, UK10K Consortium.
Nature communications Volume 6 (2015) p.7171

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F, NextGen Consortium.
Frontiers in genetics Volume 6 (2015) p.107

ArrayExpress update--simplifying data submissions.
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.
Nucleic acids research Volume 43 (2015) p.D1113-6

An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.
Nature Volume 526 (2015) p.75-81

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N.
CPT: pharmacometrics & systems pharmacology Volume 4 (2015) p.316-319

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H, FAANG Consortium.
Genome biology Volume 16 (2015) p.57

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H.
Database : the journal of biological databases and curation Volume 2015 (2015) p.

The evolution of standards and data management practices in systems biology.
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.
Molecular systems biology Volume 11 (2015) p.851

Harnessing the heart of big data.
Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR 3rd, Lindsey ML, Ping P.
Circulation research Volume 116 (2015) p.1115-1119

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.
Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P, Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS.
Nature genetics Volume 47 (2015) p.381-386

Proteins: interaction at a distance.
Laskowski RA, Thornton JM.
IUCrJ Volume 2 (2015) p.609-610

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME.
Nature methods Volume 12 (2015) p.339-342

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 15 (2015) p.930-949

Designing Experiments to Discriminate Families of Logic Models.
Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C.
Frontiers in bioengineering and biotechnology Volume 3 (2015) p.131

Open source libraries and frameworks for biological data visualisation: a guide for developers.
Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.
Proteomics Volume 15 (2015) p.1356-1374

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 370 (2015) p.

Introducing the PRIDE Archive RESTful web services.
Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA.
Nucleic acids research Volume 43 (2015) p.W599-604

Identifying novel biomarkers through data mining-a realistic scenario?
Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.
Proteomics. Clinical applications Volume 9 (2015) p.437-443

A quick guide for building a successful bioinformatics community.
Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N.
PLoS computational biology Volume 11 (2015) p.e1003972

MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.
Vuckovic D, Gasparini P, Soranzo N, Iotchkova V.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2754-2756

MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2443-2451

High-throughput phenomics.
Viti C, Decorosi F, Marchi E, Galardini M, Giovannetti L.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.99-123

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.
Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F.
Nucleic acids research Volume 43 (2015) p.D637-44

Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.
Golanowska M, Galardini M, Bazzicalupo M, Hugouvieux-Cotte-Pattat N, Mengoni A, Potrykus M, Slawiak M, Lojkowska E.
Genome announcements Volume 3 (2015) p.

Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS.
Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A.
Journal of genomics Volume 3 (2015) p.36-39

2014

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau016

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D1001-6

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, Stolovitzky G, Saez-Rodriguez J.
BMC systems biology Volume 8 (2014) p.13

KEGGViewer, a BioJS component to visualize KEGG Pathways.
Villaveces JM, Jimenez RC, Habermann BH.
F1000Research Volume 3 (2014) p.43

The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.
Courtot M, Brinkman RR, Ruttenberg A.
PloS one Volume 9 (2014) p.e92632

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers.
Villaveces JM, Jimenez RC, Habermann BH.
F1000Research Volume 3 (2014) p.44

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.E3366

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N, UK1OK Consortium Members, UK1OK Consortium Members.
Nature communications Volume 5 (2014) p.4871

Sequence, a BioJS component for visualising sequences.
Gomez J, Jimenez R.
F1000Research Volume 3 (2014) p.52

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N.
BMC bioinformatics Volume 15 (2014) p.369

Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations.
Rallapalli PM, Orengo CA, Studer RA, Perkins SJ.
Molecular biology and evolution Volume 31 (2014) p.3040-3056

A unifying model of genome evolution under parsimony.
Paten B, Zerbino DR, Hickey G, Haussler D.
BMC bioinformatics Volume 15 (2014) p.206

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1008-1009

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 42 (2014) p.D191-8

Do climatic conditions affect host and parasite phenotypes differentially? A case study of magpies and great spotted cuckoos.
Soler JJ, De Neve L, Martín-Gálvez D, Molina-Morales M, Pérez-Contreras T, Ruiz-Rodríguez M.
Oecologia Volume 174 (2014) p.327-338

Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.
Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R.
Open biology Volume 4 (2014) p.

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.
Studer RA, Christin PA, Williams MA, Orengo CA.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.2223-2228

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C.
Angewandte Chemie (International ed. in English) Volume 53 (2014) p.6720-6723

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ.
BMC bioinformatics Volume 15 (2014) p.155

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM.
Biopolymers Volume 101 (2014) p.659-668

Practical aspects of protein co-evolution.
Ochoa D, Pazos F.
Frontiers in cell and developmental biology Volume 2 (2014) p.14

Cuckoo hosts shift from accepting to rejecting parasitic eggs across their lifetime.
Molina-Morales M, Martínez JG, Martín-Gálvez D, Dawson DA, Burke T, Avilés JM.
Evolution; international journal of organic evolution Volume 68 (2014) p.3020-3029

Eavesdropping cuckoos: further insights on great spotted cuckoo preference by magpie nests and egg colour.
Soler JJ, Avilés JM, Martín-Gálvez D, de Neve L, Soler M.
Oecologia Volume 175 (2014) p.105-115

Smoothing 3D protein structure motifs through graph mining and amino acid similarities.
Dhifli W, Saidi R, Nguifo EM.
Journal of computational biology : a journal of computational molecular cell biology Volume 21 (2014) p.162-172

How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space.
Koutsoukas A, Paricharak S, Galloway WR, Spring DR, Ijzerman AP, Glen RC, Marcus D, Bender A.
Journal of chemical information and modeling Volume 54 (2014) p.230-242

Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.6131-6138

A long-term experimental study demonstrates the costs of begging that were not found over the short term.
Soler M, Ruiz-Raya F, Carra LG, Medina-Molina E, Ibáñez-Álamo JD, Martín-Gálvez D.
PloS one Volume 9 (2014) p.e111929

Structural studies of adipokinetic hormones in water and DPC micelle solution using NMR distance restrained molecular dynamics.
Jackson GE, Gamieldien R, Mugumbate G, Gäde G.
Peptides Volume 53 (2014) p.270-277

Updates to BioSamples database at European Bioinformatics Institute.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D50-2

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.
Bio Systems Volume 124 (2014) p.26-38

Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.
Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD.
Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1170-1182

DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.
Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S.
Genomics Volume 103 (2014) p.1-10

A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.
Nature biotechnology Volume 32 (2014) p.1202-1212

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Cejuela JM, McQuilton P, Ponting L, Marygold SJ, Stefancsik R, Millburn GH, Rost B, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau033

Overview of the gene ontology task at BioCreative IV.
Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z.
Database : the journal of biological databases and curation Volume 2014 (2014) p.

Exploring the biological and chemical complexity of the ligases.
Holliday GL, Rahman SA, Furnham N, Thornton JM.
Journal of molecular biology Volume 426 (2014) p.2098-2111

BC4GO: a full-text corpus for the BioCreative IV GO task.
Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z.
Database : the journal of biological databases and curation Volume 2014 (2014) p.

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.
PLoS genetics Volume 10 (2014) p.e1004798

PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Nucleic acids research Volume 42 (2014) p.D285-91

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler TJ, Clements J, Finn RD.
BMC bioinformatics Volume 15 (2014) p.7

EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.
Nature methods Volume 11 (2014) p.171-174

Editorial: Genomics and proteomics behind drug design.
Perez-Riverol Y, Carvalho PC.
Current topics in medicinal chemistry Volume 14 (2014) p.343

Computational approaches to interpreting genomic sequence variation.
Ritchie GR, Flicek P.
Genome medicine Volume 6 (2014) p.87

Data standardization and sharing-the work of the HUPO-PSI.
Orchard S.
Biochimica et biophysica acta Volume 1844 (2014) p.82-87

The EBI RDF platform: linked open data for the life sciences.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1338-1339

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P.
PloS one Volume 9 (2014) p.e96855

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Delaneau O, Marchini J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium.
Nature communications Volume 5 (2014) p.3934

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic acids research Volume 42 (2014) p.D926-32

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Genome biology Volume 15 (2014) p.R88

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Lopez R, Cowley A, Li W, McWilliam H.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 48 (2014) p.3.12.1-50

A community computational challenge to predict the activity of pairs of compounds.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community.
Nature biotechnology Volume 32 (2014) p.1213-1222

Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b.
Toribio AL, Pickard D, Cerdeño-Tárraga AM, Petty NK, Thomson N, Salmond G, Dougan G.
Genome announcements Volume 2 (2014) p.

Archaic humans: Four makes a party.
Birney E, Pritchard JK.
Nature Volume 505 (2014) p.32-34

Biomarkers in autism spectrum disorder: the old and the new.
Ruggeri B, Sarkans U, Schumann G, Persico AM.
Psychopharmacology Volume 231 (2014) p.1201-1216

PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA.
Nucleic acids research Volume 42 (2014) p.D292-6

Enly: Improving Draft Genomes through Reads Recycling.
Fondi M, Orlandini V, Corti G, Severgnini M, Galardini M, Pietrelli A, Fuligni F, Iacono M, Rizzi E, De Bellis G, Fani R.
Journal of genomics Volume 2 (2014) p.89-93

Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D (1)H-NMR data.
Gómez J, Brezmes J, Mallol R, Rodríguez MA, Vinaixa M, Salek RM, Correig X, Cañellas N.
Analytical and bioanalytical chemistry Volume 406 (2014) p.7967-7976

Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J.
G3 (Bethesda, Md.) Volume 4 (2014) p.433-445

An integrated ontology resource to explore and study host-virus relationships.
Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P.
PloS one Volume 9 (2014) p.e108075

Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.
Maina AN, Mwaura FB, Oyugi J, Goulding D, Toribio AL, Kariuki S.
Current microbiology Volume 68 (2014) p.64-70

Bioinformatics tools for the functional interpretation of quantitative proteomics results.
Villavicencio-Diaz TN, Rodriguez-Ulloa A, Guirola-Cruz O, Perez-Riverol Y.
Current topics in medicinal chemistry Volume 14 (2014) p.435-449

Anatomy of enzyme channels.
Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M.
BMC bioinformatics Volume 15 (2014) p.379

The common marmoset genome provides insight into primate biology and evolution.
Marmoset Genome Sequencing and Analysis Consortium.
Nature genetics Volume 46 (2014) p.850-857

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
Nucleic acids research Volume 42 (2014) p.D485-9

FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences.
Garcia L, Yachdav G, Martin MJ.
F1000Research Volume 3 (2014) p.47

Overview of gene structure in C. elegans.
Spieth J, Lawson D, Davis P, Williams G, Howe K.
WormBook : the online review of C. elegans biology Volume (2014) p.1-18

WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic acids research Volume 42 (2014) p.D789-93

Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.
Nature Volume 512 (2014) p.445-448

BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
Kim JK, Cho Y, Laskowski RA, Ryu SE, Sugihara K, Kim DS.
Proteins Volume 82 (2014) p.1829-1849

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.
Ochoa R, Davies M, Papadatos G, Atkinson F, Overington JP.
Bioinformatics (Oxford, England) Volume 30 (2014) p.298-300

A document classifier for medicinal chemistry publications trained on the ChEMBL corpus.
Papadatos G, van Westen GJ, Croset S, Santos R, Trubian S, Overington JP.
Journal of cheminformatics Volume 6 (2014) p.40

Screening and hit evaluation of a chemical library against blood-stage Plasmodium falciparum.
Avery VM, Bashyam S, Burrows JN, Duffy S, Papadatos G, Puthukkuti S, Sambandan Y, Singh S, Spangenberg T, Waterson D, Willis P.
Malaria journal Volume 13 (2014) p.190

The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.
Current opinion in structural biology Volume 26 (2014) p.121-130

Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.
Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q, Kamatani Y, Bennet AM, Tamm R, Trompet S, Guðbjartsson DF, Flachsbart F, Rose G, Viktorin A, Fischer K, Nygaard M, Cordell HJ, Crocco P, van den Akker EB, Böhringer S, Helmer Q, Nelson CP, Saunders GI, Alver M, Andersen-Ranberg K, Breen ME, van der Breggen R, Caliebe A, Capri M, Cevenini E, Collerton JC, Dato S, Davies K, Ford I, Gampe J, Garagnani P, de Geus EJ, Harrow J, van Heemst D, Heijmans BT, Heinsen FA, Hottenga JJ, Hofman A, Jeune B, Jonsson PV, Lathrop M, Lechner D, Martin-Ruiz C, Mcnerlan SE, Mihailov E, Montesanto A, Mooijaart SP, Murphy A, Nohr EA, Paternoster L, Postmus I, Rivadeneira F, Ross OA, Salvioli S, Sattar N, Schreiber S, Stefánsson H, Stott DJ, Tiemeier H, Uitterlinden AG, Westendorp RG, Willemsen G, Samani NJ, Galan P, Sørensen TI, Boomsma DI, Jukema JW, Rea IM, Passarino G, de Craen AJ, Christensen K, Nebel A, Stefánsson K, Metspalu A, Magnusson P, Blanché H, Christiansen L, Kirkwood TB, van Duijn CM, Franceschi C, Houwing-Duistermaat JJ, Slagboom PE.
Human molecular genetics Volume 23 (2014) p.4420-4432

Relationship between genome and epigenome--challenges and requirements for future research.
Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.
BMC genomics Volume 15 (2014) p.487

Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.
Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I.
Medical mycology Volume 52 (2014) p.472-481

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
Greger L, Su J, Rung J, Ferreira PG, Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.
PloS one Volume 9 (2014) p.e104567

The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
Davis OS, Band G, Pirinen M, Haworth CM, Meaburn EL, Kovas Y, Harlaar N, Docherty SJ, Hanscombe KB, Trzaskowski M, Curtis CJ, Strange A, Freeman C, Bellenguez C, Su Z, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Barroso I, Peltonen L, Dale PS, Petrill SA, Schalkwyk LS, Craig IW, Lewis CM, Price TS, Wellcome Trust Case Control Consortium 2, Donnelly P, Plomin R, Spencer CC.
Nature communications Volume 5 (2014) p.4204

Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery.
Schubert M, Iorio F.
Pharmacogenomics Volume 15 (2014) p.1943-1946

Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM.
Nature communications Volume 5 (2014) p.5135

DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.
Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D.
PLoS genetics Volume 10 (2014) p.e1004109

An overview of tools for the validation of protein NMR structures.
Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A.
Journal of biomolecular NMR Volume 58 (2014) p.259-285

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.
Marguerat S, Lawler K, Brazma A, Bähler J.
RNA biology Volume 11 (2014) p.702-714

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1942-1942

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.
Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC.
Nature communications Volume 5 (2014) p.2997

RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A.
PloS one Volume 9 (2014) p.e107026

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F.
Nucleic acids research Volume 42 (2014) p.D873-8

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.
Pinnick KE, Nicholson G, Manolopoulos KN, McQuaid SE, Valet P, Frayn KN, Denton N, Min JL, Zondervan KT, Fleckner J, MolPAGE Consortium, McCarthy MI, Holmes CC, Karpe F.
Diabetes Volume 63 (2014) p.3785-3797

Activities at the Universal Protein Resource (UniProt).

Nucleic acids research Volume 42 (2014) p.7486-7486

Fast randomization of large genomic datasets while preserving alteration counts.
Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 30 (2014) p.i617-23

Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
Nayduch D, Cohnstaedt LW, Saski C, Lawson D, Kersey P, Fife M, Carpenter S.
Virus research Volume 182 (2014) p.43-49

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.
Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T.
Journal of the American Society of Nephrology : JASN Volume 25 (2014) p.1509-1522

The ChEMBL database: a taster for medicinal chemists.
Papadatos G, Overington JP.
Future medicinal chemistry Volume 6 (2014) p.361-364

PIP₃ induces the recycling of receptor tyrosine kinases.
Laketa V, Zarbakhsh S, Traynor-Kaplan A, Macnamara A, Subramanian D, Putyrski M, Mueller R, Nadler A, Mentel M, Saez-Rodriguez J, Pepperkok R, Schultz C.
Science signaling Volume 7 (2014) p.ra5

Genome-wide estimates of inbreeding in unrelated individuals and their association with cognitive ability.
Power RA, Nagoshi C, DeFries JC, Plomin R, Wellcome Trust Case Control Consortium 2.
European journal of human genetics : EJHG Volume 22 (2014) p.386-390

Selectome update: quality control and computational improvements to a database of positive selection.
Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M.
Nucleic acids research Volume 42 (2014) p.D917-21

A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium 2, Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Arranz MJ, Bakker S, Bender S, Bruggeman R, Cahn W, Chandler D, Collier DA, Crespo-Facorro B, Dazzan P, de Haan L, Di Forti M, Dragović M, Giegling I, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Kravariti E, Lawrie S, Linszen DH, Mata I, McDonald C, McIntosh A, Myin-Germeys I, Ophoff RA, Pariante CM, Paunio T, Picchioni M, Psychiatric Genomics Consortium, Ripke S, Rujescu D, Sauer H, Shaikh M, Sussmann J, Suvisaari J, Tosato S, Toulopoulou T, Van Os J, Walshe M, Weisbrod M, Whalley H, Wiersma D, Blackwell JM, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Wood NW, Barroso I, Peltonen L, Lewis CM, Murray RM, Donnelly P, Powell J, Spencer CC.
Biological psychiatry Volume 75 (2014) p.386-397

Integrative knowledge management to enhance pharmaceutical R&D.
Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F.
Nature reviews. Drug discovery Volume 13 (2014) p.239-240

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R.
Molecular systems biology Volume 10 (2014) p.767

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA.
Nucleic acids research Volume 42 (2014) p.D240-5

Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy.
Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.2235-2240

Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.
Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH.
Structure (London, England : 1993) Volume 22 (2014) p.1862-1874

Big data and other challenges in the quest for orthologs.
Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs consortium.
Bioinformatics (Oxford, England) Volume 30 (2014) p.2993-2998

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA.
Journal of biomedical semantics Volume 5 (2014) p.34

TermGenie - a web-application for pattern-based ontology class generation.
Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ.
Journal of biomedical semantics Volume 5 (2014) p.48

Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription.
García P, Paulo E, Gao J, Wahls WP, Ayté J, Lowy E, Hidalgo E.
Nucleic acids research Volume 42 (2014) p.10351-10359

PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.
Lucas JM, Muffato M, Roest Crollius H.
BMC bioinformatics Volume 15 (2014) p.268

The Protein Data Bank archive as an open data resource.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Journal of computer-aided molecular design Volume 28 (2014) p.1009-1014

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.
BMC bioinformatics Volume 15 (2014) p.136

Leucine modulates dynamic phosphorylation events in insulin signaling pathway and enhances insulin-dependent glycogen synthesis in human skeletal muscle cells.
Di Camillo B, Eduati F, Nair SK, Avogaro A, Toffolo GM.
BMC cell biology Volume 15 (2014) p.9

Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats.
Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C, Jobling MA.
Human mutation Volume 35 (2014) p.609-617

Genomes and phenomes of a population of outbred rats and its progenitors.
Baud A, Guryev V, Hummel O, Johannesson M, Rat Genome Sequencing and Mapping Consortium, Flint J.
Scientific data Volume 1 (2014) p.140011

The architecture of parent-of-origin effects in mice.
Mott R, Yuan W, Kaisaki P, Gan X, Cleak J, Edwards A, Baud A, Flint J.
Cell Volume 156 (2014) p.332-342

Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat.
Falak S, Schafer S, Baud A, Hummel O, Schulz H, Gauguier D, Hubner N, Osborne-Pellegrin M.
Physiological genomics Volume 46 (2014) p.418-428

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.
eLife Volume 3 (2014) p.e02626

A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region.
Kraaijenbrink T, van der Gaag KJ, Zuniga SB, Xue Y, Carvalho-Silva DR, Tyler-Smith C, Jobling MA, Parkin EJ, Su B, Shi H, Xiao CJ, Tang WR, Kashyap VK, Trivedi R, Sitalaximi T, Banerjee J, Karma Tshering of Gaselô, Tuladhar NM, Opgenort JR, van Driem GL, Barbujani G, de Knijff P.
PloS one Volume 9 (2014) p.e91534

Ensembl 2014.
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SM.
Nucleic acids research Volume 42 (2014) p.D749-55

Response to On prompt update of literature references in the Protein Data Bank.
Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 70 (2014) p.2780

Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL.
Developmental cell Volume 28 (2014) p.351-365

Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat.
Tuncel J, Haag S, Yau AC, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, EURATRANS Consortium, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R.
PLoS genetics Volume 10 (2014) p.e1004151

Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG.
Trends in biotechnology Volume 32 (2014) p.396-399

High-resolution genome screen for bone mineral density in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T.
Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Volume 29 (2014) p.1619-1626

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.
Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D.
Aging Volume 6 (2014) p.98-117

A controlled vocabulary for pathway entities and events.
Jupe S, Jassal B, Williams M, Wu G.
Database : the journal of biological databases and curation Volume 2014 (2014) p.

The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.
Nucleic acids research Volume 42 (2014) p.D18-25

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E.
Standards in Genomic Sciences Volume 9 (2014) p.1285-1301

Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi N, Lippert C, Lawrence ND, Stegle O.
Nature communications Volume 5 (2014) p.4890

Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.
Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, Hebenstreit D, Dingler FA, Moignard V, Göttgens B, Arlt W, McKenzie AN, Teichmann SA.
Cell reports Volume 7 (2014) p.1130-1142

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F.
PLoS computational biology Volume 10 (2014) p.e1003535

Identifying cell types from spatially referenced single-cell expression datasets.
Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J.
PLoS computational biology Volume 10 (2014) p.e1003824

Bioinformatics curriculum guidelines: toward a definition of core competencies.
Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV.
PLoS computational biology Volume 10 (2014) p.e1003496

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O.
The Plant cell Volume 26 (2014) p.4298-4310

Small molecule annotation for the Protein Data Bank.
Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau116

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.
Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F.
Nature genetics Volume 46 (2014) p.753-758

The sheep genome illuminates biology of the rumen and lipid metabolism.
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SM, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Fuentes-Utrilla P, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristiansen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas JW, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP.
Science (New York, N.Y.) Volume 344 (2014) p.1168-1173

Turtle ghrelin.
Pascual-Anaya J, Zaddissa A, Aken B, Zhang G, Irie N.
Nature genetics Volume 46 (2014) p.526

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG.
Nature biotechnology Volume 32 (2014) p.1250-1255

Gibbon genome and the fast karyotype evolution of small apes.
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.
Nature Volume 513 (2014) p.195-201

The genomic substrate for adaptive radiation in African cichlid fish.
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SC, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F.
Nature Volume 513 (2014) p.375-381

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.
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PLoS computational biology Volume 10 (2014) p.e1003733

Evaluation of prompted annotation of activity data recorded from a smart phone.
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Functional annotation of noncoding sequence variants.
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Nature methods Volume 11 (2014) p.294-296

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
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Nature biotechnology Volume 32 (2014) p.903-914

Protein flexibility facilitates quaternary structure assembly and evolution.
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PLoS biology Volume 12 (2014) p.e1001870

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.
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PLoS genetics Volume 10 (2014) p.e1004120

TreeFam v9: a new website, more species and orthology-on-the-fly.
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Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.
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BioEssays : news and reviews in molecular, cellular and developmental biology Volume 36 (2014) p.209-218

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.
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BMC bioinformatics Volume 15 (2014) p.75

Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z.
PLoS genetics Volume 10 (2014) p.e1004132

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.
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BMC genomics Volume 15 (2014) p.729

Dissecting the transcriptional phenotype of ribosomal protein deficiency: implications for Diamond-Blackfan Anemia.
Aspesi A, Pavesi E, Robotti E, Crescitelli R, Boria I, Avondo F, Moniz H, Da Costa L, Mohandas N, Roncaglia P, Ramenghi U, Ronchi A, Gustincich S, Merlin S, Marengo E, Ellis SR, Follenzi A, Santoro C, Dianzani I.
Gene Volume 545 (2014) p.282-289

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
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Nucleic acids research Volume 42 (2014) p.D364-73

gitter: a robust and accurate method for quantification of colony sizes from plate images.
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G3 (Bethesda, Md.) Volume 4 (2014) p.547-552

Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
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Science (New York, N.Y.) Volume 346 (2014) p.1254346

High-flux table-top soft x-ray source driven by sub-2-cycle, CEP stable, 1.85-μm 1-kHz pulses for carbon K-edge spectroscopy.
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Optics letters Volume 39 (2014) p.5383-5386

Assembly information services in the European Nucleotide Archive.
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Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
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Methods in molecular biology (Clifton, N.J.) Volume 1079 (2014) p.59-73

Pfam: the protein families database.
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Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
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BMC proceedings Volume 8 (2014) p.S8

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
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Nature methods Volume 11 (2014) p.817-820

Current status and new features of the Consensus Coding Sequence database.
Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD.
Nucleic acids research Volume 42 (2014) p.D865-72

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
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Science (New York, N.Y.) Volume 345 (2014) p.1074-1079

Genome sequencing of normal cells reveals developmental lineages and mutational processes.
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Nature Volume 513 (2014) p.422-425

A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
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Genetics Volume 197 (2014) p.257-271

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
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Journal of proteome research Volume 13 (2014) p.433-446

Transcriptional diversity during lineage commitment of human blood progenitors.
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Visualisation of BioPAX Networks using BioLayout Express (3D).
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F1000Research Volume 3 (2014) p.246

A survey of molecular descriptors used in mass spectrometry based proteomics.
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Serum levels of mature microRNAs in DICER1-mutated pleuropulmonary blastoma.
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Journal of bioinformatics and computational biology Volume 12 (2014) p.1450026

A 3D cellular context for the macromolecular world.
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Nature structural & molecular biology Volume 21 (2014) p.841-845

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.
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Biochimica et biophysica acta Volume 1844 (2014) p.98-107

On best practices in the development of bioinformatics software.
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Frontiers in genetics Volume 5 (2014) p.199

The Nucleic Acid Database: new features and capabilities.
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Nucleic acids research Volume 42 (2014) p.D114-22

InterProScan 5: genome-scale protein function classification.
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Bioinformatics (Oxford, England) Volume 30 (2014) p.1236-1240

The Reactome pathway knowledgebase.
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Nucleic acids research Volume 42 (2014) p.D472-7

BioJS: an open source standard for biological visualisation - its status in 2014.
Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H.
F1000Research Volume 3 (2014) p.55

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.
Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J.
Molecular cancer Volume 13 (2014) p.28

qcML: an exchange format for quality control metrics from mass spectrometry experiments.
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Molecular & cellular proteomics : MCP Volume 13 (2014) p.1905-1913

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.
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Proteomics Volume 14 (2014) p.2363-2368

jmzTab: a java interface to the mzTab data standard.
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Proteomics Volume 14 (2014) p.1328-1332

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
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Nature biotechnology Volume 32 (2014) p.223-226

Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.
Denise H, Moschos SA, Sidders B, Burden F, Perkins H, Carter N, Stroud T, Kennedy M, Fancy SA, Lapthorn C, Lavender H, Kinloch R, Suhy D, Corbau R.
Molecular therapy. Nucleic acids Volume 3 (2014) p.e145

Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM.
Nucleic acids research Volume 42 (2014) p.D546-52

A predictive model for assistive technology adoption for people with dementia.
Zhang S, McClean SI, Nugent CD, Donnelly MP, Galway L, Scotney BW, Cleland I.
IEEE journal of biomedical and health informatics Volume 18 (2014) p.375-383

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.
Genome research Volume 24 (2014) p.1797-1807

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.
Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.17230-17235

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.
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Cell reports Volume 9 (2014) p.1990-2000

The cavefish genome reveals candidate genes for eye loss.
McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC.
Nature communications Volume 5 (2014) p.5307

Gramene 2013: comparative plant genomics resources.
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
Nucleic acids research Volume 42 (2014) p.D1193-9

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
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Proteomics Volume 14 (2014) p.2233-2241

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
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Bioinformatics (Oxford, England) Volume 30 (2014) p.2999-3003

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.
Nucleic acids research Volume 42 (2014) p.D358-63

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
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Biochimica et biophysica acta Volume 1844 (2014) p.63-76

BioModels linked dataset.
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BMC systems biology Volume 8 (2014) p.91

Ten simple rules for running interactive workshops.
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PLoS computational biology Volume 10 (2014) p.e1003485

A comprehensive model of the phototransduction cascade in mouse rod cells.
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Molecular bioSystems Volume 10 (2014) p.1481-1489

Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes.
Colombo M, Laayouni H, Invergo BM, Bertranpetit J, Montanucci L.
Evolution; international journal of organic evolution Volume 68 (2014) p.605-613

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.
Molecular & cellular proteomics : MCP Volume 13 (2014) p.2765-2775

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.
Cossetti C, Iraci N, Mercer TR, Leonardi T, Alpi E, Drago D, Alfaro-Cervello C, Saini HK, Davis MP, Schaeffer J, Vega B, Stefanini M, Zhao C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS, Pluchino S.
Molecular cell Volume 56 (2014) p.193-204

A comparative encyclopedia of DNA elements in the mouse genome.
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Nature Volume 515 (2014) p.355-364

Transporter taxonomy - a comparison of different transport protein classification schemes.
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Drug discovery today. Technologies Volume 12 (2014) p.e37-46

Ten recommendations for software engineering in research.
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GigaScience Volume 3 (2014) p.31

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
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Nucleic acids research Volume 42 (2014) p.D802-9

A formal re-description of the cockroach Hebardina concinna anchored on DNA Barcodes confirms wing polymorphism and identifies morphological characters for field identification.
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PloS one Volume 9 (2014) p.e106789

UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers.
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Journal of cheminformatics Volume 6 (2014) p.43

Posterior localization of ApVas1 positions the preformed germ plasm in the sexual oviparous pea aphid Acyrthosiphon pisum.
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EvoDevo Volume 5 (2014) p.18

Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.
Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C.
Scientific data Volume 1 (2014) p.140029

The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.
Venkata C, Forster MJ, Howe PW, Steinbeck C.
PloS one Volume 9 (2014) p.e111576

A molecular fragment cheminformatics roadmap for mesoscopic simulation.
Truszkowski A, Daniel M, Kuhn H, Neumann S, Steinbeck C, Zielesny A, Epple M.
Journal of cheminformatics Volume 6 (2014) p.45

Efficient ring perception for the Chemistry Development Kit.
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MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.
Beisken S, Earll M, Portwood D, Seymour M, Steinbeck C.
Molecular informatics Volume 33 (2014) p.307-310

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
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Nucleic acids research Volume 42 (2014) p.D503-9

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.
Jayaseelan KV, Steinbeck C.
BMC bioinformatics Volume 15 (2014) p.234

The ChEMBL bioactivity database: an update.
Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP.
Nucleic acids research Volume 42 (2014) p.D1083-90

Evolution of transcription factor binding in metazoans - mechanisms and functional implications.
Villar D, Flicek P, Odom DT.
Nature reviews. Genetics Volume 15 (2014) p.221-233

Characterizing genetic variants for clinical action.
Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJ, Jarvik GP, O'Donnell C, Sherry ST, Aronson N, Biesecker LG, Blumberg B, Calonge N, Colhoun HM, Epstein RS, Flicek P, Gordon ES, Green ED, Green RC, Hurles M, Kawamoto K, Knaus W, Ledbetter DH, Levy HP, Lyon E, Maglott D, McLeod HL, Rahman N, Randhawa G, Wicklund C, Manolio TA, Chisholm RL, Williams MS.
American journal of medical genetics. Part C, Seminars in medical genetics Volume 166C (2014) p.93-104

A standardized framing for reporting protein identifications in mzIdentML 1.2.
Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR.
Proteomics Volume 14 (2014) p.2389-2399

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y, Mashima J, Nakamura Y, Cochrane G, Karsch-Mizrachi I.
Standards in genomic sciences Volume 9 (2014) p.1275-1277

Genomic standards consortium projects.
Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.
Standards in genomic sciences Volume 9 (2014) p.599-601

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
Huntley RP, Sawford T, Martin MJ, O'Donovan C.
GigaScience Volume 3 (2014) p.4

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.
Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I, UniProt Consortium.
Human mutation Volume 35 (2014) p.927-935

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA.
Nucleic acids research Volume 42 (2014) p.D600-6

Representing kidney development using the gene ontology.
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP.
PloS one Volume 9 (2014) p.e99864

OAE: The Ontology of Adverse Events.
He Y, Sarntivijai S, Lin Y, Xiang Z, Guo A, Zhang S, Jagannathan D, Toldo L, Tao C, Smith B.
Journal of biomedical semantics Volume 5 (2014) p.29

Use of internet search logs to evaluate potential drug adverse events.
Sarntivijai S, Abernethy DR.
Clinical pharmacology and therapeutics Volume 96 (2014) p.149-150

Chemical, target, and bioactive properties of allosteric modulation.
van Westen GJ, Gaulton A, Overington JP.
PLoS computational biology Volume 10 (2014) p.e1003559

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression.
Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AE, Wardle FC.
BMC biology Volume 12 (2014) p.81

Transporter assays and assay ontologies: useful tools for drug discovery.
Zdrazil B, Chichester C, Zander Balderud L, Engkvist O, Gaulton A, Overington JP.
Drug discovery today. Technologies Volume 12 (2014) p.e47-54

Large-scale identification of phosphorylation sites for profiling protein kinase selectivity.
Imamura H, Sugiyama N, Wakabayashi M, Ishihama Y.
Journal of proteome research Volume 13 (2014) p.3410-3419

Single Cell Genomics meeting in Stockholm: from single cells to cell types.
Scialdone A, Achim K, Marioni JC.
Genome biology Volume 15 (2014) p.496

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange.
Beer R, Herbst K, Ignatiadis N, Kats I, Adlung L, Meyer H, Niopek D, Christiansen T, Georgi F, Kurzawa N, Meichsner J, Rabe S, Riedel A, Sachs J, Schessner J, Schmidt F, Walch P, Niopek K, Heinemann T, Eils R, Di Ventura B.
Molecular bioSystems Volume 10 (2014) p.1709-1718

Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.
Rawlings ND, Barrett AJ, Bateman A.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 48 (2014) p.1.25.1-33

Reliable protocols for whole-mount fluorescent in situ hybridization (FISH) in the pea aphid Acyrthosiphon pisum: a comprehensive survey and analysis.
Chung CY, Cook CE, Lin GW, Huang TY, Chang CC.
Insect science Volume 21 (2014) p.265-277

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.
Journal of biomedical semantics Volume 5 (2014) p.25

CLO: The cell line ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.
Journal of biomedical semantics Volume 5 (2014) p.37

Maximum likelihood inference of small trees in the presence of long branches.
Parks SL, Goldman N.
Systematic biology Volume 63 (2014) p.798-811

Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM.
Nature methods Volume 11 (2014) p.171-174

Assessing the state of substitution models describing noncoding RNA evolution.
Allen JE, Whelan S.
Genome biology and evolution Volume 6 (2014) p.65-75

2013

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.
Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L.
Journal of proteomics Volume 95 (2013) p.89-92

Novel anti-plasmodial hits identified by virtual screening of the ZINC database.
Mugumbate G, Newton AS, Rosenthal PJ, Gut J, Moreira R, Chibale K, Guedes RC.
Journal of computer-aided molecular design Volume 27 (2013) p.859-871

In silico comparison of antimycobacterial natural products with known antituberculosis drugs.
Espinoza-Moraga M, Njuguna NM, Mugumbate G, Caballero J, Chibale K.
Journal of chemical information and modeling Volume 53 (2013) p.649-660

Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.
BMC systems biology Volume 7 (2013) p.116

Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.
Wallach T, Schellenberg K, Maier B, Kalathur RK, Porras P, Wanker EE, Futschik ME, Kramer A.
PLoS genetics Volume 9 (2013) p.e1003398

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
Rebholz-Schuhmann D, Kafkas S, Kim JH, Li C, Jimeno Yepes A, Hoehndorf R, Backofen R, Lewin I.
Journal of biomedical semantics Volume 4 (2013) p.28

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M.
Genome research Volume 23 (2013) p.2066-2077

Proteomics data exchange and storage: the need for common standards and public repositories.
Jiménez RC, Vizcaíno JA.
Methods in molecular biology (Clifton, N.J.) Volume 1007 (2013) p.317-333

BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1103-1104

Evolutionary biology: The handiwork of tinkering.
Flicek P.
Nature Volume 500 (2013) p.158-159

ChEMBLSpace--a graphical explorer of the chemogenomic space covered by the ChEMBL database.
Fechner N, Papadatos G, Evans D, Morphy JR, Brewerton SC, Thorner D, Bodkin M.
Bioinformatics (Oxford, England) Volume 29 (2013) p.523-524

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M, HUPO-PSI Group.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat009

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
Nature methods Volume 10 (2013) p.676-682

Monitoring named entity recognition: the League Table.
Rebholz-Schuhmann D, Kafkas S, Kim JH, Jimeno Yepes A, Lewin I.
Journal of biomedical semantics Volume 4 (2013) p.19

Synthesis and in vitro and in vivo pharmacological evaluation of new 4-aminoquinoline-based compounds.
Tukulula M, Njoroge M, Abay ET, Mugumbate GC, Wiesner L, Taylor D, Gibhard L, Norman J, Swart KJ, Gut J, Rosenthal PJ, Barteau S, Streckfuss J, Kameni-Tcheudji J, Chibale K.
ACS medicinal chemistry letters Volume 4 (2013) p.1198-1202

Estimating error rates in bioactivity databases.
Tiikkainen P, Bellis L, Light Y, Franke L.
Journal of chemical information and modeling Volume 53 (2013) p.2499-2505

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.
Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.
Proteomics Volume 13 (2013) p.2931-2937

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.
Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, Guirola O, Bringas R, Cabrera G, Guillen G, Padron G, Gonzalez LJ, Besada V.
Journal of proteomics Volume 87 (2013) p.134-138

Evolution and functional cross-talk of protein post-translational modifications.
Beltrao P, Bork P, Krogan NJ, van Noort V.
Molecular systems biology Volume 9 (2013) p.714

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I.
BMC bioinformatics Volume 14 (2013) p.104

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.
BMC systems biology Volume 7 (2013) p.135

A decadal view of biodiversity informatics: challenges and priorities.
Hardisty A, Roberts D, Biodiversity Informatics Community, Addink W, Aelterman B, Agosti D, Amaral-Zettler L, Ariño AH, Arvanitidis C, Backeljau T, Bailly N, Belbin L, Berendsohn W, Bertrand N, Caithness N, Campbell D, Cochrane G, Conruyt N, Culham A, Damgaard C, Davies N, Fady B, Faulwetter S, Feest A, Field D, Garnier E, Geser G, Gilbert J, Grosche, Grosser D, Hardisty A, Herbinet B, Hobern D, Jones A, de Jong Y, King D, Knapp S, Koivula H, Los W, Meyer C, Morris RA, Morrison N, Morse D, Obst M, Pafilis E, Page LM, Page R, Pape T, Parr C, Paton A, Patterson D, Paymal E, Penev L, Pollet M, Pyle R, von Raab-Straube E, Robert V, Roberts D, Robertson T, Rovellotti O, Saarenmaa H, Schalk P, Schaminee J, Schofield P, Sier A, Sierra S, Smith V, van Spronsen E, Thornton-Wood S, van Tienderen P, van Tol J, Tuama ÉÓ, Uetz P, Vaas L, Vignes Lebbe R, Vision T, Vu D, De Wever A, White R, Willis K, Young F.
BMC ecology Volume 13 (2013) p.16

Reconstructing Native American migrations from whole-genome and whole-exome data.
Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, 1000 Genomes Project, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD.
PLoS genetics Volume 9 (2013) p.e1004023

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.
Genome research Volume 23 (2013) p.749-761

Development and application of a DNA microarray-based yeast two-hybrid system.
Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE.
Nucleic acids research Volume 41 (2013) p.1496-1507

Critical assessment of automated flow cytometry data analysis techniques.
Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.
Nature methods Volume 10 (2013) p.228-238

PRIDE Cluster: building a consensus of proteomics data.
Griss J, Foster JM, Hermjakob H, Vizcaíno JA.
Nature methods Volume 10 (2013) p.95-96

Towards the collaborative curation of the registry underlying Identifiers.org.
Juty N, Le Novère N, Hermjakob H, Laibe C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat017

Adhesion to carbon nanotube conductive scaffolds forces action-potential appearance in immature rat spinal neurons.
Fabbro A, Sucapane A, Toma FM, Calura E, Rizzetto L, Carrieri C, Roncaglia P, Martinelli V, Scaini D, Masten L, Turco A, Gustincich S, Prato M, Ballerini L.
PloS one Volume 8 (2013) p.e73621

Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways.
Mancini C, Roncaglia P, Brussino A, Stevanin G, Lo Buono N, Krmac H, Maltecca F, Gazzano E, Bartoletti Stella A, Calvaruso MA, Iommarini L, Cagnoli C, Forlani S, Le Ber I, Durr A, Brice A, Ghigo D, Casari G, Porcelli AM, Funaro A, Gasparre G, Gustincich S, Brusco A.
BMC medical genomics Volume 6 (2013) p.22

The International Nucleotide Sequence Database Collaboration.
Nakamura Y, Cochrane G, Karsch-Mizrachi I, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 41 (2013) p.D21-4

A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones.
Hirani N, Westenberg M, Gami MS, Davis P, Hope IA, Dolphin CT.
BMC biotechnology Volume 13 (2013) p.1

Genetic susceptibility to non-necrotizing erysipelas/cellulitis.
Hannula-Jouppi K, Massinen S, Siljander T, Mäkelä S, Kivinen K, Leinonen R, Jiao H, Aitos P, Karppelin M, Vuopio J, Syrjänen J, Kere J.
PloS one Volume 8 (2013) p.e56225

Shorthand notation for lipid structures derived from mass spectrometry.
Liebisch G, Vizcaíno JA, Köfeler H, Trötzmüller M, Griffiths WJ, Schmitz G, Spener F, Wakelam MJ.
Journal of lipid research Volume 54 (2013) p.1523-1530

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR.
Molecular & cellular proteomics : MCP Volume 12 (2013) p.2332-2340

An estimated 5% of new protein structures solved today represent a new Pfam family.
Mistry J, Kloppmann E, Rost B, Punta M.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2186-2193

Recommendations of the wwPDB NMR Validation Task Force.
Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL.
Structure (London, England : 1993) Volume 21 (2013) p.1563-1570

DNA damage in mammalian neural stem cells leads to astrocytic differentiation mediated by BMP2 signaling through JAK-STAT.
Schneider L, Pellegatta S, Favaro R, Pisati F, Roncaglia P, Testa G, Nicolis SK, Finocchiaro G, d'Adda di Fagagna F.
Stem cell reports Volume 1 (2013) p.123-138

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR 3rd, Apweiler R, Ge J, Hermjakob H, Ping P.
Circulation research Volume 113 (2013) p.1043-1053

Biomarkers of food intake and metabolite differences between plasma and red blood cell matrices; a human metabolomic profile approach.
Catalán Ú, Rodríguez MÁ, Ras MR, Maciá A, Mallol R, Vinaixa M, Fernández-Castillejo S, Valls RM, Pedret A, Griffin JL, Salek R, Correig X, Motilva MJ, Solà R.
Molecular bioSystems Volume 9 (2013) p.1411-1422

Scientific competency questions as the basis for semantically enriched open pharmacological space development.
Azzaoui K, Jacoby E, Senger S, Rodríguez EC, Loza M, Zdrazil B, Pinto M, Williams AJ, de la Torre V, Mestres J, Pastor M, Taboureau O, Rarey M, Chichester C, Pettifer S, Blomberg N, Harland L, Williams-Jones B, Ecker GF.
Drug discovery today Volume 18 (2013) p.843-852

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Saez-Rodriguez J.
F1000Research Volume 2 (2013) p.192

Bioinformatics workflows and web services in systems biology made easy for experimentalists.
Jimenez RC, Corpas M.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.299-310

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V.
Analytical chemistry Volume 85 (2013) p.3515-3520

BioServices: a common Python package to access biological Web Services programmatically.
Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.3241-3242

Capturing cooperative interactions with the PSI-MI format.
Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat066

Construction of cell type-specific logic models of signaling networks using CellNOpt.
Morris MK, Melas I, Saez-Rodriguez J.
Methods in molecular biology (Clifton, N.J.) Volume 930 (2013) p.179-214

A new reference implementation of the PSICQUIC web service.
del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.
Nucleic acids research Volume 41 (2013) p.W601-6

Network based elucidation of drug response: from modulators to targets.
Iorio F, Saez-Rodriguez J, di Bernardo D.
BMC systems biology Volume 7 (2013) p.139

Genome-wide meta-analysis identifies new susceptibility loci for migraine.
Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G, Medland SE, Todt U, McArdle WL, Quaye L, Koiranen M, Ikram MA, Lehtimäki T, Stam AH, Ligthart L, Wedenoja J, Dunham I, Neale BM, Palta P, Hamalainen E, Schürks M, Rose LM, Buring JE, Ridker PM, Steinberg S, Stefansson H, Jakobsson F, Lawlor DA, Evans DM, Ring SM, Färkkilä M, Artto V, Kaunisto MA, Freilinger T, Schoenen J, Frants RR, Pelzer N, Weller CM, Zielman R, Heath AC, Madden PA, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FM, Hartikainen AL, Pouta A, van den Ende J, Uitterlinden AG, Hofman A, Amin N, Hottenga JJ, Vink JM, Heikkilä K, Alexander M, Muller-Myhsok B, Schreiber S, Meitinger T, Wichmann HE, Aromaa A, Eriksson JG, Traynor BJ, Trabzuni D, Rossin E, Lage K, Jacobs SB, Gibbs JR, Birney E, Kaprio J, Penninx BW, Boomsma DI, van Duijn C, Raitakari O, Jarvelin MR, Zwart JA, Cherkas L, Strachan DP, Kubisch C, Ferrari MD, van den Maagdenberg AM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman DI, Palotie A, North American Brain Expression Consortium, UK Brain Expression Consortium, International Headache Genetics Consortium.
Nature genetics Volume 45 (2013) p.912-917

From Peptidome to PRIDE: public proteomics data migration at a large scale.
Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H.
Proteomics Volume 13 (2013) p.1692-1695

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.
Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.
PLoS computational biology Volume 9 (2013) p.e1003253

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P.
Genome biology Volume 14 (2013) p.R148

Modeling signaling networks with different formalisms: a preview.
MacNamara A, Henriques D, Saez-Rodriguez J.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.89-105

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.
Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR.
Molecular & cellular proteomics : MCP Volume 12 (2013) p.3026-3035

Policy challenges of clinical genome sequencing.
Wright CF, Middleton A, Burton H, Cunningham F, Humphries SE, Hurst J, Birney E, Firth HV.
BMJ (Clinical research ed.) Volume 347 (2013) p.f6845

Visualization and analysis of biological networks.
Millán PP.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.63-88

Improving the performance of Transposable Elements detection tools.
Loureiro T, Camacho R, Vieira J, Fonseca NA.
Journal of integrative bioinformatics Volume 10 (2013) p.231

Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG.
Nature methods Volume 10 (2013) p.1093-1095

Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G.
Nucleic acids research Volume 41 (2013) p.5189-5198

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.
Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM.
Structure (London, England : 1993) Volume 21 (2013) p.875-881

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.
Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S.
Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.4009-4014

bioWeb3D: an online webGL 3D data visualisation tool.
Pettit JB, Marioni JC.
BMC bioinformatics Volume 14 (2013) p.185

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2320-2326

Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.
Nucleic acids research Volume 41 (2013) p.827-841

A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.
Bioinformatics (Oxford, England) Volume 29 (2013) p.206-214

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z.
Nucleic acids research Volume 41 (2013) p.D171-6

Database citation in full text biomedical articles.
Kafkas Ş, Kim JH, McEntyre JR.
PloS one Volume 8 (2013) p.e63184

Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.
Nature biotechnology Volume 31 (2013) p.126-134

A community-driven global reconstruction of human metabolism.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.
Nature biotechnology Volume 31 (2013) p.419-425

Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.
Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE.
British journal of cancer Volume 109 (2013) p.983-993

Controlled annotations for systems biology.
Juty N, Laibe C, Le Novère N.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.227-245

Transcriptional data: a new gateway to drug repositioning?
Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J.
Drug discovery today Volume 18 (2013) p.350-357

Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.
Hamilton-Williams EE, Rainbow DB, Cheung J, Christensen M, Lyons PA, Peterson LB, Steward CA, Sherman LA, Wicker LS.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 24 (2013) p.358-375

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM.
PLoS genetics Volume 9 (2013) p.e1003803

The future of the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Biopolymers Volume 99 (2013) p.218-222

Maximising proteomics data for the scientific community
Hermjakob H, Apweiler R.
European Pharmaceutical Review Volume 9 (2013) p.23-29

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.
Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J.
PloS one Volume 8 (2013) p.e61318

How community has shaped the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure (London, England : 1993) Volume 21 (2013) p.1485-1491

Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium.
Nature methods Volume 10 (2013) p.1185-1191

IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.
Kurbatova N, Chartier M, Zylber MI, Najmanovich R.
F1000Research Volume 2 (2013) p.117

Genomicus: five genome browsers for comparative genomics in eukaryota.
Louis A, Muffato M, Roest Crollius H.
Nucleic acids research Volume 41 (2013) p.D700-5

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC.
Genome biology Volume 14 (2013) p.R7

The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2013) p.456-458

Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1382-1389

A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
Ryberg M, Sandberg S, Mellberg C, Stegle O, Lindahl B, Larsson C, Hauksson J, Olsson T.
Journal of internal medicine Volume 274 (2013) p.67-76

A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden.
Funnell AP, Wilson MD, Ballester B, Mak KS, Burdach J, Magan N, Pearson RC, Lemaigre FP, Stowell KM, Odom DT, Flicek P, Crossley M.
American journal of human genetics Volume 92 (2013) p.460-467

Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case.
Kogej T, Blomberg N, Greasley PJ, Mundt S, Vainio MJ, Schamberger J, Schmidt G, Hüser J.
Drug discovery today Volume 18 (2013) p.1014-1024

Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.
Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M, Naghra H, Cotton JA, Berriman M, Britton C, Gilleard JS.
International journal for parasitology Volume 43 (2013) p.465-475

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E.
Nature Volume 494 (2013) p.77-80

Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.
Fonseca NA, Morales-Hojas R, Reis M, Rocha H, Vieira CP, Nolte V, Schlötterer C, Vieira J.
Genome biology and evolution Volume 5 (2013) p.661-679

The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.
Araújo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, Macedo-Ribeiro S, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Vieira J.
PloS one Volume 8 (2013) p.e63747

Crystal structure of the entire respiratory complex I.
Baradaran R, Berrisford JM, Minhas GS, Sazanov LA.
Nature Volume 494 (2013) p.443-448

A long road towards the structure of respiratory complex I, a giant molecular proton pump.
Sazanov LA, Baradaran R, Efremov RG, Berrisford JM, Minhas G.
Biochemical Society transactions Volume 41 (2013) p.1265-1271

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.
Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G, Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire P, Birney E, Müller F, Stupka E.
Nucleic acids research Volume 41 (2013) p.3600-3618

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.
Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.
Genome biology Volume 14 (2013) p.R37

Drug metabolite generation using a laboratory evolved NADPH independent cytochrome P450: application of in vitro and in silico approaches.
Chigorimbo-Murefu NT, Njoroge M, Louw S, Mugumbate G, Chibale K.
Drug metabolism letters Volume 7 (2013) p.68-77

High-resolution analysis of cis-acting regulatory networks at the α-globin locus.
Hughes JR, Lower KM, Dunham I, Taylor S, De Gobbi M, Sloane-Stanley JA, McGowan S, Ragoussis J, Vernimmen D, Gibbons RJ, Higgs DR.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 368 (2013) p.20120361

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.
Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L.
Nucleic acids research Volume 41 (2013) p.W591-6

Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2296

Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Raspé O, Vieira CP.
Journal of experimental botany Volume 64 (2013) p.2423-2434

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.
GigaScience Volume 2 (2013) p.10

Optimal placement of accelerometers for the detection of everyday activities.
Cleland I, Kikhia B, Nugent C, Boytsov A, Hallberg J, Synnes K, McClean S, Finlay D.
Sensors (Basel, Switzerland) Volume 13 (2013) p.9183-9200

Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.
Nature methods Volume 10 (2013) p.723-729

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N.
Nature genetics Volume 45 (2013) p.701-706

The mutational landscape of phosphorylation signaling in cancer.
Reimand J, Wagih O, Bader GD.
Scientific reports Volume 3 (2013) p.2651

Tetrazole-based deoxyamodiaquines: synthesis, ADME/PK profiling and pharmacological evaluation as potential antimalarial agents.
Tukulula M, Njoroge M, Mugumbate GC, Gut J, Rosenthal PJ, Barteau S, Streckfuss J, Heudi O, Kameni-Tcheudji J, Chibale K.
Bioorganic & medicinal chemistry Volume 21 (2013) p.4904-4913

Comment on on the propagation of errors by Jaskolski (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2297

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.
Nucleic acids research Volume 41 (2013) p.D490-8

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ.
Cell Volume 154 (2013) p.691-703

Anopheles gambiae, Anoga-HrTH hormone, free and bound structure--a nuclear magnetic resonance experiment.
Mugumbate G, Jackson GE, van der Spoel D, Kövér KE, Szilágyi L.
Peptides Volume 41 (2013) p.94-100

Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.
Science (New York, N.Y.) Volume 342 (2013) p.1235587

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J.
Journal of biomedical semantics Volume 4 (2013) p.20

The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.
Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA.
Genome biology Volume 14 (2013) p.R88

CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system.
Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG.
Cell reports Volume 5 (2013) p.271-282

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W.
Nature genetics Volume 45 (2013) p.415-21, 421e1-2

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes.
Studer RA, Dessailly BH, Orengo CA.
The Biochemical journal Volume 449 (2013) p.581-594

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.
Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F.
Molecular bioSystems Volume 9 (2013) p.70-76

The Drosophila phenotype ontology.
Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.
Journal of biomedical semantics Volume 4 (2013) p.30

High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.
Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IR, Horsburgh GJ, Potter J, Molina-Morales M, Bicknell AW, Preston SA, Ekblom R, Slate J, Burke T.
BMC genomics Volume 14 (2013) p.176

A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus.
Crossman LC, Chen H, Cerdeño-Tárraga AM, Brooks K, Quail MA, Pineiro SA, Hobley L, Sockett RE, Bentley SD, Parkhill J, Williams HN, Stine OC.
The ISME journal Volume 7 (2013) p.148-160

Evidence of long-term structured cuckoo parasitism on individual magpie hosts.
Molina-Morales M, Gabriel Martínez J, Martín-Gálvez D, A Dawson D, Rodríguez-Ruiz J, Burke T, Avilés JM.
The Journal of animal ecology Volume 82 (2013) p.389-398

Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes.
Gendrel AV, Tang YA, Suzuki M, Godwin J, Nesterova TB, Greally JM, Heard E, Brockdorff N.
Molecular and cellular biology Volume 33 (2013) p.3150-3165

Systematic analysis of experimental phenotype data reveals gene functions.
Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.
PloS one Volume 8 (2013) p.e60847

[Genome sequencing and genetic mapping to dissect the genetic basis of complex traits].
Baud A, Calderari S, Mott R, Flint J, Gauguier D, Rat Genome Sequencing and Mapping Consortium.
Medecine sciences : M/S Volume 29 (2013) p.671-674

Latent regulatory potential of human-specific repetitive elements.
Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT.
Molecular cell Volume 49 (2013) p.262-272

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau MT, Heinig M, Lee YA, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FP, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, Jones EY, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hubner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J.
Nature genetics Volume 45 (2013) p.767-775

Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.
White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Sanger Institute Mouse Genetics Project, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP.
Cell Volume 154 (2013) p.452-464

FlyBase: improvements to the bibliography.
Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ, FlyBase consortium.
Nucleic acids research Volume 41 (2013) p.D751-7

Do first-time breeding females imprint on their own eggs?
Soler M, Ruiz-Castellano C, Carra LG, Ontanilla J, Martín-Galvez D.
Proceedings. Biological sciences / The Royal Society Volume 280 (2013) p.20122518

Immunology meets genomics.
Teichmann SA.
Briefings in functional genomics Volume 12 (2013) p.469-470

Structural and functional annotation of the porcine immunome.
Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK.
BMC genomics Volume 14 (2013) p.332

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV.
Briefings in bioinformatics Volume 14 (2013) p.548-555

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ.
Nucleic acids research Volume 41 (2013) p.D483-9

Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium.
Nucleic acids research Volume 41 (2013) p.D43-7

HAMAP in 2013, new developments in the protein family classification and annotation system.
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium.
Nucleic acids research Volume 41 (2013) p.D584-9

Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ.
G3 (Bethesda, Md.) Volume 3 (2013) p.2031-2047

UniChem: a unified chemical structure cross-referencing and identifier tracking system.
Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP.
Journal of cheminformatics Volume 5 (2013) p.3

HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Hickey G, Paten B, Earl D, Zerbino D, Haussler D.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1341-1342

Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P, RGASP Consortium.
Nature methods Volume 10 (2013) p.1177-1184

Analysis Tool Web Services from the EMBL-EBI.
McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R.
Nucleic acids research Volume 41 (2013) p.W597-600

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1325-1332

Ensembl 2013.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SM.
Nucleic acids research Volume 41 (2013) p.D48-55

Association of gut microbiota with post-operative clinical course in Crohn's disease.
Dey N, Soergel DA, Repo S, Brenner SE.
BMC gastroenterology Volume 13 (2013) p.131

T-cell activation induces selective changes of cellular lipidome.
Lonnberg T, Yetukuri L, Seppanen-Laakso T, Lahesmaa R, Oresic M.
Frontiers in bioscience (Elite edition) Volume 5 (2013) p.558-573

Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.
Nature Volume 501 (2013) p.506-511

Large-scale association analysis identifies new risk loci for coronary artery disease.
CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, DIAGRAM Consortium, CARDIOGENICS Consortium, Doney AS, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, MuTHER Consortium, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AF, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wellcome Trust Case Control Consortium, Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O'Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CN, Roberts R, Watkins H, Schunkert H, Samani NJ.
Nature genetics Volume 45 (2013) p.25-33

DbVar and DGVa: public archives for genomic structural variation.
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM.
Nucleic acids research Volume 41 (2013) p.D936-41

HSM - a hybrid system based approach for modelling intracellular networks.
Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J.
Gene Volume 518 (2013) p.70-77

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
Lawler K, Hammond-Kosack K, Brazma A, Coulson RM.
BMC systems biology Volume 7 (2013) p.52

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.
Nature biotechnology Volume 31 (2013) p.1015-1022

Update on the Kelch-like (KLHL) gene family.
Dhanoa BS, Cogliati T, Satish AG, Bruford EA, Friedman JS.
Human genomics Volume 7 (2013) p.13

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.
Cell Volume 154 (2013) p.530-540

Genenames.org: the HGNC resources in 2013.
Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA.
Nucleic acids research Volume 41 (2013) p.D545-52

Response to Diaz.
Bögershausen N, Bruford E, Wollnik B.
Clinical genetics Volume 83 (2013) p.296

Skirting the pitfalls: a clear-cut nomenclature for H3K4 methyltransferases.
Bögershausen N, Bruford E, Wollnik B.
Clinical genetics Volume 83 (2013) p.212-214

The ABCs of membrane transporters in health and disease (SLC series): introduction.
Hediger MA, Clémençon B, Burrier RE, Bruford EA.
Molecular aspects of medicine Volume 34 (2013) p.95-107

Reuse of public genome-wide gene expression data.
Rung J, Brazma A.
Nature reviews. Genetics Volume 14 (2013) p.89-99

Implication of a rare deletion at distal 16p11.2 in schizophrenia.
Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, Malhotra AK, Rietschel M, Nöthen MM, Degenhardt F, Priebe L, Breuer R, Strohmaier J, Ruderfer DM, Moran JL, Chambert KD, Sanders AR, Shi J, Kendler K, Riley B, O'Neill T, Walsh D, Malhotra D, Corvin A, Purcell S, Sklar P, Iwata N, Hultman CM, Sullivan PF, Sebat J, McCarthy S, Gejman PV, Levinson DF, Owen MJ, O'Donovan MC, Lencz T, Kirov G, Molecular Genetics of Schizophrenia Consortium, Wellcome Trust Case Control Consortium 2.
JAMA psychiatry Volume 70 (2013) p.253-260

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC), Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL.
Nature genetics Volume 45 (2013) p.1353-1360

Epimutation profiling in Beckwith-Wiedemann syndrome: relationship with assisted reproductive technology.
Tee L, Lim DH, Dias RP, Baudement MO, Slater AA, Kirby G, Hancocks T, Stewart H, Hardy C, Macdonald F, Maher ER.
Clinical epigenetics Volume 5 (2013) p.23

Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R.
Immunity Volume 38 (2013) p.1271-1284

Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Chen Z, Lönnberg T, Lahesmaa R.
Scandinavian journal of immunology Volume 78 (2013) p.172-180

From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Lönnberg T, Chen Z, Lahesmaa R.
Briefings in functional genomics Volume 12 (2013) p.471-482

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.
Hill AF, Pegtel DM, Lambertz U, Leonardi T, O'Driscoll L, Pluchino S, Ter-Ovanesyan D, Nolte-'t Hoen EN.
Journal of extracellular vesicles Volume 2 (2013) p.

Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Magnusson PK, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Psychosis Endophenotypes International Consortium, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Wellcome Trust Case Control Consortium 2, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CC, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CC, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF.
Nature genetics Volume 45 (2013) p.1150-1159

A genome-wide study shows a limited contribution of rare copy number variants to Alzheimer's disease risk.
Chapman J, Rees E, Harold D, Ivanov D, Gerrish A, Sims R, Hollingworth P, Stretton A, GERAD1 Consortium, Holmans P, Owen MJ, O'Donovan MC, Williams J, Kirov G.
Human molecular genetics Volume 22 (2013) p.816-824

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM.
Molecular bioSystems Volume 9 (2013) p.1756-1764

Serotonin: from top to bottom.
Fidalgo S, Ivanov DK, Wood SH.
Biogerontology Volume 14 (2013) p.21-45

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.
Genome biology Volume 14 (2013) p.R70

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bas062

Meta-analysis of gene-level associations for rare variants based on single-variant statistics.
Hu YJ, Berndt SI, Gustafsson S, Ganna A, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn J, North KE, Ingelsson E, Lin DY.
American journal of human genetics Volume 93 (2013) p.236-248

World Health Organization International Standard to harmonize assays for detection of hepatitis E virus RNA.
Baylis SA, Blümel J, Mizusawa S, Matsubayashi K, Sakata H, Okada Y, Nübling CM, Hanschmann KM, HEV Collaborative Study Group.
Emerging infectious diseases Volume 19 (2013) p.729-735

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D781-6

Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling.
Invergo BM, Montanucci L, Koch KW, Bertranpetit J, Dell'orco D.
Cell communication and signaling : CCS Volume 11 (2013) p.36

A system-level, molecular evolutionary analysis of mammalian phototransduction.
Invergo BM, Montanucci L, Laayouni H, Bertranpetit J.
BMC evolutionary biology Volume 13 (2013) p.52

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.
de Matos P, Cham JA, Cao H, Alcántara R, Rowland F, Lopez R, Steinbeck C.
BMC bioinformatics Volume 14 (2013) p.103

Hepatitis E virus infection in Ghanaian blood donors - the importance of immunoassay selection and confirmation.
Meldal BH, Sarkodie F, Owusu-Ofori S, Allain JP.
Vox sanguinis Volume 104 (2013) p.30-36

A large-scale evaluation of computational protein function prediction.
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.
Nature methods Volume 10 (2013) p.221-227

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ.
Journal of structural biology Volume 184 (2013) p.173-181

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.
BMC genomics Volume 14 (2013) p.513

The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat029

Emdatabank: Unified Data Resource for 3DEM
Catherine Lawson, Ardan Patwardhan, Grigore D Pintilie, Eduardo Sanz Garcia, Ingvar Lagerstedt, Matthew L Baker, Raul Sala, Steven J Ludtke, Helen M Berman, Gerard Kleywegt, Wah Chiu.
Biophysical journal Volume 104 (2013) p.351a

SMIM1 underlies the Vel blood group and influences red blood cell traits.
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, Karjalainen J, Kerstens HH, Kiddle G, Lloyd-Jones H, Needs M, Poole J, Soussan AA, Rendon A, Rieneck K, Sambrook JG, Schepers H, Silljé HH, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA.
Nature genetics Volume 45 (2013) p.542-545

OntoQuery: easy-to-use web-based OWL querying.
Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2955-2957

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.
Science (New York, N.Y.) Volume 342 (2013) p.1516-1517

Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer.
Feig C, Jones JO, Kraman M, Wells RJ, Deonarine A, Chan DS, Connell CM, Roberts EW, Zhao Q, Caballero OL, Teichmann SA, Janowitz T, Jodrell DI, Tuveson DA, Fearon DT.
Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.20212-20217

Protein complexes are under evolutionary selection to assemble via ordered pathways.
Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA.
Cell Volume 153 (2013) p.461-470

Structural, evolutionary, and assembly principles of protein oligomerization.
Levy ED, Teichmann S.
Progress in molecular biology and translational science Volume 117 (2013) p.25-51

Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia.
Roberts EW, Deonarine A, Jones JO, Denton AE, Feig C, Lyons SK, Espeli M, Kraman M, McKenna B, Wells RJ, Zhao Q, Caballero OL, Larder R, Coll AP, O'Rahilly S, Brindle KM, Teichmann SA, Tuveson DA, Fearon DT.
The Journal of experimental medicine Volume 210 (2013) p.1137-1151

LifeTrain: towards a European framework for continuing professional development in biomedical sciences
Brooksbank C.
Nature reviews. Drug discovery Volume (2013) p.

The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.
Hall Z, Hernández H, Marsh JA, Teichmann SA, Robinson CV.
Structure (London, England : 1993) Volume 21 (2013) p.1325-1337

iAnn: an event sharing platform for the life sciences.
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1919-1921

The role of reporting standards for metabolite annotation and identification in metabolomic studies.
Salek RM, Steinbeck C, Viant MR, Goodacre R, Dunn WB.
GigaScience Volume 2 (2013) p.13

The Amborella genome and the evolution of flowering plants.
Amborella Genome Project.
Science (New York, N.Y.) Volume 342 (2013) p.1241089

Best practices in bioinformatics training for life scientists.
Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.
Briefings in bioinformatics Volume 14 (2013) p.528-537

Expanding natural product chemistry resources at the EBI.
Hastings J, Conesa P, Dekker A, Ennis M, Haug K, Jayaseelan K, Kale N, Mahendraker T, Moreno P, Muthukrishnan V, Owen G, Salek R, Turner S, Steinbeck C.
Journal of Cheminformatics Volume 5 (2013) p.P43-P43

Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes.
Nishi H, Fong JH, Chang C, Teichmann SA, Panchenko AR.
Molecular bioSystems Volume 9 (2013) p.1620-1626

Cryo-electron microscopy--a primer for the non-microscopist.
Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S.
The FEBS journal Volume 280 (2013) p.28-45

Review of “Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)” by Mikhail E Elyashberg, Antony Williams and Kirill Blinov.
Steinbeck C.
Journal of Cheminformatics Volume 5 (2013) p.29-29

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D456-63

Noncanonical expression of caudal during early embryogenesis in the pea aphid Acyrthosiphon pisum: maternal cad-driven posterior development is not conserved.
Chang CC, Hsiao YM, Huang TY, Cook CE, Shigenobu S, Chang TH.
Insect molecular biology Volume 22 (2013) p.442-455

Dissemination of metabolomics results: role of MetaboLights and COSMOS.
Salek RM, Haug K, Steinbeck C.
GigaScience Volume 2 (2013) p.8

The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.
Moulos P, Klein J, Jupp S, Stevens R, Bascands JL, Schanstra JP.
BMC bioinformatics Volume 14 (2013) p.235

Evolution of protein structures and interactions from the perspective of residue contact networks.
Zhang X, Perica T, Teichmann SA.
Current opinion in structural biology Volume 23 (2013) p.954-963

The zebrafish reference genome sequence and its relationship to the human genome.
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL.
Nature Volume 496 (2013) p.498-503

Detection and imaging the expression of the trans-membrane protein CD44 in RT112 cells by use of enzyme-labeled antibodies and SECM.
Roberts WS, Davis F, Holmes JL, Collyer SD, Larcombe LD, Morgan SL, Higson SP.
Biosensors & bioelectronics Volume 41 (2013) p.282-288

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson WO, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimäki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt MF, Mohlke KL, O'Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E.
Nature genetics Volume 45 (2013) p.501-512

A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2808-2809

miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs.
Lupini L, Bassi C, Ferracin M, Bartonicek N, D'Abundo L, Zagatti B, Callegari E, Musa G, Moshiri F, Gramantieri L, Corrales FJ, Enright AJ, Sabbioni S, Negrini M.
Frontiers in genetics Volume 4 (2013) p.64

Detecting and comparing non-coding RNAs in the high-throughput era.
Bussotti G, Notredame C, Enright AJ.
International journal of molecular sciences Volume 14 (2013) p.15423-15458

Supporting SBML as a model exchange format in software applications.
Keating SM, Le Novère N.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.201-225

Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene.
Hanning JE, Saini HK, Murray MJ, van Dongen S, Davis MP, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR, Coleman N.
British journal of cancer Volume 108 (2013) p.450-460

Enhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice.
Clare S, John V, Walker AW, Hill JL, Abreu-Goodger C, Hale C, Goulding D, Lawley TD, Mastroeni P, Frankel G, Enright AJ, Vigorito E, Dougan G.
Infection and immunity Volume 81 (2013) p.723-732

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.
Petrov AI, Zirbel CL, Leontis NB.
RNA (New York, N.Y.) Volume 19 (2013) p.1327-1340

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic acids research Volume 41 (2013) p.W15-21

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H.
Nucleic acids research Volume 41 (2013) p.D1063-9

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA.
PloS one Volume 8 (2013) p.e61951

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D773-80

Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state.
Hanning JE, Saini HK, Murray MJ, Caffarel MM, van Dongen S, Ward D, Barker EM, Scarpini CG, Groves IJ, Stanley MA, Enright AJ, Pett MR, Coleman N.
The Journal of pathology Volume 231 (2013) p.354-366

LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.
Murray MJ, Saini HK, Siegler CA, Hanning JE, Barker EM, van Dongen S, Ward DM, Raby KL, Groves IJ, Scarpini CG, Pett MR, Thornton CM, Enright AJ, Nicholson JC, Coleman N, CCLG.
Cancer research Volume 73 (2013) p.4872-4884

KNIME-CDK: Workflow-driven cheminformatics.
Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C.
BMC bioinformatics Volume 14 (2013) p.257

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ.
Methods (San Diego, Calif.) Volume 63 (2013) p.41-49

Metingear: a development environment for annotating genome-scale metabolic models.
May JW, James AG, Steinbeck C.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2213-2215

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D.
Molecular cell Volume 50 (2013) p.601-608

Vive la difference: naming structural variants in the human reference genome.
Seal RL, Wright MW, Gray KA, Bruford EA.
Human genomics Volume 7 (2013) p.12

Brood parasitism correlates with the strength of spatial autocorrelation of life history and defensive traits in Magpies.
Soler JJ, Martín-Gálvez D, de Neve L, Soler M.
Ecology Volume 94 (2013) p.1338-1346

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI).
Rebholz-Schuhmann D, Kim JH, Yan Y, Dixit A, Friteyre C, Hoehndorf R, Backofen R, Lewin I.
PloS one Volume 8 (2013) p.e75185

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC.
Journal of proteomics Volume 89 (2013) p.179-182

SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping.
Betancourt LH, De Bock PJ, Staes A, Timmerman E, Perez-Riverol Y, Sanchez A, Besada V, Gonzalez LJ, Vandekerckhove J, Gevaert K.
Journal of proteomics Volume 91 (2013) p.164-171

The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M.
Database: The Journal of Biological Databases and Curation Volume 2013 (2013) p.

Facing growth in the European Nucleotide Archive.
Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V.
Nucleic acids research Volume 41 (2013) p.D30-5

Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1343-1344

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic acids research Volume 41 (2013) p.D530-5

ISCB computational biology Wikipedia competition.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.
PLoS computational biology Volume 9 (2013) p.e1003242

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.
Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ.
Genome biology Volume 14 (2013) p.R11

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
Ziehm M, Thornton JM.
Aging cell Volume 12 (2013) p.910-916

ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.
Nucleic acids research Volume 41 (2013) p.D987-90

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.
Proteins Volume 81 (2013) p.1980-1987

ROCK: a resource for integrative breast cancer data analysis.
Ur-Rehman S, Gao Q, Mitsopoulos C, Zvelebil M.
Breast cancer research and treatment Volume 139 (2013) p.907-921

JBioWH: an open-source Java framework for bioinformatics data integration.
Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat051

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat077

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.
Nucleic acids research Volume 41 (2013) p.D499-507

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Ziehm M, Piper MD, Thornton JM.
Aging cell Volume 12 (2013) p.917-922

Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus.
Corona M, Libbrecht R, Wurm Y, Riba-Grognuz O, Studer RA, Keller L.
PLoS genetics Volume 9 (2013) p.e1003730

Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.
Nucleic acids research Volume 41 (2013) p.D226-32

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M.
Nucleic acids research Volume 41 (2013) p.e121

LUD, a new protein domain associated with lactate utilization.
Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A.
BMC bioinformatics Volume 14 (2013) p.341

The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat023

The annotation-enriched non-redundant patent sequence databases.
Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat005

IPD--the Immuno Polymorphism Database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG.
Nucleic acids research Volume 41 (2013) p.D1234-40

The IMGT/HLA database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic acids research Volume 41 (2013) p.D1222-7

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM.
Current opinion in structural biology Volume 23 (2013) p.443-450

Filling out the structural map of the NTF2-like superfamily.
Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L.
BMC bioinformatics Volume 14 (2013) p.327

The SHOCT domain: a widespread domain under-represented in model organisms.
Eberhardt RY, Bartholdson SJ, Punta M, Bateman A.
PloS one Volume 8 (2013) p.e57848

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.
Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A.
BMC bioinformatics Volume 14 (2013) p.265

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP.
Nucleic acids research Volume 41 (2013) p.4549-4564

Abstracting knowledge from the Protein Data Bank.
Furnham N, Laskowski RA, Thornton JM.
Biopolymers Volume 99 (2013) p.183-188

Elucidating human phosphatase-substrate networks.
Li X, Wilmanns M, Thornton J, Köhn M.
Science signaling Volume 6 (2013) p.rs10

The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.
PLoS biology Volume 11 (2013) p.e1001638

The role of structural bioinformatics resources in the era of integrative structural biology.
Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.710-721

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2395-2402

Using phenotypic heterogeneity to increase the power of genome-wide association studies: application to age at onset of ischaemic stroke subphenotypes.
Traylor M, Bevan S, Rothwell PM, Sudlow C, Wellcome Trust Case Control Consortium 2 (WTCCC2), Dichgans M, Markus HS, Lewis CM.
Genetic epidemiology Volume 37 (2013) p.495-503

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM.
PLoS computational biology Volume 9 (2013) p.e1003382

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.
Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J.
Molecular bioSystems Volume 9 (2013) p.1576-1583

The impact of mathematical modeling on the understanding of diabetes and related complications.
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V.
CPT: pharmacometrics & systems pharmacology Volume 2 (2013) p.e54

A variant in LDLR is associated with abdominal aortic aneurysm.
Bradley DT, Hughes AE, Badger SA, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Grétarsdóttir S, Burnand K, Child AH, Clough RE, Cockerill G, Hafez H, Scott DJ, Ariëns RA, Johnson A, Sohrabi S, Smith A, Thompson MM, van Bockxmeer FM, Waltham M, Matthíasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Wild JB, Edkins S, Gwilliam R, Hunt SE, Potter S, Lindholt JS, Golledge J, Norman PE, van Rij A, Powell JT, Eriksson P, Stefánsson K, Thompson JR, Humphries SE, Sayers RD, Deloukas P, Samani NJ, Bown MJ.
Circulation. Cardiovascular genetics Volume 6 (2013) p.498-504

BioModels Database: a repository of mathematical models of biological processes.
Chelliah V, Laibe C, Le Novère N.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.189-199

Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF.
Nolen LD, Boyle S, Ansari M, Pritchard E, Bickmore WA.
Human molecular genetics Volume 22 (2013) p.4180-4193

17q25 Locus is associated with white matter hyperintensity volume in ischemic stroke, but not with lacunar stroke status.
Adib-Samii P, Rost N, Traylor M, Devan W, Biffi A, Lanfranconi S, Fitzpatrick K, Bevan S, Kanakis A, Valant V, Gschwendtner A, Malik R, Richie A, Gamble D, Segal H, Parati EA, Ciusani E, Holliday EG, Maguire J, Wardlaw J, Worrall B, Bis J, Wiggins KL, Longstreth W, Kittner SJ, Cheng YC, Mosley T, Falcone GJ, Furie KL, Leiva-Salinas C, Lau BC, Saleem Khan M, Australian Stroke Genetics Collaborative, Wellcome Trust Case-Control Consortium-2 (WTCCC2), METASTROKE, Sharma P, Fornage M, Mitchell BD, Psaty BM, Sudlow C, Levi C, Boncoraglio GB, Rothwell PM, Meschia J, Dichgans M, Rosand J, Markus HS, International Stroke Genetics Consortium.
Stroke; a journal of cerebral circulation Volume 44 (2013) p.1609-1615

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins Volume 81 (2013) p.583-591

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.
Anderson JW, Haas PA, Mathieson LA, Volynkin V, Lyngsø R, Tataru P, Hein J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.704-710

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.132-134

Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.
LeishGEN Consortium, Wellcome Trust Case Control Consortium 2, Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SM, Sundar S, Spencer CC, Blackwell JM, Donnelly P.
Nature genetics Volume 45 (2013) p.208-213

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.
Sanseverino W, Hermoso A, D'Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR.
Nucleic acids research Volume 41 (2013) p.D1167-71

Characterization of a versatile organometallic pro-drug (CORM) for experimental CO based therapeutics.
Seixas JD, Mukhopadhyay A, Santos-Silva T, Otterbein LE, Gallo DJ, Rodrigues SS, Guerreiro BH, Gonçalves AM, Penacho N, Marques AR, Coelho AC, Reis PM, Romão MJ, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 42 (2013) p.5985-5998

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
Lahti L, Torrente A, Elo LL, Brazma A, Rung J.
Nucleic acids research Volume 41 (2013) p.e110

Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus.
Blue Mountains Eye Study (BMES), Wellcome Trust Case Control Consortium 2 (WTCCC2).
Human molecular genetics Volume 22 (2013) p.4653-4660

CySBGN: a Cytoscape plug-in to integrate SBGN maps.
Gonçalves E, van Iersel M, Saez-Rodriguez J.
BMC bioinformatics Volume 14 (2013) p.17

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.
Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R.
The Journal of pathology Volume 230 (2013) p.270-276

Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.
Hinks A, Cobb J, Marion MC, Prahalad S, Sudman M, Bowes J, Martin P, Comeau ME, Sajuthi S, Andrews R, Brown M, Chen WM, Concannon P, Deloukas P, Edkins S, Eyre S, Gaffney PM, Guthery SL, Guthridge JM, Hunt SE, James JA, Keddache M, Moser KL, Nigrovic PA, Onengut-Gumuscu S, Onslow ML, Rosé CD, Rich SS, Steel KJ, Wakeland EK, Wallace CA, Wedderburn LR, Woo P, Boston Children's JIA Registry, British Society of Paediatric and Adolescent Rheumatology (BSPAR) Study Group, Childhood Arthritis Prospective Study (CAPS), Childhood Arthritis Response to Medication Study (CHARMS), German Society for Pediatric Rheumatology (GKJR), JIA Gene Expression Study, NIAMS JIA Genetic Registry, TREAT Study, United Kingdom Juvenile Idiopathic Arthritis Genetics Consortium (UKJIAGC), Bohnsack JF, Haas JP, Glass DN, Langefeld CD, Thomson W, Thompson SD.
Nature genetics Volume 45 (2013) p.664-669

2012

The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.
Nucleic acids research Volume 40 (2012) p.D841-6

Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.
Tamuri AU, dos Reis M, Goldstein RA.
Genetics Volume 190 (2012) p.1101-1115

InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong S.
Nucleic acids research Volume 40 (2012) p.4725-4725

The UniProt-GO Annotation database in 2011.
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R.
Nucleic acids research Volume 40 (2012) p.D565-70

The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic acids research Volume 40 (2012) p.D559-64

The HUPO initiative on Model Organism Proteomes, iMOP.
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.
Proteomics Volume 12 (2012) p.340-345

Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 40 (2012) p.D71-5

First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans?
Matos KS, da Cunha EF, da Silva Gonçalves A, Wilter A, Kuča K, França TC, Ramalho TC.
Journal of biomolecular structure & dynamics Volume 30 (2012) p.546-558

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND.
PLoS computational biology Volume 8 (2012) p.e1002330

The bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling.
Quin MB, Berrisford JM, Newman JA, Baslé A, Lewis RJ, Marles-Wright J.
Structure (London, England : 1993) Volume 20 (2012) p.350-363

ACPYPE - AnteChamber PYthon Parser interfacE.
Sousa da Silva AW, Vranken WF.
BMC research notes Volume 5 (2012) p.367

The YARHG domain: an extracellular domain in search of a function.
Coggill P, Bateman A.
PloS one Volume 7 (2012) p.e35575

The BioSample Database (BioSD) at the European Bioinformatics Institute.
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research Volume 40 (2012) p.D64-70

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Stegle O, Parts L, Piipari M, Winn J, Durbin R.
Nature protocols Volume 7 (2012) p.500-507

Improvements in the Protein Identifier Cross-Reference service.
Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA.
Nucleic acids research Volume 40 (2012) p.W276-80

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ.
The Plant cell Volume 24 (2012) p.3530-3557

Patterns of cis regulatory variation in diverse human populations.
Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.
PLoS genetics Volume 8 (2012) p.e1002639

Making your database available through Wikipedia: the pros and cons.
Finn RD, Gardner PP, Bateman A.
Nucleic acids research Volume 40 (2012) p.D9-12

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Bateman A.
Nucleic acids research Volume 40 (2012) p.D343-50

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.
Proteomics Volume 12 (2012) p.795-798

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks.
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM.
Molecular cell Volume 46 (2012) p.871-883

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y.
Genome research Volume 22 (2012) p.602-610

CING: an integrated residue-based structure validation program suite.
Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW.
Journal of biomolecular NMR Volume 54 (2012) p.267-283

OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR.
Nature methods Volume 9 (2012) p.245-253

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.
Cancers Volume 4 (2012) p.1180-1211

PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA.
Nature biotechnology Volume 30 (2012) p.135-137

PRIDE: quality control in a proteomics data repository.
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas004

HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.
Lam MP, Vivanco F, Scholten A, Hermjakob H, Van Eyk J, Ping P.
Proteomics Volume 12 (2012) p.749-751

Data management challenges in three-dimensional EM.
Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ.
Nature structural & molecular biology Volume 19 (2012) p.1203-1207

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.
Journal of proteome research Volume 11 (2012) p.1412-1419

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.
Nature methods Volume 9 (2012) p.345-350

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Nature Volume 491 (2012) p.56-65

The interface of protein structure, protein biophysics, and molecular evolution.
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.
Protein science : a publication of the Protein Society Volume 21 (2012) p.769-785

Bioinformatics meets user-centred design: a perspective.
Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C.
PLoS computational biology Volume 8 (2012) p.e1002554

The mzIdentML data standard for mass spectrometry-based proteomics results.
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.
Molecular & cellular proteomics : MCP Volume 11 (2012) p.M111.014381

Bioimage informatics: a new category in Bioinformatics.
Peng H, Bateman A, Valencia A, Wren JD.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1057

The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium.
Nature methods Volume 9 (2012) p.459-462

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.
Wimalaratne SM, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B.
Bioinformatics (Oxford, England) Volume 28 (2012) p.448-450

Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.
Teichmann SA, Wigge PA, Charoensawan V.
Cell cycle (Georgetown, Tex.) Volume 11 (2012) p.4487-4488

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.
Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A.
Cell stem cell Volume 10 (2012) p.157-170

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.
Vaquerizas JM, Teichmann SA, Luscombe NM.
Methods in molecular biology (Clifton, N.J.) Volume 786 (2012) p.3-19

PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.
Nucleic acids research Volume 40 (2012) p.D445-52

Blind testing of routine, fully automated determination of protein structures from NMR data.
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM.
Structure (London, England : 1993) Volume 20 (2012) p.227-236

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1001-1008

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA.
Molecular cell Volume 47 (2012) p.183-192

Probing the diverse landscape of protein flexibility and binding.
Marsh JA, Teichmann SA, Forman-Kay JD.
Current opinion in structural biology Volume 22 (2012) p.643-650

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.
Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA.
Biochemical Society transactions Volume 40 (2012) p.475-491

The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions.
Fonseca NA, Vieira CP, Schlötterer C, Vieira J.
Fly Volume 6 (2012) p.71-74

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
Briefings in bioinformatics Volume 13 (2012) p.383-389

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
Reisinger F, Krishna R, Ghali F, Ríos D, Hermjakob H, Vizcaíno JA, Jones AR.
Proteomics Volume 12 (2012) p.790-794

Annotating cancer variants and anti-cancer therapeutics in reactome.
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.
Cancers Volume 4 (2012) p.1180-1211

A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR.
Omics : a journal of integrative biology Volume 16 (2012) p.431-442

InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.
Nucleic acids research Volume 40 (2012) p.D306-12

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.
Proteomics Volume 12 (2012) p.11-20

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.
Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H.
Proteomics Volume 12 (2012) p.2767-2772

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H.
Proteomics Volume 12 (2012) p.351-355

European initiative towards quality standards in education and training for discovery, development and use of medicines.
Klech H, Brooksbank C, Price S, Verpillat P, Bühler FR, Dubois D, Haider N, Johnson C, Lindén HH, Payton T, Renn O, See W.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences Volume 45 (2012) p.515-520

Analyzing protein-protein interaction networks.
Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE.
Journal of proteome research Volume 11 (2012) p.2014-2031

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.
Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas036

The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.
Nucleic acids research Volume 40 (2012) p.D290-301

The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium.
Nature Volume 485 (2012) p.635-641

PomBase: a comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG.
Nucleic acids research Volume 40 (2012) p.D695-9

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.
BMC bioinformatics Volume 13 (2012) p.324

Predicting the secondary structure of proteins using machine learning algorithms.
Camacho R, Ferreira R, Rosa N, Guimarães V, Fonseca NA, Costa VS, de Sousa M, Magalhães A.
International journal of data mining and bioinformatics Volume 6 (2012) p.571-584

Transcription factors of Lotus: regulation of isoflavonoid biosynthesis requires coordinated changes in transcription factor activity.
Shelton D, Stranne M, Mikkelsen L, Pakseresht N, Welham T, Hiraka H, Tabata S, Sato S, Paquette S, Wang TL, Martin C, Bailey P.
Plant physiology Volume 159 (2012) p.531-547

ADOPS--Automatic Detection Of Positively Selected Sites.
Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Fonseca NA, Vieira J.
Journal of integrative bioinformatics Volume 9 (2012) p.200

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA.
Molecular & cellular proteomics : MCP Volume 11 (2012) p.1682-1689

A network-oriented perspective on cardiac calcium signaling.
George CH, Parthimos D, Silvester NC.
American journal of physiology. Cell physiology Volume 303 (2012) p.C897-910

Access and use of the GUDMAP database of genitourinary development.
Davies JA, Little MH, Aronow B, Armstrong J, Brennan J, Lloyd-MacGilp S, Armit C, Harding S, Piu X, Roochun Y, Haggarty B, Houghton D, Davidson D, Baldock R.
Methods in molecular biology (Clifton, N.J.) Volume 886 (2012) p.185-201

Opportunities for text mining in the FlyBase genetic literature curation workflow.
McQuilton P, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas039

Directly e-mailing authors of newly published papers encourages community curation.
Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas024

A suggested new bacteriophage genus: "Viunalikevirus".
Adriaenssens EM, Ackermann HW, Anany H, Blasdel B, Connerton IF, Goulding D, Griffiths MW, Hooton SP, Kutter EM, Kropinski AM, Lee JH, Maes M, Pickard D, Ryu S, Sepehrizadeh Z, Shahrbabak SS, Toribio AL, Lavigne R.
Archives of virology Volume 157 (2012) p.2035-2046

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.
Bioinformatics (Oxford, England) Volume 28 (2012) p.3163-3165

State-time spectrum of signal transduction logic models.
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.
Physical biology Volume 9 (2012) p.045003

Ensembl 2012.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.
Nucleic acids research Volume 40 (2012) p.D84-90

Integrating literature-constrained and data-driven inference of signalling networks.
Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 28 (2012) p.2311-2317

FlyBase 101--the basics of navigating FlyBase.
McQuilton P, St Pierre SE, Thurmond J, FlyBase Consortium.
Nucleic acids research Volume 40 (2012) p.D706-14

PSI-Search: iterative HOE-reduced profile SSEARCH searching.
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1650-1651

An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium.
Nature Volume 489 (2012) p.57-74

Populous: a tool for building OWL ontologies from templates.
Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R.
BMC bioinformatics Volume 13 Suppl 1 (2012) p.S5

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.
Jupp S, Stevens R, Hoehndorf R.
Journal of biomedical semantics Volume 3 Suppl 1 (2012) p.S3

Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L.
Drug discovery today Volume 17 Suppl (2012) p.S3-15

A parallel systematic-Monte Carlo algorithm for exploring conformational space.
Perez-Riverol Y, Vera R, Mazola Y, Musacchio A.
Current topics in medicinal chemistry Volume 12 (2012) p.1790-1796

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Nucleic acids research Volume 40 (2012) p.D91-7

BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.
Bioinformatics (Oxford, England) Volume 28 (2012) p.2693-2695

MyDas, an extensible Java DAS server.
Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.
PloS one Volume 7 (2012) p.e44180

Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets.
Jupe S, Akkerman JW, Soranzo N, Ouwehand WH.
Journal of thrombosis and haemostasis : JTH Volume 10 (2012) p.2399-2402

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.
Prins P, Goto N, Yates A, Gautier L, Willis S, Fields C, Katayama T.
Methods in molecular biology (Clifton, N.J.) Volume 856 (2012) p.513-527

Insights into hominid evolution from the gorilla genome sequence.
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.
Nature Volume 483 (2012) p.169-175

Mapping the human phosphatome on growth pathways.
Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G.
Molecular systems biology Volume 8 (2012) p.603

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, 1000 Genomes Project Consortium.
American journal of human genetics Volume 91 (2012) p.1022-1032

Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.
Schulte I, Batty EM, Pole JC, Blood KA, Mo S, Cooke SL, Ng C, Howe KL, Chin SF, Brenton JD, Caldas C, Howarth KD, Edwards PA.
BMC genomics Volume 13 (2012) p.719

The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer.
Ng CK, Cooke SL, Howe K, Newman S, Xian J, Temple J, Batty EM, Pole JC, Langdon SP, Edwards PA, Brenton JD.
The Journal of pathology Volume 226 (2012) p.703-712

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.
Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG.
PloS one Volume 7 (2012) p.e50085

Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.
Emery L, Whelan S, Hirschi KD, Pittman JK.
Frontiers in plant science Volume 3 (2012) p.1

Extracellular membrane vesicles and immune regulation in the brain.
Cossetti C, Smith JA, Iraci N, Leonardi T, Alfaro-Cervello C, Pluchino S.
Frontiers in physiology Volume 3 (2012) p.117

MageComet--web application for harmonizing existing large-scale experiment descriptions.
Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1402-1403

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S.
Bioinformatics (Oxford, England) Volume 28 (2012) p.246-253

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome research Volume 22 (2012) p.2376-2384

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.
Melas IN, Mitsos A, Messinis DE, Weiss TS, Rodriguez JS, Alexopoulos LG.
Molecular bioSystems Volume 8 (2012) p.1571-1584

Modeling signaling networks using high-throughput phospho-proteomics.
Terfve C, Saez-Rodriguez J.
Advances in experimental medicine and biology Volume 736 (2012) p.19-57

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.
Nucleic acids research Volume 40 (2012) p.D1077-81

Systematic identification of genomic markers of drug sensitivity in cancer cells.
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O'Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH.
Nature Volume 483 (2012) p.570-575

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.
Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA.
Integrative biology : quantitative biosciences from nano to macro Volume 4 (2012) p.1038-1048

Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome.
Gendrel AV, Apedaile A, Coker H, Termanis A, Zvetkova I, Godwin J, Tang YA, Huntley D, Montana G, Taylor S, Giannoulatou E, Heard E, Stancheva I, Brockdorff N.
Developmental cell Volume 23 (2012) p.265-279

Efficient photocatalytic hydrogen production by platinum-loaded carbon-doped cadmium indate nanoparticles.
Thornton JM, Raftery D.
ACS applied materials & interfaces Volume 4 (2012) p.2426-2431

ELIXIR: a distributed infrastructure for European biological data.
Crosswell LC, Thornton JM.
Trends in biotechnology Volume 30 (2012) p.241-242

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.
BMC systems biology Volume 6 (2012) p.29

Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Schwarz MA, Thornton J, Xu H, Awasthi N, Schwarz RE.
PloS one Volume 7 (2012) p.e33101

Current challenges in genome annotation through structural biology and bioinformatics.
Furnham N, de Beer TA, Thornton JM.
Current opinion in structural biology Volume 22 (2012) p.594-601

Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer.
Sanchez A, Sun W, Ma J, Betancourt L, Perez-Riverol Y, de-Cossio JF, Padron G, Jiang Y, He F, Gonzalez LJ, Besada V.
European journal of mass spectrometry (Chichester, England) Volume 18 (2012) p.505-508

graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1665-1667

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I.
PloS one Volume 7 (2012) p.e41762

Extent, causes, and consequences of small RNA expression variation in human adipose tissue.
Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J, MuTHER Consortium, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM.
PLoS genetics Volume 8 (2012) p.e1002704

Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177

Evaluation of a technology enabled garment for older walkers.
Burns WP, Nugent CD, McCullagh PJ, Finlay DD, Cleland I, Scotney BW, McClean SI, McCann J, Gueldenring D.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2012 (2012) p.2100-2103

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X, Coffey AJ, Turner DJ, Swerdlow H, Burton J, Quail MA, Conrad DF, Enright AJ, Tyler-Smith C, Xue Y.
Human genetics Volume 131 (2012) p.665-674

MELTING, a flexible platform to predict the melting temperatures of nucleic acids.
Dumousseau M, Rodriguez N, Juty N, Le Novère N.
BMC bioinformatics Volume 13 (2012) p.101

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.
Juty N, Le Novère N, Laibe C.
Nucleic acids research Volume 40 (2012) p.D580-6

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation.
Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N, Hunter S.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bar068

Metagenomic analysis: the challenge of the data bonanza.
Hunter CI, Mitchell A, Jones P, McAnulla C, Pesseat S, Scheremetjew M, Hunter S.
Briefings in bioinformatics Volume 13 (2012) p.743-746

Isoelectric point optimization using peptide descriptors and support vector machines.
Perez-Riverol Y, Audain E, Millan A, Ramos Y, Sanchez A, Vizcaíno JA, Wang R, Müller M, Machado YJ, Betancourt LH, González LJ, Padrón G, Besada V.
Journal of proteomics Volume 75 (2012) p.2269-2274

The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012.
Attwood TK, Coletta A, Muirhead G, Pavlopoulou A, Philippou PB, Popov I, Romá-Mateo C, Theodosiou A, Mitchell AL.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas019

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs.
Manakov SA, Morton A, Enright AJ, Grant SG.
Frontiers in neuroscience Volume 6 (2012) p.156

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ Jr, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A.
Circulation Volume 125 (2012) p.2751-2761

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.1204-1209

Large-scale analysis of microRNA evolution.
Guerra-Assunção JA, Enright AJ.
BMC genomics Volume 13 (2012) p.218

Biocurators and biocuration: surveying the 21st century challenges.
Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios L, Gaudet P.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bar059

Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting.
Zheng-Bradley X, Flicek P.
Human mutation Volume 33 (2012) p.1016-1019

Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis.
Masforrol Y, Gil J, González LJ, Pérez-Riverol Y, Fernández-de-Cossío J, Sánchez A, Betancourt LH, Garay HE, Cabrales A, Albericio F, Yang H, Zubarev RA, Besada V, Acosta OR.
ACS combinatorial science Volume 14 (2012) p.145-149

Safe, long-term hepatic expression of anti-HCV shRNA in a nonhuman primate model.
Suhy DA, Kao SC, Mao T, Whiteley L, Denise H, Souberbielle B, Burdick AD, Hayes K, Wright JF, Lavender H, Roelvink P, Kolykhalov A, Brady K, Moschos SA, Hauck B, Zelenaia O, Zhou S, Scribner C, High KA, Renison SH, Corbau R.
Molecular therapy : the journal of the American Society of Gene Therapy Volume 20 (2012) p.1737-1749

In vitro characterization of the activity of PF-05095808, a novel biological agent for hepatitis C virus therapy.
Lavender H, Brady K, Burden F, Delpuech-Adams O, Denise H, Palmer A, Perkins H, Savic B, Scott S, Smith-Burchnell C, Troke P, Wright JF, Suhy D, Corbau R.
Antimicrobial agents and chemotherapy Volume 56 (2012) p.1364-1375

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.
Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C.
The Journal of biological chemistry Volume 287 (2012) p.29516-29528

The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models.
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ.
Journal of biological rhythms Volume 27 (2012) p.328-332

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A, Vilella AJ, Goldman N.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1684-1691

The KUPKB: a novel Web application to access multiomics data on kidney disease.
Klein J, Jupp S, Moulos P, Fernandez M, Buffin-Meyer B, Casemayou A, Chaaya R, Charonis A, Bascands JL, Stevens R, Schanstra JP.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 26 (2012) p.2145-2153

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM.
PLoS computational biology Volume 8 (2012) p.e1002403

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM.
PloS one Volume 7 (2012) p.e50881

Women in science.
Dean C, Osborn M, Oshlack A, Thornton J.
Genome biology Volume 13 (2012) p.148

Major submissions tool developments at the European Nucleotide Archive.
Amid C, Birney E, Bower L, Cerdeño-Tárraga A, Cheng Y, Cleland I, Faruque N, Gibson R, Goodgame N, Hunter C, Jang M, Leinonen R, Liu X, Oisel A, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Rivière S, Rossello M, Senf A, Smirnov D, Ten Hoopen P, Vaughan D, Vaughan R, Zalunin V, Cochrane G.
Nucleic acids research Volume 40 (2012) p.D43-7

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.E944-53

ChEMBL: a large-scale bioactivity database for drug discovery.
Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP.
Nucleic acids research Volume 40 (2012) p.D1100-7

An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.
Sipos B, Massingham T, Stütz AM, Goldman N.
PloS one Volume 7 (2012) p.e43359

Shouldn't enantiomeric purity be included in the minimum information about a bioactive entity? Response from the MIABE group
Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.
Nature reviews. Drug discovery Volume 11 (2012) p.730

Annotating Human P-Glycoprotein Bioassay Data.
Zdrazil B, Pinto M, Vasanthanathan P, Williams AJ, Balderud LZ, Engkvist O, Chichester C, Hersey A, Overington JP, Ecker GF.
Molecular informatics Volume 31 (2012) p.599-609

MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.
Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P.
PloS one Volume 7 (2012) p.e40938

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N.
Molecular biology and evolution Volume 29 (2012) p.1125-1139

Looking for Darwin in genomic sequences--validity and success of statistical methods.
Zhai W, Nielsen R, Goldman N, Yang Z.
Molecular biology and evolution Volume 29 (2012) p.2889-2893

Open data for drug discovery: learning from the biological community.
Hersey A, Senger S, Overington JP.
Future medicinal chemistry Volume 4 (2012) p.1865-1867

Error-correcting properties of the SOLiD Exact Call Chemistry.
Massingham T, Goldman N.
BMC bioinformatics Volume 13 (2012) p.145

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM.
Nucleic acids research Volume 40 (2012) p.D776-82

Toxicogenomics Investigation Under the eTOX Project
Taboureau O, Hersey A, Audouze K, Gautier L, Jacobsen UP, Akhtar R, Atkinson F, Overington JP, Brunak S.
Journal of pharmacogenomics & pharmacoproteomics Volume S7 (2012) p.1-5

All Your Base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.
Genome biology Volume 13 (2012) p.R13

AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas003

Hepatitis B virus in transfusion medicine: still a problem?
Allain JP, Candotti D, ISBT HBV Safety Collaborative Group.
Biologicals : journal of the International Association of Biological Standardization Volume 40 (2012) p.180-186

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P.
Genome research Volume 22 (2012) p.2163-2175

Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression.
Gonçalves E, Pereira R, Rocha I, Rocha M.
Journal of computational biology : a journal of computational molecular cell biology Volume 19 (2012) p.102-114

An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
Nelson AC, Pillay N, Henderson S, Presneau N, Tirabosco R, Halai D, Berisha F, Flicek P, Stemple DL, Stern CD, Wardle FC, Flanagan AM.
The Journal of pathology Volume 228 (2012) p.274-285

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J.
BMC systems biology Volume 6 (2012) p.133

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M.
Genome biology Volume 13 (2012) p.R48

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
Levy ED, De S, Teichmann SA.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.20461-20466

A combined functional annotation score for non-synonymous variants.
Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E.
Human heredity Volume 73 (2012) p.47-51

De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.
Nature genetics Volume 44 (2012) p.226-232

Toward community standards in the quest for orthologs.
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J, Quest for Orthologs Consortium.
Bioinformatics (Oxford, England) Volume 28 (2012) p.900-904

Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.
arcOGEN Consortium, arcOGEN Collaborators, Zeggini E, Panoutsopoulou K, Southam L, Rayner NW, Day-Williams AG, Lopes MC, Boraska V, Esko T, Evangelou E, Hoffman A, Houwing-Duistermaat JJ, Ingvarsson T, Jonsdottir I, Jonnson H, Kerkhof HJ, Kloppenburg M, Bos SD, Mangino M, Metrustry S, Slagboom PE, Thorleifsson G, Raine EV, Ratnayake M, Ricketts M, Beazley C, Blackburn H, Bumpstead S, Elliott KS, Hunt SE, Potter SC, Shin SY, Yadav VK, Zhai G, Sherburn K, Dixon K, Arden E, Aslam N, Battley PK, Carluke I, Doherty S, Gordon A, Joseph J, Keen R, Koller NC, Mitchell S, O'Neill F, Paling E, Reed MR, Rivadeneira F, Swift D, Walker K, Watkins B, Wheeler M, Birrell F, Ioannidis JP, Meulenbelt I, Metspalu A, Rai A, Salter D, Stefansson K, Stykarsdottir U, Uitterlinden AG, van Meurs JB, Chapman K, Deloukas P, Ollier WE, Wallis GA, Arden N, Carr A, Doherty M, McCaskie A, Willkinson JM, Ralston SH, Valdes AM, Spector TD, Loughlin J.
Lancet (London, England) Volume 380 (2012) p.815-823

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ, Swertz MA.
Human mutation Volume 33 (2012) p.867-873

Evolution of oligomeric state through geometric coupling of protein interfaces.
Perica T, Chothia C, Teichmann SA.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.8127-8132

Accessing and using chemical property databases.
Hastings J, Josephs Z, Steinbeck C.
Methods in molecular biology (Clifton, N.J.) Volume 929 (2012) p.193-219

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.
Genome research Volume 22 (2012) p.1798-1812

Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells.
Hebenstreit D, Deonarine A, Babu MM, Teichmann SA.
Current opinion in cell biology Volume 24 (2012) p.350-358

Molecular interaction databases.
Orchard S.
Proteomics Volume 12 (2012) p.1656-1662

The making of ENCODE: Lessons for big-data projects.
Birney E.
Nature Volume 489 (2012) p.49-51

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT.
Cell Volume 148 (2012) p.335-348

BLUEPRINT to decode the epigenetic signature written in blood.
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S.
Nature biotechnology Volume 30 (2012) p.224-226

On the need for an international effort to capture, share and use crystallization screening data.
Newman J, Bolton EE, Müller-Dieckmann J, Fazio VJ, Gallagher DT, Lovell D, Luft JR, Peat TS, Ratcliffe D, Sayle RA, Snell EH, Taylor K, Vallotton P, Velanker S, von Delft F.
Acta crystallographica. Section F, Structural biology and crystallization communications Volume 68 (2012) p.253-258

Correction: Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival.
Sokolowski B, Orchard S, Harvey M, Sridhar S, Sakai Y.
PLoS ONE Volume 7 (2012) p.

Journey to the genetic interior. Interview by Stephen S Hall.
Birney E.
Scientific American Volume 307 (2012) p.80-2, 84

Rhea--a manually curated resource of biochemical reactions.
Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C.
Nucleic acids research Volume 40 (2012) p.D754-60

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.
Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 23 (2012) p.641-652

MetaboLights: towards a new COSMOS of metabolomics data management.
Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL.
Metabolomics : Official journal of the Metabolomic Society Volume 8 (2012) p.757-760

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Genome research Volume 22 (2012) p.9-24

Rare and functional SIAE variants are not associated with autoimmune disease risk in up to 66,924 individuals of European ancestry.
Hunt KA, Smyth DJ, Balschun T, Ban M, Mistry V, Ahmad T, Anand V, Barrett JC, Bhaw-Rosun L, Bockett NA, Brand OJ, Brouwer E, Concannon P, Cooper JD, Dias KR, van Diemen CC, Dubois PC, Edkins S, Fölster-Holst R, Fransen K, Glass DN, Heap GA, Hofmann S, Huizinga TW, Hunt S, Langford C, Lee J, Mansfield J, Marrosu MG, Mathew CG, Mein CA, Müller-Quernheim J, Nutland S, Onengut-Gumuscu S, Ouwehand W, Pearce K, Prescott NJ, Posthumus MD, Potter S, Rosati G, Sambrook J, Satsangi J, Schreiber S, Shtir C, Simmonds MJ, Sudman M, Thompson SD, Toes R, Trynka G, Vyse TJ, Walker NM, Weidinger S, Zhernakova A, Zoledziewska M, Type 1 Diabetes Genetics Consortium, UK Inflammatory Bowel Disease (IBD) Genetics Consortium, Wellcome Trust Case Control Consortium, Weersma RK, Gough SC, Sawcer S, Wijmenga C, Parkes M, Cucca F, Franke A, Deloukas P, Rich SS, Todd JA, van Heel DA.
Nature genetics Volume 44 (2012) p.3-5

Three hybrid classifiers for the detection of emotions in suicide notes.
Liakata M, Kim JH, Saha S, Hastings J, Rebholz-Schuhmann D.
Biomedical informatics insights Volume 5 (2012) p.175-184

Gene family matters: expanding the HGNC resource.
Daugherty LC, Seal RL, Wright MW, Bruford EA.
Human genomics Volume 6 (2012) p.4

In the beginning there was babble...
Klionsky DJ, Bruford EA, Cherry JM, Hodgkin J, Laulederkind SJ, Singer AG.
Autophagy Volume 8 (2012) p.1165-1167

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
Su Z, Gay LJ, Strange A, Palles C, Band G, Whiteman DC, Lescai F, Langford C, Nanji M, Edkins S, van der Winkel A, Levine D, Sasieni P, Bellenguez C, Howarth K, Freeman C, Trudgill N, Tucker AT, Pirinen M, Peppelenbosch MP, van der Laan LJ, Kuipers EJ, Drenth JP, Peters WH, Reynolds JV, Kelleher DP, McManus R, Grabsch H, Prenen H, Bisschops R, Krishnadath K, Siersema PD, van Baal JW, Middleton M, Petty R, Gillies R, Burch N, Bhandari P, Paterson S, Edwards C, Penman I, Vaidya K, Ang Y, Murray I, Patel P, Ye W, Mullins P, Wu AH, Bird NC, Dallal H, Shaheen NJ, Murray LJ, Koss K, Bernstein L, Romero Y, Hardie LJ, Zhang R, Winter H, Corley DA, Panter S, Risch HA, Reid BJ, Sargeant I, Gammon MD, Smart H, Dhar A, McMurtry H, Ali H, Liu G, Casson AG, Chow WH, Rutter M, Tawil A, Morris D, Nwokolo C, Isaacs P, Rodgers C, Ragunath K, MacDonald C, Haigh C, Monk D, Davies G, Wajed S, Johnston D, Gibbons M, Cullen S, Church N, Langley R, Griffin M, Alderson D, Deloukas P, Hunt SE, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Anderson M, Brooks C, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood N, Trynka G, Wijmenga C, Cazier JB, Atherfold P, Nicholson AM, Gellatly NL, Glancy D, Cooper SC, Cunningham D, Lind T, Hapeshi J, Ferry D, Rathbone B, Brown J, Love S, Attwood S, MacGregor S, Watson P, Sanders S, Ek W, Harrison RF, Moayyedi P, de Caestecker J, Barr H, Stupka E, Vaughan TL, Peltonen L, Spencer CC, Tomlinson I, Donnelly P, Jankowski JA, Esophageal Adenocarcinoma Genetics Consortium, Wellcome Trust Case Control Consortium 2.
Nature genetics Volume 44 (2012) p.1131-1136

Seven newly identified loci for autoimmune thyroid disease.
Cooper JD, Simmonds MJ, Walker NM, Burren O, Brand OJ, Guo H, Wallace C, Stevens H, Coleman G, Wellcome Trust Case Control Consortium, Franklyn JA, Todd JA, Gough SC.
Human molecular genetics Volume 21 (2012) p.5202-5208

Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke.
International Stroke Genetics Consortium (ISGC), Wellcome Trust Case Control Consortium 2 (WTCCC2), Bellenguez C, Bevan S, Gschwendtner A, Spencer CC, Burgess AI, Pirinen M, Jackson CA, Traylor M, Strange A, Su Z, Band G, Syme PD, Malik R, Pera J, Norrving B, Lemmens R, Freeman C, Schanz R, James T, Poole D, Murphy L, Segal H, Cortellini L, Cheng YC, Woo D, Nalls MA, Müller-Myhsok B, Meisinger C, Seedorf U, Ross-Adams H, Boonen S, Wloch-Kopec D, Valant V, Slark J, Furie K, Delavaran H, Langford C, Deloukas P, Edkins S, Hunt S, Gray E, Dronov S, Peltonen L, Gretarsdottir S, Thorleifsson G, Thorsteinsdottir U, Stefansson K, Boncoraglio GB, Parati EA, Attia J, Holliday E, Levi C, Franzosi MG, Goel A, Helgadottir A, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Worrall BB, Kittner SJ, Mitchell BD, Kissela B, Meschia JF, Thijs V, Lindgren A, Macleod MJ, Slowik A, Walters M, Rosand J, Sharma P, Farrall M, Sudlow CL, Rothwell PM, Dichgans M, Donnelly P, Markus HS.
Nature genetics Volume 44 (2012) p.328-333

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.
Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJ, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WH, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JR, Platou CG, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney AS, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CN, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Wellcome Trust Case Control Consortium, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Investigators, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Asian Genetic Epidemiology Network–Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.
Nature genetics Volume 44 (2012) p.981-990

The International Nucleotide Sequence Database Collaboration.
Karsch-Mizrachi I, Nakamura Y, Cochrane G, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 40 (2012) p.D33-7

The Sequence Read Archive: explosive growth of sequencing data.
Kodama Y, Shumway M, Leinonen R, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 40 (2012) p.D54-6

GrameneMart: the BioMart data portal for the Gramene project.
Spooner W, Youens-Clark K, Staines D, Ware D.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bar056

Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N.
Nature Volume 491 (2012) p.705-710

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.
Li JW, Robison K, Martin M, Sjödin A, Usadel B, Young M, Olivares EC, Bolser DM.
Nucleic acids research Volume 40 (2012) p.D1313-7

A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C.
Science (New York, N.Y.) Volume 335 (2012) p.823-828

UniProtKB amid the turmoil of plant proteomics research.
Schneider M, UniProt Consortium, Poux S.
Frontiers in plant science Volume 3 (2012) p.270

Identification and localisation of the NB-LRR gene family within the potato genome.
Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I.
BMC genomics Volume 13 (2012) p.75

MetaBase--the wiki-database of biological databases.
Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, González V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J.
Nucleic acids research Volume 40 (2012) p.D1250-4

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium.
Nature Volume 487 (2012) p.94-98

RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011.
Robbins RJ, Cochrane G, Davies N, Dawyndt P, Kottmann R, Krishtalka LK, Morrison N, Tuama EÓ, San Gil I, Wooley J.
Standards in genomic sciences Volume 7 (2012) p.153-158

De novo induction of amyloid-β deposition in vivo.
Morales R, Duran-Aniotz C, Castilla J, Estrada LD, Soto C.
Molecular psychiatry Volume 17 (2012) p.1347-1353

De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.
Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M, Ruderfer D, Moran J, Chambert K, Toncheva D, Georgieva L, Grozeva D, Fjodorova M, Wollerton R, Rees E, Nikolov I, van de Lagemaat LN, Bayés A, Fernandez E, Olason PI, Böttcher Y, Komiyama NH, Collins MO, Choudhary J, Stefansson K, Stefansson H, Grant SG, Purcell S, Sklar P, O'Donovan MC, Owen MJ.
Molecular psychiatry Volume 17 (2012) p.142-153

The role of variation at AβPP, PSEN1, PSEN2, and MAPT in late onset Alzheimer's disease.
Gerrish A, Russo G, Richards A, Moskvina V, Ivanov D, Harold D, Sims R, Abraham R, Hollingworth P, Chapman J, Hamshere M, Pahwa JS, Dowzell K, Williams A, Jones N, Thomas C, Stretton A, Morgan AR, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Morgan K, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Johnston JA, Holmes C, Mann D, Smith AD, Love S, Kehoe PG, Hardy J, Mead S, Fox N, Rossor M, Collinge J, Maier W, Jessen F, Kölsch H, Heun R, Schürmann B, van den Bussche H, Heuser I, Kornhuber J, Wiltfang J, Dichgans M, Frölich L, Hampel H, Hüll M, Rujescu D, Goate AM, Kauwe JS, Cruchaga C, Nowotny P, Morris JC, Mayo K, Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Davies G, Harris SE, Starr JM, Deary IJ, Al-Chalabi A, Shaw CE, Tsolaki M, Singleton AB, Guerreiro R, Mühleisen TW, Nöthen MM, Moebus S, Jöckel KH, Klopp N, Wichmann HE, Carrasquillo MM, Pankratz VS, Younkin SG, Jones L, Holmans PA, O'Donovan MC, Owen MJ, Williams J.
Journal of Alzheimer's disease : JAD Volume 28 (2012) p.377-387

Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.
Shen PS, Domek MJ, Sanz-García E, Makaju A, Taylor RM, Hoggan R, Culumber MD, Oberg CJ, Breakwell DP, Prince JT, Belnap DM.
Journal of virology Volume 86 (2012) p.7907-7917

WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW.
Worm Volume 1 (2012) p.15-21

WormBase 2012: more genomes, more data, new website.
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic acids research Volume 40 (2012) p.D735-41

Analyses of pig genomes provide insight into porcine demography and evolution.
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.
Nature Volume 491 (2012) p.393-398

Implementing an X-ray validation pipeline for the Protein Data Bank.
Gore S, Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 68 (2012) p.478-483

The Protein Data Bank at 40: reflecting on the past to prepare for the future.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure (London, England : 1993) Volume 20 (2012) p.391-396

The 2010 cryo-EM modeling challenge.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W.
Biopolymers Volume 97 (2012) p.651-654

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.
Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K, Amos CI, Padyukov L, Toes RE, Huizinga TW, Wijmenga C, Trynka G, Franke L, Westra HJ, Alfredsson L, Hu X, Sandor C, de Bakker PI, Davila S, Khor CC, Heng KK, Andrews R, Edkins S, Hunt SE, Langford C, Symmons D, Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate, Wellcome Trust Case Control Consortium, Concannon P, Onengut-Gumuscu S, Rich SS, Deloukas P, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Ärlsetig L, Martin J, Rantapää-Dahlqvist S, Plenge RM, Raychaudhuri S, Klareskog L, Gregersen PK, Worthington J.
Nature genetics Volume 44 (2012) p.1336-1340

The future of DNA sequence archiving.
Cochrane G, Cook CE, Birney E.
GigaScience Volume 1 (2012) p.2

Outcome of the first electron microscopy validation task force meeting.
Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL.
Structure (London, England : 1993) Volume 20 (2012) p.205-214

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.
Schmidt D, Schwalie P, Wilson M, Ballester B, Gonçalves Â, Kutter C, Brown G, Marshall A, Flicek P, Odom D.
Cell Volume 148 (2012) p.832-832

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1086-1092

Diverse epigenetic strategies interact to control epidermal differentiation.
Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, Sirokmány G, Donati G, Uribe-Lewis S, Pavlidis P, Murrell A, Markowetz F, Watt FM.
Nature cell biology Volume 14 (2012) p.753-763

Self-organizing ontology of biochemically relevant small molecules.
Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M.
BMC bioinformatics Volume 13 (2012) p.3

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.
Yuan Y, Failmezger H, Rueda OM, Ali HR, Gräf S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F.
Science translational medicine Volume 4 (2012) p.157ra143

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D, VectorBase Consortium.
Nucleic acids research Volume 40 (2012) p.D729-34

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.
Genome research Volume 22 (2012) p.1658-1667

A database for chemical proteomics: ChEBI.
de Matos P, Adams N, Hastings J, Moreno P, Steinbeck C.
Methods in molecular biology (Clifton, N.J.) Volume 803 (2012) p.273-296

GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.
Britto R, Sallou O, Collin O, Michaux G, Primig M, Chalmel F.
Nucleic acids research Volume 40 (2012) p.W458-65

The mammalian gene function resource: the International Knockout Mouse Consortium.
Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 23 (2012) p.580-586

Toward interoperable bioscience data.
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.
Nature genetics Volume 44 (2012) p.121-126

WormBase: Annotating many nematode genomes
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg P.
Worm Volume 1 (2012) p.15-21

Structured chemical class definitions and automated matching for chemical ontology evolution.
Duan L, Hastings J, de Matos P, Ennis M, Steinbeck C.
Journal of Cheminformatics Volume 4 (2012) p.P5-P5

In support of the BMRB.
Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S.
Nature structural & molecular biology Volume 19 (2012) p.854-860

Structure-based classification and ontology in chemistry.
Hastings J, Magka D, Batchelor C, Duan L, Stevens R, Ennis M, Steinbeck C.
Journal of cheminformatics Volume 4 (2012) p.8

Analysis of variation at transcription factor binding sites in Drosophila and humans.
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E.
Genome biology Volume 13 (2012) p.R49

Paralogous annotation of disease-causing variants in long QT syndrome genes.
Ware JS, Walsh R, Cunningham F, Birney E, Cook SA.
Human mutation Volume 33 (2012) p.1188-1191

Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC.
PLoS computational biology Volume 8 (2012) p.e1002789

Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery.
Denkert C, Bucher E, Hilvo M, Salek R, Orešič M, Griffin J, Brockmöller S, Klauschen F, Loibl S, Barupal DK, Budczies J, Iljin K, Nekljudova V, Fiehn O.
Genome medicine Volume 4 (2012) p.37

The genomic basis of adaptive evolution in threespine sticklebacks.
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C, Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM.
Nature Volume 484 (2012) p.55-61

Modeling gene expression using chromatin features in various cellular contexts.
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z.
Genome biology Volume 13 (2012) p.R53

Low budget analysis of Direct-To-Consumer genomic testing familial data.
Glusman G, Cariaso M, Jimenez R, Swan D, Greshake B, Bhak J, Logan DW, Corpas M.
F1000Research Volume 1 (2012) p.3

Automatic categorization of diverse experimental information in the bioscience literature.
Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold SJ, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW.
BMC bioinformatics Volume 13 (2012) p.16

The Origin and Function of Anti-Fungal Peptides in C. elegans: Open Questions.
Pujol N, Davis PA, Ewbank JJ.
Frontiers in immunology Volume 3 (2012) p.237

HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.
PloS one Volume 7 (2012) p.e31826

A transcription factor collective defines cardiac cell fate and reflects lineage history.
Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE.
Cell Volume 148 (2012) p.473-486

Natural product-likeness score revisited: an open-source, open-data implementation.
Jayaseelan KV, Moreno P, Truszkowski A, Ertl P, Steinbeck C.
BMC bioinformatics Volume 13 (2012) p.106

Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study.
Budczies J, Denkert C, Müller BM, Brockmöller SF, Klauschen F, Györffy B, Dietel M, Richter-Ehrenstein C, Marten U, Salek RM, Griffin JL, Hilvo M, Orešič M, Wohlgemuth G, Fiehn O.
BMC genomics Volume 13 (2012) p.334

2011

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
Molecular systems biology Volume 7 (2011) p.539

Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.
Genome research Volume 21 (2011) p.734-740

The representation of heart development in the gene ontology.
Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC.
Developmental biology Volume 354 (2011) p.9-17

Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman HM, Chiu W.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2011) p.369-373

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs.
Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC.
Nucleic acids research Volume 39 (2011) p.W190-6

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.
Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F.
BMC microbiology Volume 11 (2011) p.105

Ensembl 2011.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM.
Nucleic acids research Volume 39 (2011) p.D800-6

A new generation of crystallographic validation tools for the protein data bank.
Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.
Structure (London, England : 1993) Volume 19 (2011) p.1395-1412

EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W.
Nucleic acids research Volume 39 (2011) p.D456-64

Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors.
Pelé J, Abdi H, Moreau M, Thybert D, Chabbert M.
PloS one Volume 6 (2011) p.e19094

myKaryoView: a light-weight client for visualization of genomic data.
Jimenez RC, Salazar GA, Gel B, Dopazo J, Mulder N, Corpas M.
PloS one Volume 6 (2011) p.e26345

The Protein Data Bank in Europe (PDBe): bringing structure to biology.
Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 67 (2011) p.324-330

Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC.
Gut Volume 60 (2011) p.1317-1326

The IMGT/HLA database.
Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic acids research Volume 39 (2011) p.D1171-6

1,000 structures and more from the MCSG.
Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA.
BMC structural biology Volume 11 (2011) p.2

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses.
Vilella AJ, Birney E, Flicek P, Herrero J.
Genome biology Volume 12 (2011) p.401

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.6-8

New gene functions in megakaryopoiesis and platelet formation.
Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Mägi R, Meacham S, Okada Y, Pirastu N, Sorice R, Teumer A, Voss K, Zhang W, Ramirez-Solis R, Bis JC, Ellinghaus D, Gögele M, Hottenga JJ, Langenberg C, Kovacs P, O'Reilly PF, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, Ellen van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, D'Adamo P, Davies G, de Boer RA, de Geus EJ, Döring A, Elliott P, Erdmann J, Evans DM, Falchi M, Feng W, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kühnel B, Kyrtsonis MC, Lagou V, Lloyd-Jones H, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nakamura Y, Nauck M, Navis G, Nöthlings U, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Tang WH, Taylor K, Tenesa A, Lay Thein S, Tönjes A, Uda M, Ulivi S, van Veldhuisen DJ, Visscher PM, Völker U, Wichmann HE, Wiggins KL, Willemsen G, Yang TP, Hua Zhao J, Zitting P, Bradley JR, Dedoussis GV, Gasparini P, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, Joost van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Rendon A, Ferreira MA, Ouwehand WH, Soranzo N.
Nature Volume 480 (2011) p.201-208

BioMart Central Portal: an open database network for the biological community.
Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, Chelala C, Croft D, Cros A, Cutts RJ, Di Génova A, Forbes S, Fujisawa T, Gadaleta E, Goodstein DM, Gundem G, Haggarty B, Haider S, Hall M, Harris T, Haw R, Hu S, Hubbard S, Hsu J, Iyer V, Jones P, Katayama T, Kinsella R, Kong L, Lawson D, Liang Y, Lopez-Bigas N, Luo J, Lush M, Mason J, Moreews F, Ndegwa N, Oakley D, Perez-Llamas C, Primig M, Rivkin E, Rosanoff S, Shepherd R, Simon R, Skarnes B, Smedley D, Sperling L, Spooner W, Stevenson P, Stone K, Teague J, Wang J, Wang J, Whitty B, Wong DT, Wong-Erasmus M, Yao L, Youens-Clark K, Yung C, Zhang J, Kasprzyk A.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar041

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS.
Genome research Volume 21 (2011) p.456-464

easyDAS: automatic creation of DAS servers.
Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H.
BMC bioinformatics Volume 12 (2011) p.23

Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C, BioDBCore Working Group.
Nucleic acids research Volume 39 (2011) p.D7-10

Celebrating structural biology.

Nature structural & molecular biology Volume 18 (2011) p.1304-1316

The sequence read archive.
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 39 (2011) p.D19-21

The International Nucleotide Sequence Database Collaboration.
Cochrane G, Karsch-Mizrachi I, Nakamura Y, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 39 (2011) p.D15-8

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.
Galperin MY, Cochrane GR.
Nucleic acids research Volume 39 (2011) p.D1-6

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.
Nature biotechnology Volume 29 (2011) p.415-420

Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C, BioDBCore Working Group.
Database : the journal of biological databases and curation Volume 2011 (2011) p.baq027

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.
Morris C, Pajon A, Griffiths SL, Daniel E, Savitsky M, Lin B, Diprose JM, da Silva AW, Pilicheva K, Troshin P, van Niekerk J, Isaacs N, Naismith J, Nave C, Blake R, Wilson KS, Stuart DI, Henrick K, Esnouf RM.
Acta crystallographica. Section D, Biological crystallography Volume 67 (2011) p.249-260

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y.
PLoS genetics Volume 7 (2011) p.e1001316

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
Holliday GL, Fischer JD, Mitchell JB, Thornton JM.
The FEBS journal Volume 278 (2011) p.3835-3845

Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA.
Nucleic acids research Volume 39 (2011) p.D420-6

Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D.
Nucleic acids research Volume 39 (2011) p.D1085-94

A novel strategy for NMR resonance assignment and protein structure determination.
Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH.
Journal of biomolecular NMR Volume 49 (2011) p.27-38

Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding blaCTX-M-14.
Cottell JL, Webber MA, Coldham NG, Taylor DL, Cerdeño-Tárraga AM, Hauser H, Thomson NR, Woodward MJ, Piddock LJ.
Emerging infectious diseases Volume 17 (2011) p.645-652

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.
Nature Volume 477 (2011) p.419-423

Overcoming the ontology enrichment bottleneck with Quick Term Templates
Rocca-Serra P, Ruttenberg A, O'Connor MJ, Whetzel PL, Schober D, Greenbaum J, Courtot M, Brinkman RR, Sansone SA, Scheuermann R, Peters B.
Applied ontology Volume 6 (2011) p.13-22

MIREOT: The minimum information to reference an external ontology term
Courtot M, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A.
Applied ontology Volume 6 (2011) p.23-33

PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.
Nucleic acids research Volume 39 (2011) p.D402-10

Genome sequence and analysis of the tuber crop potato.
Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sønderkær M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert Bt, Goverse A, van Ham RC, Visser RG.
Nature Volume 475 (2011) p.189-195

Genome of Streptococcus oralis strain Uo5.
Reichmann P, Nuhn M, Denapaite D, Brückner R, Henrich B, Maurer P, Rieger M, Klages S, Reinhard R, Hakenbeck R.
Journal of bacteriology Volume 193 (2011) p.2888-2889

The European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G.
Nucleic acids research Volume 39 (2011) p.D28-31

Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar030

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.
Alic N, Andrews TD, Giannakou ME, Papatheodorou I, Slack C, Hoddinott MP, Cochemé HM, Schuster EF, Thornton JM, Partridge L.
Molecular systems biology Volume 7 (2011) p.502

Human metabolic profiles are stably controlled by genetic and environmental variation.
Nicholson G, Rantalainen M, Maher AD, Li JV, Malmodin D, Ahmadi KR, Faber JH, Hallgrímsdóttir IB, Barrett A, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, The Molpage Consortium, Silverman BW, Donnelly P, Nicholson JK, Allen M, Zondervan KT, Lindon JC, Spector TD, McCarthy MI, Holmes E, Baunsgaard D, Holmes CC.
Molecular systems biology Volume 7 (2011) p.525

A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium.
PLoS biology Volume 9 (2011) p.e1001046

Chromatin and heritability: how epigenetic studies can complement genetic approaches.
Birney E.
Trends in genetics : TIG Volume 27 (2011) p.172-176

Contributions of the EMERALD project to assessing and improving microarray data quality.
Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.
BioTechniques Volume 50 (2011) p.27-31

Conserved BK channel-protein interactions reveal signals relevant to cell death and survival.
Sokolowski B, Orchard S, Harvey M, Sridhar S, Sakai Y.
PloS one Volume 6 (2011) p.e28532

Omics technologies, data and bioinformatics principles.
Schneider MV, Orchard S.
Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.3-30

Peptide fractionation by acid pH SDS-free electrophoresis.
Ramos Y, Garcia Y, Pérez-Riverol Y, Leyva A, Padrón G, Sánchez A, Castellanos-Serra L, González LJ, Besada V.
Electrophoresis Volume 32 (2011) p.1323-1326

Structural annotation of Mycobacterium tuberculosis proteome.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R, OSDD Consortium, Brahmachari SK, Chandra N.
PloS one Volume 6 (2011) p.e27044

ontoCAT: an R package for ontology traversal and search.
Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2468-2470

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
Journal of chemical information and modeling Volume 51 (2011) p.2778-2786

Minimum Information About a Simulation Experiment (MIASE).
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N.
PLoS computational biology Volume 7 (2011) p.e1001122

Protein structure databases.
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Molecular biotechnology Volume 48 (2011) p.183-198

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.
Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP.
Genome biology Volume 12 (2011) p.R90

A revised nomenclature for transcribed human endogenous retroviral loci.
Mayer J, Blomberg J, Seal RL.
Mobile DNA Volume 2 (2011) p.7

Comparing signaling networks between normal and transformed hepatocytes using discrete logical models.
Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK.
Cancer research Volume 71 (2011) p.5400-5411

Crowdsourcing network inference: the DREAM predictive signaling network challenge.
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.
Science signaling Volume 4 (2011) p.mr7

The GUDMAP database--an online resource for genitourinary research.
Harding SD, Armit C, Armstrong J, Brennan J, Cheng Y, Haggarty B, Houghton D, Lloyd-MacGilp S, Pi X, Roochun Y, Sharghi M, Tindal C, McMahon AP, Gottesman B, Little MH, Georgas K, Aronow BJ, Potter SS, Brunskill EW, Southard-Smith EM, Mendelsohn C, Baldock RA, Davies JA, Davidson D.
Development (Cambridge, England) Volume 138 (2011) p.2845-2853

Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: evaluation in proteomic studies using peptide-centric database searches.
Betancourt LH, Sánchez A, Pérez Y, Fernandez de Cossio J, Gil J, Toledo P, Iguchi S, Aimoto S, González LJ, Padrón G, Takao T, Besada V.
Journal of proteomics Volume 74 (2011) p.2210-2213

In silico analysis of accurate proteomics, complemented by selective isolation of peptides.
Perez-Riverol Y, Sánchez A, Ramos Y, Schmidt A, Müller M, Betancourt L, González LJ, Vera R, Padron G, Besada V.
Journal of proteomics Volume 74 (2011) p.2071-2082

Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
Science signaling Volume 4 (2011) p.pe10

Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.
PLoS computational biology Volume 7 (2011) p.e1001099

Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily.
Bingle CD, Seal RL, Craven CJ.
Biochemical Society transactions Volume 39 (2011) p.977-983

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.
Nucleic acids research Volume 39 (2011) p.D1002-4

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2156-2158

A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.
Nature Volume 478 (2011) p.476-482

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M.
Bioinformatics (Oxford, England) Volume 27 (2011) p.589-591

Reactome: a database of reactions, pathways and biological processes.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.
Nucleic acids research Volume 39 (2011) p.D691-7

Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project.
Nature Volume 470 (2011) p.59-65

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.
Genome research Volume 21 (2011) p.1757-1767

Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project.
Nature genetics Volume 43 (2011) p.712-714

Demographic history and rare allele sharing among human populations.
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, 1000 Genomes Project, Bustamante CD.
Proceedings of the National Academy of Sciences of the United States of America Volume 108 (2011) p.11983-11988

Gene expression differences among primates are associated with changes in a histone epigenetic modification.
Cain CE, Blekhman R, Marioni JC, Gilad Y.
Genetics Volume 187 (2011) p.1225-1234

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.
Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D.
BMC plant biology Volume 11 (2011) p.104

genenames.org: the HGNC resources in 2011.
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Nucleic acids research Volume 39 (2011) p.D514-9

Signatures of selection and sex-specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family.
Keays MC, Barker D, Wicker-Thomas C, Ritchie MG.
Molecular ecology Volume 20 (2011) p.3617-3630

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, MolPAGE Consortium, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan KT, Spector TD, Nicholson JK, Lindon JC, Baunsgaard D, Holmes E, McCarthy MI, Holmes CC.
PLoS genetics Volume 7 (2011) p.e1002270

Methods and strategies for gene structure curation in WormBase.
Williams GW, Davis PA, Rogers AS, Bieri T, Ozersky P, Spieth J.
Database : the journal of biological databases and curation Volume 2011 (2011) p.baq039

Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature.
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Human genomics Volume 5 (2011) p.90-98

Computational biology for ageing.
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Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.51-63

A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics (Oxford, England) Volume 27 (2011) p.867-869

PRIDE and "Database on Demand" as valuable tools for computational proteomics.
Vizcaíno JA, Reisinger F, Côté R, Martens L.
Methods in molecular biology (Clifton, N.J.) Volume 696 (2011) p.93-105

EST analysis pipeline: use of distributed computing resources.
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Methods in molecular biology (Clifton, N.J.) Volume 722 (2011) p.103-120

Mouse genomic variation and its effect on phenotypes and gene regulation.
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ.
Nature Volume 477 (2011) p.289-294

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.
Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT.
Nature genetics Volume 43 (2011) p.948-955

Proteomic temporal profile of human brain endothelium after oxidative stress.
Ning M, Sarracino DA, Kho AT, Guo S, Lee SR, Krastins B, Buonanno FS, Vizcaíno JA, Orchard S, McMullin D, Wang X, Lo EH.
Stroke; a journal of cerebral circulation Volume 42 (2011) p.37-43

Physiological and molecular evidence that environmental changes elicit morphological interconversion in the model diatom Phaeodactylum tricornutum.
De Martino A, Bartual A, Willis A, Meichenin A, Villazán B, Maheswari U, Bowler C.
Protist Volume 162 (2011) p.462-481

Quality control in proteomics.
Martens L, Vizcaíno JA, Banks R.
Proteomics Volume 11 (2011) p.1015-1016

Submitting proteomics data to PRIDE using PRIDE Converter.
Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.237-253

The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P, Köhn M.
Biochemistry Volume 50 (2011) p.7579-7590

Modernizing reference genome assemblies.
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T.
PLoS biology Volume 9 (2011) p.e1001091

Assemblies: the good, the bad, the ugly.
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Nature methods Volume 8 (2011) p.59-60

Controlled vocabularies and semantics in systems biology.
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.
Molecular systems biology Volume 7 (2011) p.543

Data standards for Omics data: the basis of data sharing and reuse.
Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA.
Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.31-69

A model for collaborative curation, the IEDB and ChEBI curation of non-peptidic epitopes
Vita R, Peters B, Josephs Z, De Matos P, Ennis M, Turner S, Steinbeck C, Seymour E, Zarebski LO, Sette A.
Immunome research Volume 7 (2011) p.1-8

Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A.
Bioinformatics (Oxford, England) Volume 27 (2011) p.973-979

Revision history aware repositories of computational models of biological systems.
Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PM.
BMC bioinformatics Volume 12 (2011) p.22

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P.
BMC research notes Volume 4 (2011) p.313

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.
Lakner C, Holder MT, Goldman N, Naylor GJ.
Systematic biology Volume 60 (2011) p.161-174

Atomic resolution insights into curli fiber biogenesis.
Taylor JD, Zhou Y, Salgado PS, Patwardhan A, McGuffie M, Pape T, Grabe G, Ashman E, Constable SC, Simpson PJ, Lee WC, Cota E, Chapman MR, Matthews SJ.
Structure (London, England : 1993) Volume 19 (2011) p.1307-1316

Ongoing and future developments at the Universal Protein Resource.
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Nucleic acids research Volume 39 (2011) p.D214-9

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel HR, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC.
Genome biology Volume 12 (2011) p.R81

Comparative and demographic analysis of orang-utan genomes.
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.
Nature Volume 469 (2011) p.529-533

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lef?vre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng Z, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song X, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC.
Genome biology Volume 12 (2011) p.414-414

Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R.
Genome biology Volume 12 (2011) p.402

A common layer of interoperability for biomedical ontologies based on OWL EL.
Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV.
Bioinformatics (Oxford, England) Volume 27 (2011) p.1001-1008

Integrating systems biology models and biomedical ontologies.
Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV.
BMC systems biology Volume 5 (2011) p.124

Effects of BMI and abdominal volume on the accuracy of step count obtained from a tri-axial accelerometer.
Cleland I, Nugent CD, Finlay DD, Burns W, Bougourd J, Stevens K, Armitage R.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2011 (2011) p.3656-3659

Anatomy ontologies and potential users: bridging the gap.
Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H.
Journal of biomedical semantics Volume 2 Suppl 4 (2011) p.S3

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.
BMC bioinformatics Volume 12 (2011) p.218

Messenger RNA and microRNA profiling during early mouse EB formation.
Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S, Enright AJ.
Gene expression patterns : GEP Volume 11 (2011) p.334-344

The impact of focused Gene Ontology curation of specific mammalian systems.
Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC.
PloS one Volume 6 (2011) p.e27541

Using semantic web technologies to manage complexity and change in biomedical data.
Stevens R, Jupp S, Klein J, Schanstra J.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2011 (2011) p.3708-3711

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.
Puri V, Goyal A, Sankaranarayanan R, Enright AJ, Vaidya T.
BMC evolutionary biology Volume 11 (2011) p.334

MiR-221 influences effector functions and actin cytoskeleton in mast cells.
Mayoral RJ, Deho L, Rusca N, Bartonicek N, Saini HK, Enright AJ, Monticelli S.
PloS one Volume 6 (2011) p.e26133

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus.
Rebholz-Schuhmann D, Jimeno Yepes A, Li C, Kafkas S, Lewin I, Kang N, Corbett P, Milward D, Buyko E, Beisswanger E, Hornbostel K, Kouznetsov A, Witte R, Laurila JB, Baker CJ, Kuo CJ, Clematide S, Rinaldi F, Farkas R, Móra G, Hara K, Furlong LI, Rautschka M, Neves ML, Pascual-Montano A, Wei Q, Collier N, Chowdhury MF, Lavelli A, Berlanga R, Morante R, Van Asch V, Daelemans W, Marina JL, van Mulligen E, Kors J, Hahn U.
Journal of biomedical semantics Volume 2 Suppl 5 (2011) p.S11

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements.
De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D.
Nature Volume 480 (2011) p.259-263

The functional spectrum of low-frequency coding variation.
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project.
Genome biology Volume 12 (2011) p.R84

Developing a kidney and urinary pathway knowledge base.
Jupp S, Klein J, Schanstra J, Stevens R.
Journal of biomedical semantics Volume 2 Suppl 2 (2011) p.S7

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts.
Caiazzo M, Dell'Anno MT, Dvoretskova E, Lazarevic D, Taverna S, Leo D, Sotnikova TD, Menegon A, Roncaglia P, Colciago G, Russo G, Carninci P, Pezzoli G, Gainetdinov RR, Gustincich S, Dityatev A, Broccoli V.
Nature Volume 476 (2011) p.224-227

Developmental influence of the cellular prion protein on the gene expression profile in mouse hippocampus.
Benvegnù S, Roncaglia P, Agostini F, Casalone C, Corona C, Gustincich S, Legname G.
Physiological genomics Volume 43 (2011) p.711-725

Chemical ontologies: what are they, what are they for and what are the challenges.
Hastings J, Adams N, Ennis M, Hull D, Steinbeck C.
Journal of Cheminformatics Volume 3 (2011) p.O4-O4

Modularization requirements in bio-ontologies: A case study of ChEbi
Hastings J, Batchelor C, Steinbeck C, Schulz S.
Advances in molecular bioinformatics Volume 230 (2011) p.63-70

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution.
Truszkowski A, Neumann S, Zielesny A, Willighagen E, Steinbeck C.
Journal of Cheminformatics Volume 3 (2011) p.P5-P5

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.
Genome research Volume 21 (2011) p.2224-2241

Computational metabolomics – a field at the boundaries of cheminformatics and bioinformatics.
Steinbeck C, Kuhn S, Jayaseelan KV, Moreno P.
Journal of Cheminformatics Volume 3 (2011) p.O6-O6

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, Murray-Rust P.
Journal of cheminformatics Volume 3 (2011) p.37

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.
Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M.
PloS one Volume 6 (2011) p.e25513

New developments on the cheminformatics open workflow environment CDK-Taverna.
Truszkowski A, Jayaseelan KV, Neumann S, Willighagen EL, Zielesny A, Steinbeck C.
Journal of cheminformatics Volume 3 (2011) p.54

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.
Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.M111.008490

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H.
Proteomics Volume 11 (2011) p.4284-4290

DAS writeback: a collaborative annotation system.
Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.
BMC bioinformatics Volume 12 (2011) p.143

Reactome pathway analysis to enrich biological discovery in proteomics data sets.
Haw R, Hermjakob H, D'Eustachio P, Stein L.
Proteomics Volume 11 (2011) p.3598-3613

Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues.
Moreno P, Jayaseelan K, Steinbeck C.
Journal of Cheminformatics Volume 3 (2011) p.P19-P19

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.
Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, Fonseca NA.
International journal of legal medicine Volume 125 (2011) p.629-636

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.O111.015446

The Reactome BioMart.
Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar031

mzML--a community standard for mass spectrometry data.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.R110.000133

Predicting Malignancy from Mammography Findings and Surgical Biopsies.
Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Volume 2011 (2011) p.

Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2616-2617

Preparing molecular interaction data for publication.
Orchard S, Hermjakob H.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.229-236

Data standardization by the HUPO-PSI: how has the community benefitted?
Orchard S, Hermjakob H.
Methods in molecular biology (Clifton, N.J.) Volume 696 (2011) p.149-160

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.
Camacho R, Pereira M, Costa VS, Fonseca NA, Adriano C, Simões CJ, Brito RM.
Journal of integrative bioinformatics Volume 8 (2011) p.182

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.
de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL.
Journal of theoretical biology Volume 271 (2011) p.136-144

Motor neuron impairment mediated by a sumoylated fragment of the glial glutamate transporter EAAT2.
Foran E, Bogush A, Goffredo M, Roncaglia P, Gustincich S, Pasinelli P, Trotti D.
Glia Volume 59 (2011) p.1719-1731

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar047

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.
Proteomics. Clinical applications Volume 5 (2011) p.580-589

A guide to UniProt for protein scientists.
O'Donovan C, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.25-35

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".
Griffin JL, Atherton HJ, Steinbeck C, Salek RM.
BMC research notes Volume 4 (2011) p.272

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 11 (2011) p.4434-4438

Collation and data-mining of literature bioactivity data for drug discovery.
Bellis LJ, Akhtar R, Al-Lazikani B, Atkinson F, Bento AP, Chambers J, Davies M, Gaulton A, Hersey A, Ikeda K, Krüger FA, Light Y, McGlinchey S, Santos R, Stauch B, Overington JP.
Biochemical Society transactions Volume 39 (2011) p.1365-1370

Minimum information about a bioactive entity (MIABE).
Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.
Nature reviews. Drug discovery Volume 10 (2011) p.661-669

The Genomic Standards Consortium.
Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J.
PLoS biology Volume 9 (2011) p.e1001088

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited.
Hess J, Goldman N.
PloS one Volume 6 (2011) p.e22783

In-silico ADME models: a general assessment of their utility in drug discovery applications.
Gleeson MP, Hersey A, Hannongbua S.
Current topics in medicinal chemistry Volume 11 (2011) p.358-381

UKPMC: a full text article resource for the life sciences.
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, Lewin I, Lyte V, MacIntyre R, Mansoor S, Mason L, McNaught J, Newbold E, Nobata C, Ong E, Pillai S, Rebholz-Schuhmann D, Rosie H, Rowbotham R, Rupp CJ, Stoehr P, Vaughan P.
Nucleic acids research Volume 39 (2011) p.D58-65

Oxygen consumption rate of cells in 3D culture: the use of experiment and simulation to measure kinetic parameters and optimise culture conditions.
Streeter I, Cheema U.
The Analyst Volume 136 (2011) p.4013-4019

Mechanisms of structure generation during plastic compression of nanofibrillar collagen hydrogel scaffolds: towards engineering of collagen.
Hadjipanayi E, Ananta M, Binkowski M, Streeter I, Lu Z, Cui ZF, Brown RA, Mudera V.
Journal of tissue engineering and regenerative medicine Volume 5 (2011) p.505-519

Probing the links between in vitro potency, ADMET and physicochemical parameters.
Gleeson MP, Hersey A, Montanari D, Overington J.
Nature reviews. Drug discovery Volume 10 (2011) p.197-208

A molecular dynamics study of the interprotein interactions in collagen fibrils.
Streeter I, de Leeuw NH.
Soft matter Volume 7 (2011) p.3373-3382

Binding of glycosaminoglycan saccharides to hydroxyapatite surfaces: A density functional theory study.
Streeter I, de Leeuw NH.
Proceedings. Mathematical, physical, and engineering sciences / the Royal Society Volume 467 (2011) p.2084-2101

UniProt Knowledgebase: a hub of integrated protein data.
Magrane M, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar009

The genomic standards consortium: bringing standards to life for microbial ecology.
Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glöckner FO, Field D.
The ISME journal Volume 5 (2011) p.1565-1567

Solving the Problem: Genome Annotation Standards before the Data Deluge.
Klimke W, O'Donovan C, White O, Brister JR, Clark K, Fedorov B, Mizrachi I, Pruitt KD, Tatusova T.
Standards in genomic sciences Volume 5 (2011) p.168-193

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
Nature methods Volume 8 (2011) p.528-529

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA (New York, N.Y.) Volume 17 (2011) p.578-594

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.
Kosiol C, Goldman N.
Journal of molecular biology Volume 411 (2011) p.910-923

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.
BMC bioinformatics Volume 12 (2011) p.104

RNAcentral: A vision for an international database of RNA sequences.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNA (New York, N.Y.) Volume 17 (2011) p.1941-1946

Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts.
Malone CM, Domaschenz R, Amagase Y, Dunham I, Murai K, Jones PH.
Experimental cell research Volume 317 (2011) p.1590-1602

2010

Allele-specific and heritable chromatin signatures in humans.
Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Human molecular genetics Volume 19 (2010) p.R204-9

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8.
Kyrpides N, Field D, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J.
Standards in genomic sciences Volume 3 (2010) p.93-96

A new strategy for genome assembly using short sequence reads and reduced representation libraries.
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.
Genome research Volume 20 (2010) p.249-256

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome biology Volume 11 (2010) p.402

Ensembl variation resources.
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P.
BMC genomics Volume 11 (2010) p.293

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan AW, Laskowski RA, Selwood DL.
Journal of medicinal chemistry Volume 53 (2010) p.3086-3094

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ.
Genome research Volume 20 (2010) p.791-803

Pyrazolopyridazine alpha-2-delta-1 ligands for the treatment of neuropathic pain.
Myatt JW, Healy MP, Bravi GS, Billinton A, Johnson CN, Matthews KL, Jandu KS, Meng W, Hersey A, Livermore DG, Douault CB, Witherington J, Bit RA, Rowedder JE, Brown JD, Clayton NM.
Bioorganic & medicinal chemistry letters Volume 20 (2010) p.4683-4688

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.
Berka K, Laskowski RA, Hobza P, Vondrášek J.
Journal of chemical theory and computation Volume 6 (2010) p.2191-2203

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium.
The Plant cell Volume 22 (2010) p.2530-2536

Free computational resources for designing selected reaction monitoring transitions.
Cham Mead JA, Bianco L, Bessant C.
Proteomics Volume 10 (2010) p.1106-1126

PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ.
Nucleic acids research Volume 38 (2010) p.D308-17

Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.
Nature methods Volume 7 (2010) p.S42-55

The publication and database deposition of molecular interaction data.
Orchard S, Aranda B, Hermjakob H.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] Volume Chapter 25 (2010) p.Unit 25.3

The IntAct molecular interaction database in 2010.
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.
Nucleic acids research Volume 38 (2010) p.D525-31

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri AU, Laskowski RA.
Bioinformatics (Oxford, England) Volume 26 (2010) p.1260-1261

A small-cell lung cancer genome with complex signatures of tobacco exposure.
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordoñez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ.
Nature Volume 463 (2010) p.184-190

Protein structure databases.
Laskowski RA.
Methods in molecular biology (Clifton, N.J.) Volume 609 (2010) p.59-82

The systematic annotation of the three main GPCR families in Reactome.
Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P.
Database : the journal of biological databases and curation Volume 2010 (2010) p.baq018

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.
Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.
Molecular & cellular proteomics : MCP Volume 9 (2010) p.2642-2653

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2470-2471

Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation.
Abad-Zapatero C, Perišić O, Wass J, Bento AP, Overington J, Al-Lazikani B, Johnson ME.
Drug discovery today Volume 15 (2010) p.804-811

Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2.
Alexopoulos LG, Melas IN, Chairakaki AD, Saez-Rodriguez J, Mitsos A.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2010 (2010) p.6717-6720

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.
PLoS biology Volume 8 (2010) p.

A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease.
Perreau VM, Orchard S, Adlard PA, Bellingham SA, Cappai R, Ciccotosto GD, Cowie TF, Crouch PJ, Duce JA, Evin G, Faux NG, Hill AF, Hung YH, James SA, Li QX, Mok SS, Tew DJ, White AR, Bush AI, Hermjakob H, Masters CL.
Proteomics Volume 10 (2010) p.2377-2395

Gene expression atlas at the European bioinformatics institute.
Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A.
Nucleic acids research Volume 38 (2010) p.D690-8

The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J.
Nucleic acids research Volume 38 (2010) p.D17-25

Modeling sample variables with an Experimental Factor Ontology.
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.
Bioinformatics (Oxford, England) Volume 26 (2010) p.1112-1118

Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus.
Marx P, Nuhn M, Kovács M, Hakenbeck R, Brückner R.
BMC genomics Volume 11 (2010) p.661

The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.
Nucleic acids research Volume 38 (2010) p.D736-42

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.
Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H.
Nucleic acids research Volume 38 (2010) p.W78-83

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N.
BMC bioinformatics Volume 11 (2010) p.579

The consequence of natural selection on genetic variation in the mouse.
Reuveni E, Birney E, Gross CT.
Genomics Volume 95 (2010) p.196-202

International network of cancer genome projects.
International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, Easton DF, Spellman PT, Martin S, Barker AD, Chin L, Collins FS, Compton CC, Ferguson ML, Gerhard DS, Getz G, Gunter C, Guttmacher A, Guyer M, Hayes DN, Lander ES, Ozenberger B, Penny R, Peterson J, Sander C, Shaw KM, Speed TP, Spellman PT, Vockley JG, Wheeler DA, Wilson RK, Hudson TJ, Chin L, Knoppers BM, Lander ES, Lichter P, Stein LD, Stratton MR, Anderson W, Barker AD, Bell C, Bobrow M, Burke W, Collins FS, Compton CC, DePinho RA, Easton DF, Futreal PA, Gerhard DS, Green AR, Guyer M, Hamilton SR, Hubbard TJ, Kallioniemi OP, Kennedy KL, Ley TJ, Liu ET, Lu Y, Majumder P, Marra M, Ozenberger B, Peterson J, Schafer AJ, Spellman PT, Stunnenberg HG, Wainwright BJ, Wilson RK, Yang H.
Nature Volume 464 (2010) p.993-998

Organelle proteomics experimental designs and analysis.
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS.
Proteomics Volume 10 (2010) p.3957-3969

The genome of Streptococcus mitis B6--what is a commensal?
Denapaite D, Brückner R, Nuhn M, Reichmann P, Henrich B, Maurer P, Schähle Y, Selbmann P, Zimmermann W, Wambutt R, Hakenbeck R.
PloS one Volume 5 (2010) p.e9426

PRIDE: Data submission and analysis.
Vizcaíno JA, Reisinger F, Côté R, Martens L.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] Volume Chapter 25 (2010) p.Unit 25.4

Fast and efficient searching of biological data resources--using EB-eye.
Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R.
Briefings in bioinformatics Volume 11 (2010) p.375-384

Molecular fragments chemoinformatics.
Kuhn H, Neumann S, Steinbeck C, Wittekindt C, Zielesny A.
Journal of Cheminformatics Volume 2 (2010) p.P14-P14

A database and API for variation, dense genotyping and resequencing data.
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F.
BMC bioinformatics Volume 11 (2010) p.238

A new bioinformatics analysis tools framework at EMBL-EBI.
Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R.
Nucleic acids research Volume 38 (2010) p.W695-9

Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E.
Science (New York, N.Y.) Volume 328 (2010) p.235-239

Ensembl's 10th year.
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM.
Nucleic acids research Volume 38 (2010) p.D557-62

Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A.
Nucleic acids research Volume 38 (2010) p.D563-9

Meeting Report: BioSharing at ISMB 2010.
Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A.
Standards in genomic sciences Volume 3 (2010) p.254-258

IPD--the Immuno Polymorphism Database.
Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG.
Nucleic acids research Volume 38 (2010) p.D863-9

A community standard format for the representation of protein affinity reagents.
Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H.
Molecular & cellular proteomics : MCP Volume 9 (2010) p.1-10

Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea.
Orchard S, Jones A, Albar JP, Cho SY, Kwon KH, Lee C, Hermjakob H.
Proteomics Volume 10 (2010) p.3062-3066

Straightforward and complete deposition of NMR data to the PDBe.
Penkett CJ, van Ginkel G, Velankar S, Swaminathan J, Ulrich EL, Mading S, Stevens TJ, Fogh RH, Gutmanas A, Kleywegt GJ, Henrick K, Vranken WF.
Journal of biomolecular NMR Volume 48 (2010) p.85-92

An effective model for natural selection in promoters.
Hoffman MM, Birney E.
Genome research Volume 20 (2010) p.685-692

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.
Cochrane GR, Galperin MY.
Nucleic acids research Volume 38 (2010) p.D1-4

A large-scale protein-function database.
Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K.
Nature chemical biology Volume 6 (2010) p.785

OrChem: an open source chemistry search engine for Oracle.
Rijnbeek ML, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.P28-P28

Progress on an open source computer-assisted structure elucidation suite (SENECA).
Kuhn S, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.P34-P34

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010.
Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O.
Standards in genomic sciences Volume 3 (2010) p.232-234

Non-redundant patent sequence databases with value-added annotations at two levels.
Li W, McWilliam H, de la Torre AR, Grodowski A, Benediktovich I, Goujon M, Nauche S, Lopez R.
Nucleic acids research Volume 38 (2010) p.D52-6

Role of open chemical data in aiding drug discovery and design.
Gaulton A, Overington JP.
Future medicinal chemistry Volume 2 (2010) p.903-907

EMMA--mouse mutant resources for the international scientific community.
Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M, Massimi M, Pickford K, Butler RH, Marschall S, Mallon AM, Pickard A, Raspa M, Scavizzi F, Fray M, Larrigaldie V, Leyritz J, Birney E, Tocchini-Valentini GP, Brown S, Herault Y, Montoliu L, de Angelis MH, Smedley D.
Nucleic acids research Volume 38 (2010) p.D570-6

Functional comparison of innate immune signaling pathways in primates.
Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y.
PLoS genetics Volume 6 (2010) p.e1001249

Mining proteomic MS/MS data for MRM transitions.
Chem Mead JA, Bianco L, Bessant C.
Methods in molecular biology (Clifton, N.J.) Volume 604 (2010) p.187-199

Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.
Wright VA, Vaughan BW, Laurent T, Lopez R, Brooksbank C, Schneider MV.
Briefings in bioinformatics Volume 11 (2010) p.552-562

implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H.
Proteomics Volume 10 (2010) p.1895-1898

Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.
Vizcaíno JA, Foster JM, Martens L.
Journal of proteomics Volume 73 (2010) p.2136-2146

Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK.
Nature Volume 464 (2010) p.768-772

Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.
Genome research Volume 20 (2010) p.180-189

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR.
Proteomics Volume 10 (2010) p.3073-3081

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P.
Standards in genomic sciences Volume 2 (2010) p.357-360

Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L.
Drug discovery today Volume 15 (2010) p.3-15

BioCatalogue: a universal catalogue of web services for the life sciences.
Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.
Nucleic acids research Volume 38 (2010) p.W689-94

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Béroud C, Dobson G, Lehväslaiho H, Taschner PE, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR.
Genome medicine Volume 2 (2010) p.24

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.
Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Hériché JK, Lyall A, Mallon AM, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M, Thorisson GA, Zouberakis M, Hancock JM.
Database : the journal of biological databases and curation Volume 2010 (2010) p.baq014

Genomic-scale capture and sequencing of endogenous DNA from feces.
Perry GH, Marioni JC, Melsted P, Gilad Y.
Molecular ecology Volume 19 (2010) p.5332-5344

ChEBI: a chemistry ontology and database.
de Matos P, Dekker A, Ennis M, Hastings J, Haug K, Turner S, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.P6-P6

The Ontology Lookup Service: bigger and better.
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.
Nucleic acids research Volume 38 (2010) p.W155-60

A global map of human gene expression.
Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.
Nature biotechnology Volume 28 (2010) p.322-324

Diversity of human copy number variation and multicopy genes.
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler EE.
Science (New York, N.Y.) Volume 330 (2010) p.641-646

iMotifs: an integrated sequence motif visualization and analysis environment.
Piipari M, Down TA, Saini H, Enright A, Hubbard TJ.
Bioinformatics (Oxford, England) Volume 26 (2010) p.843-844

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM.
Proteins Volume 78 (2010) p.1120-1136

So what have data standards ever done for us? The view from metabolomics.
Griffin JL, Steinbeck C.
Genome medicine Volume 2 (2010) p.38

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.
Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J.
Microbiology (Reading, England) Volume 156 (2010) p.3255-3269

The miR-144/451 locus is required for erythroid homeostasis.
Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, Horos R, Von Lindern M, Enright AJ, O'Carroll D.
The Journal of experimental medicine Volume 207 (2010) p.1351-1358

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B.
Nucleic acids research Volume 38 (2010) p.D443-7

Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach.
Kafkas Ş, Varoğlu E, Rebholz-Schuhmann D, Taneri B.
BMC Bioinformatics Volume 11 (2010) p.P1-P1

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.
Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.
Genome biology Volume 11 (2010) p.R27

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease.
McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM, Pollard AJ, Macary PA, Chaudhry AN, Smith KG.
Nature medicine Volume 16 (2010) p.586-91, 1p following 591

The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.
Petty NK, Bulgin R, Crepin VF, Cerdeño-Tárraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A, Clark L, Toribio AL, Parkhill J, Dougan G, Frankel G, Thomson NR.
Journal of bacteriology Volume 192 (2010) p.525-538

A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.
Nature Volume 467 (2010) p.1061-1073

The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam.
Nguyen NT, Ha V, Tran NV, Stabler R, Pham DT, Le TM, van Doorn HR, Cerdeño-Tárraga A, Thomson N, Campbell J, Nguyen VM, Tran TT, Pham MV, Cao TT, Wren B, Farrar J, Baker S.
PLoS neglected tropical diseases Volume 4 (2010) p.e702

Heme proteins--diversity in structural characteristics, function, and folding.
Smith LJ, Kahraman A, Thornton JM.
Proteins Volume 78 (2010) p.2349-2368

Transcription factor families inferred from genome sequences of photosynthetic stramenopiles.
Rayko E, Maumus F, Maheswari U, Jabbari K, Bowler C.
The New phytologist Volume 188 (2010) p.52-66

Digital expression profiling of novel diatom transcripts provides insight into their biological functions.
Maheswari U, Jabbari K, Petit JL, Porcel BM, Allen AE, Cadoret JP, De Martino A, Heijde M, Kaas R, La Roche J, Lopez PJ, Martin-Jézéquel V, Meichenin A, Mock T, Schnitzler Parker M, Vardi A, Armbrust EV, Weissenbach J, Katinka M, Bowler C.
Genome biology Volume 11 (2010) p.R85

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.
Slack C, Werz C, Wieser D, Alic N, Foley A, Stocker H, Withers DJ, Thornton JM, Hafen E, Partridge L.
PLoS genetics Volume 6 (2010) p.e1000881

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.
Schuster E, McElwee JJ, Tullet JM, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D.
Molecular systems biology Volume 6 (2010) p.399

Comparative ecophysiology and genomics of the toxic unicellular alga Fibrocapsa japonica.
Guidi-Rontani C, Maheswari U, Jabbari K, Bowler C.
The New phytologist Volume 185 (2010) p.446-458

The CoFactor database: organic cofactors in enzyme catalysis.
Fischer JD, Holliday GL, Thornton JM.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2496-2497

Domain-ligand mapping for enzymes.
Bashton M, Thornton JM.
Journal of molecular recognition : JMR Volume 23 (2010) p.194-208

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.
Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.
Standards in genomic sciences Volume 3 (2010) p.259-266

Modeling biomedical experimental processes with OBI.
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J, OBI consortium.
Journal of biomedical semantics Volume 1 Suppl 1 (2010) p.S7

Safeguarding the integrity of protein archive.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley SK.
Nature Volume 463 (2010) p.425

SylArray: a web server for automated detection of miRNA effects from expression data.
Bartonicek N, Enright AJ.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2900-2901

MapMi: automated mapping of microRNA loci.
Guerra-Assunção JA, Enright AJ.
BMC bioinformatics Volume 11 (2010) p.133

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.
Palmer RD, Murray MJ, Saini HK, van Dongen S, Abreu-Goodger C, Muralidhar B, Pett MR, Thornton CM, Nicholson JC, Enright AJ, Coleman N, Children's Cancer and Leukaemia Group.
Cancer research Volume 70 (2010) p.2911-2923

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.
Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, Forrest MS, Campino S, Clark TG, Stanier P, Kwiatkowski D, Deloukas P, Dermitzakis ET, Tavaré S, Moore GE, Dunham I.
BMC genetics Volume 11 (2010) p.25

The Renal Gene Ontology Annotation Initiative.
Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R.
Organogenesis Volume 6 (2010) p.71-75

Integration of chemical information with protein sequences and 3D structures.
Golovin A, Henrick K, Kleywegt G.
Journal of Cheminformatics Volume 2 (2010) p.O17-O17

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic acids research Volume 38 (2010) p.D331-5

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution.
Dhami P, Saffrey P, Bruce AW, Dillon SC, Chiang K, Bonhoure N, Koch CM, Bye J, James K, Foad NS, Ellis P, Watkins NA, Ouwehand WH, Langford C, Andrews RM, Dunham I, Vetrie D.
PloS one Volume 5 (2010) p.e12339

MRMaid-DB: a repository of published SRM transitions.
Cham JA, Bianco L, Barton C, Bessant C.
Journal of proteome research Volume 9 (2010) p.620-625

Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs.
Santhakumar D, Forster T, Laqtom NN, Fragkoudis R, Dickinson P, Abreu-Goodger C, Manakov SA, Choudhury NR, Griffiths SJ, Vermeulen A, Enright AJ, Dutia B, Kohl A, Ghazal P, Buck AH.
Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.13830-13835

Anterior development in the parthenogenetic and viviparous form of the pea aphid, Acyrthosiphon pisum: hunchback and orthodenticle expression.
Huang TY, Cook CE, Davis GK, Shigenobu S, Chen RP, Chang CC.
Insect molecular biology Volume 19 Suppl 2 (2010) p.75-85

Practical application of bioinformatics by the multidisciplinary VIZIER consortium.
Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA.
Antiviral research Volume 87 (2010) p.95-110

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.
BMC bioinformatics Volume 11 Suppl 12 (2010) p.S12

Highlights of the 'gene nomenclature across species' meeting.
Bruford EA.
Human genomics Volume 4 (2010) p.213-217

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression.
Murray MJ, Saini HK, van Dongen S, Palmer RD, Muralidhar B, Pett MR, Piipari M, Thornton CM, Nicholson JC, Enright AJ, Coleman N.
Molecular cancer Volume 9 (2010) p.290

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.
Sudbery I, Enright AJ, Fraser AG, Dunham I.
BMC genomics Volume 11 (2010) p.175

WormBase: a comprehensive resource for nematode research.
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW.
Nucleic acids research Volume 38 (2010) p.D463-7

ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner.
Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ.
Cell Volume 143 (2010) p.367-378

Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H.
Nucleic acids research Volume 38 (2010) p.D870-1

Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges.
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
PLoS ONE Volume 5 (2010) p.

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M.
Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.4135-4140

A draft sequence of the Neandertal genome.
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.
Science (New York, N.Y.) Volume 328 (2010) p.710-722

Mining Unique-m Substrings from Genomes
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R.
Journal of proteomics & bioinformatics Volume 3 (2010) p.99-100

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
Li C, Courtot M, Le Novère N, Laibe C.
Briefings in bioinformatics Volume 11 (2010) p.270-277

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic acids research Volume 38 (2010) p.D142-8

Improvements to services at the European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G.
Nucleic acids research Volume 38 (2010) p.D39-45

Public data archives for genomic structural variation.
Church DM, Lappalainen I, Sneddon TP, Hinton J, Maguire M, Lopez J, Garner J, Paschall J, DiCuccio M, Yaschenko E, Scherer SW, Feuk L, Flicek P.
Nature genetics Volume 42 (2010) p.813-814

Visualizing chromosome mosaicism and detecting ethnic outliers by the method of "rare" heterozygotes and homozygotes (RHH).
McGinnis RE, Deloukas P, McLaren WM, Inouye M.
Human molecular genetics Volume 19 (2010) p.2539-2553

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC.
PLoS genetics Volume 6 (2010) p.e1001023

Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B.
Molecular cell Volume 38 (2010) p.603-613

Molecular interactions and data standardisation.
Orchard S, Kerrien S.
Methods in molecular biology (Clifton, N.J.) Volume 604 (2010) p.309-318

Integrating common and rare genetic variation in diverse human populations.
International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE.
Nature Volume 467 (2010) p.52-58

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium.
Cellular and molecular life sciences : CMLS Volume 67 (2010) p.1049-1064

The structures and physicochemical properties of organic cofactors in biocatalysis.
Fischer JD, Holliday GL, Rahman SA, Thornton JM.
Journal of molecular biology Volume 403 (2010) p.803-824

The genome of a songbird.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.
Nature Volume 464 (2010) p.757-762

The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.
Nature biotechnology Volume 28 (2010) p.935-942

Characterization and prediction of protein nucleolar localization sequences.
Scott MS, Boisvert FM, McDowall MD, Lamond AI, Barton GJ.
Nucleic acids research Volume 38 (2010) p.7388-7399

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
PloS one Volume 5 (2010) p.e9202

Logic-based models for the analysis of cell signaling networks.
Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA.
Biochemistry Volume 49 (2010) p.3216-3224

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT.
Science (New York, N.Y.) Volume 328 (2010) p.1036-1040

Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes.
Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK.
Molecular & cellular proteomics : MCP Volume 9 (2010) p.1849-1865

Bioinformatics training: a review of challenges, actions and support requirements.
Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Judge DP, van der Gool W, Brooksbank C.
Briefings in bioinformatics Volume 11 (2010) p.544-551

Elevated cyclic AMP levels in T lymphocytes transformed by human T-cell lymphotropic virus type 1.
Kress AK, Schneider G, Pichler K, Kalmer M, Fleckenstein B, Grassmann R.
Journal of virology Volume 84 (2010) p.8732-8742

Minimum information about a protein affinity reagent (MIAPAR).
Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren PA, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H, Sherman D.
Nature biotechnology Volume 28 (2010) p.650-653

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J.
Nucleic acids research Volume 38 (2010) p.4325-4336

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
Vainshtein Y, Sanchez M, Brazma A, Hentze MW, Dandekar T, Muckenthaler MU.
BMC bioinformatics Volume 11 (2010) p.112

Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
Naukkarinen J, Surakka I, Pietiläinen KH, Rissanen A, Salomaa V, Ripatti S, Yki-Järvinen H, van Duijn CM, Wichmann HE, Kaprio J, Taskinen MR, Peltonen L, ENGAGE Consortium.
PLoS genetics Volume 6 (2010) p.e1000976

A CTCF-independent role for cohesin in tissue-specific transcription.
Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT.
Genome research Volume 20 (2010) p.578-588

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids.
Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KG, Enright AJ, Gait MJ, Vigorito E.
Nucleic acids research Volume 38 (2010) p.4466-4475

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2069-2070

How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010.
Kohonen-Corish MR, Al-Aama JY, Auerbach AD, Axton M, Barash CI, Bernstein I, Béroud C, Burn J, Cunningham F, Cutting GR, den Dunnen JT, Greenblatt MS, Kaput J, Katz M, Lindblom A, Macrae F, Maglott D, Möslein G, Povey S, Ramesar R, Richards S, Seminara D, Sobrido MJ, Tavtigian S, Taylor G, Vihinen M, Winship I, Cotton RG, Human Variome Project Meeting.
Human mutation Volume 31 (2010) p.1374-1381

A standard variation file format for human genome sequences.
Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K.
Genome biology Volume 11 (2010) p.R88

Interaction modes at protein hetero-dimer interfaces.
Vaishnavi A, Sowmya G, Kalaivanii J, Ilakya S, Kangueane U, Kangueane P.
Bioinformation Volume 4 (2010) p.310-319

Chemical Entities of Biological Interest: an update.
de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C.
Nucleic acids research Volume 38 (2010) p.D249-54

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.
Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T.
The Plant cell Volume 22 (2010) p.997-1005

eHive: an artificial intelligence workflow system for genomic analysis.
Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, Ureta-Vidal A, Flicek P, Herrero J.
BMC bioinformatics Volume 11 (2010) p.240

Consistent annotation of gene expression arrays.
Ballester B, Johnson N, Proctor G, Flicek P.
BMC genomics Volume 11 (2010) p.294

Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC).
Hilner JE, Perdue LH, Sides EG, Pierce JJ, Wägner AM, Aldrich A, Loth A, Albret L, Wagenknecht LE, Nierras C, Akolkar B, T1DGC.
Clinical trials (London, England) Volume 7 (2010) p.S5-S32

Journal club. A computational geneticist looks at mechanisms of chromosomal evolution.
Flicek P.
Nature Volume 463 (2010) p.713

CDK-Taverna: an open workflow environment for cheminformatics.
Kuhn T, Willighagen EL, Zielesny A, Steinbeck C.
BMC bioinformatics Volume 11 (2010) p.159

The (non)malignancy of cancerous amino acidic substitutions.
Talavera D, Taylor MS, Thornton JM.
Proteins Volume 78 (2010) p.518-529

Large scale comparison of global gene expression patterns in human and mouse.
Zheng-Bradley X, Rung J, Parkinson H, Brazma A.
Genome biology Volume 11 (2010) p.R124

OntoFox: web-based support for ontology reuse.
Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y.
BMC research notes Volume 3 (2010) p.175

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C.
BMC systems biology Volume 4 (2010) p.92

2009

MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions.
Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C.
Molecular & cellular proteomics : MCP Volume 8 (2009) p.696-705

Recent developments in public proteomic MS repositories and pipelines.
Mead JA, Bianco L, Bessant C.
Proteomics Volume 9 (2009) p.861-881

Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets.
Blanco L, Mead JA, Bessant C.
Journal of proteome research Volume 8 (2009) p.1782-1791

InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic acids research Volume 37 (2009) p.D211-5

Biophysical annotation and representation of CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2263-2270

Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.
Experimental physiology Volume 94 (2009) p.472-485

A method for visualizing CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.
Bioinformatics (Oxford, England) Volume 25 (2009) p.3012-3019

CellML metadata standards, associated tools and repositories.
Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Volume 367 (2009) p.1845-1867

A protein interaction network for the large conductance Ca(2+)-activated K(+) channel in the mouse cochlea.
Kathiresan T, Harvey M, Orchard S, Sakai Y, Sokolowski B.
Molecular & cellular proteomics : MCP Volume 8 (2009) p.1972-1987

Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified.
Mehta A, Orchard S.
Molecular and cellular biochemistry Volume 329 (2009) p.3-15

HUPO World Congress Publication Committee meeting. August 2008, Amsterdam, The Netherlands.
Orchard S, Ping P.
Proteomics Volume 9 (2009) p.502-503

Ending the "publish and vanish" culture: how the data standardization process will assist in data harvesting.
Orchard S.
Journal of proteome research Volume 8 (2009) p.3219

Debunking minimum information myths: one hat need not fit all.
Orchard S, Taylor CF.
New biotechnology Volume 25 (2009) p.171-172

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase Consortium, Aebersold R, Hafen E.
BMC bioinformatics Volume 10 (2009) p.59

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
Reference Genome Group of the Gene Ontology Consortium.
PLoS computational biology Volume 5 (2009) p.e1000431

Haplotype-based search for SNPs associated with differential type 1 diabetes risk among chromosomes carrying a specific HLA DRB1-DQA1-DQB1 haplotype.
McGinnis R, McLaren W, Ranganath V, Whittaker P, Hunt S, Deloukas P, Type 1 Diabetes Genetics Consortium.
Diabetes, obesity & metabolism Volume 11 Suppl 1 (2009) p.8-16

A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose.
Takeuchi F, McGinnis R, Bourgeois S, Barnes C, Eriksson N, Soranzo N, Whittaker P, Ranganath V, Kumanduri V, McLaren W, Holm L, Lindh J, Rane A, Wadelius M, Deloukas P.
PLoS genetics Volume 5 (2009) p.e1000433

Large scale association analysis of novel genetic loci for coronary artery disease.
Coronary Artery Disease Consortium, Samani NJ, Deloukas P, Erdmann J, Hengstenberg C, Kuulasmaa K, McGinnis R, Schunkert H, Soranzo N, Thompson J, Tiret L, Ziegler A.
Arteriosclerosis, thrombosis, and vascular biology Volume 29 (2009) p.774-780

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS, Type 1 Diabetes Genetics Consortium.
Nature genetics Volume 41 (2009) p.703-707

ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles.
Li W, Gracey AY, Mello LV, Brass A, Cossins AR.
BMC genomics Volume 10 (2009) p.560

Update of the Diatom EST Database: a new tool for digital transcriptomics.
Maheswari U, Mock T, Armbrust EV, Bowler C.
Nucleic acids research Volume 37 (2009) p.D1001-5

Probing the "dark matter" of protein fold space.
Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I.
Structure (London, England : 1993) Volume 17 (2009) p.1244-1252

Application of ESTs in microarray analysis.
Li W, Olohan L, Williams D, Hughes M, Gracey A, Cossins A.
Methods in molecular biology (Clifton, N.J.) Volume 533 (2009) p.289-309

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.
Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, Binz PA.
Proteomics Volume 9 (2009) p.499-501

FlyBase: enhancing Drosophila Gene Ontology annotations.
Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium.
Nucleic acids research Volume 37 (2009) p.D555-9

Evolution. Uniting alignments and trees.
Löytynoja A, Goldman N.
Science (New York, N.Y.) Volume 324 (2009) p.1528-1529

In defense of statistical methods for detecting positive selection.
Yang Z, Nielsen R, Goldman N.
Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.E95; author reply E96

Genomic DNA k-mer spectra: models and modalities.
Chor B, Horn D, Goldman N, Levy Y, Massingham T.
Genome biology Volume 10 (2009) p.R108

The Systems Biology Graphical Notation.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.
Nature biotechnology Volume 27 (2009) p.735-741

Infrastructure for the life sciences: design and implementation of the UniProt website.
Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E.
BMC bioinformatics Volume 10 (2009) p.136

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group.
Nature methods Volume 6 (2009) p.423-430

PRIDE Converter: making proteomics data-sharing easy.
Barsnes H, Vizcaíno JA, Eidhammer I, Martens L.
Nature biotechnology Volume 27 (2009) p.598-599

Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray.
Samolski I, de Luis A, Vizcaíno JA, Monte E, Suárez MB.
BMC microbiology Volume 9 (2009) p.217

Designing and encoding models for synthetic biology.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N.
Journal of the Royal Society, Interface / the Royal Society Volume 6 Suppl 4 (2009) p.S405-17

Planning the human variome project: the Spain report.
Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS, Contributors to the Human Variome Project Planning Meeting.
Human mutation Volume 30 (2009) p.496-510

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJ, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AF, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C.
Nature genetics Volume 41 (2009) p.1182-1190

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.
Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J.
Journal of chemical theory and computation Volume 5 (2009) p.982-992

PDBsum new things.
Laskowski RA.
Nucleic acids research Volume 37 (2009) p.D355-9

Web services at the European Bioinformatics Institute-2009.
McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R.
Nucleic acids research Volume 37 (2009) p.W6-10

The IMGT/HLA database.
Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic acids research Volume 37 (2009) p.D1013-7

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.
Morley RH, Lachani K, Keefe D, Gilchrist MJ, Flicek P, Smith JC, Wardle FC.
Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.3829-3834

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.
Carlile M, Swan D, Jackson K, Preston-Fayers K, Ballester B, Flicek P, Werner A.
Nucleic acids research Volume 37 (2009) p.2274-2282

The need for speed.
Flicek P.
Genome biology Volume 10 (2009) p.212

Finding query suggestions for PubMed.
Lu Z, Wilbur WJ, McEntyre JR, Iskhakov A, Szilagyi L.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Volume 2009 (2009) p.396-400

Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.
Pink CJ, Swaminathan SK, Dunham I, Rogers J, Ward A, Hurst LD.
Genome biology and evolution Volume 1 (2009) p.13-22

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace M, Maiwald T, Thornton JM.
PLoS computational biology Volume 5 (2009) p.e1000440

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.
Galperin MY, Cochrane GR.
Nucleic acids research Volume 37 (2009) p.D1-4

Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.
Nature Volume 461 (2009) p.168-170

Correction: Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome biology Volume 10 (2009) p.402-402

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ.
Genes & development Volume 23 (2009) p.619-632

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.
Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP.
Nature genetics Volume 41 (2009) p.614-618

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne A, Holloway E, Malone J, Williams E, Parkinson H.
Bioinformatics (Oxford, England) Volume 25 (2009) p.279-280

Network visualization and analysis of gene expression data using BioLayout Express(3D).
Theocharidis A, van Dongen S, Enright AJ, Freeman TC.
Nature protocols Volume 4 (2009) p.1535-1550

Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I.
Journal of chemical information and modeling Volume 49 (2009) p.2272-2289

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.
PLoS computational biology Volume 5 (2009) p.e1000585

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U.
Chemico-biological interactions Volume 178 (2009) p.94-98

Drug target central.
Harland L, Gaulton A.
Expert opinion on drug discovery Volume 4 (2009) p.857-872

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Paten B, Herrero J, Beal K, Birney E.
Bioinformatics (Oxford, England) Volume 25 (2009) p.295-301

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009.
Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J, Gilbert J.
Standards in genomic sciences Volume 1 (2009) p.278-282

Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion.
Bonaglia MC, Giorda R, Beri S, Bigoni S, Sensi A, Baroncini A, Capucci A, De Agostini C, Gwilliam R, Deloukas P, Dunham I, Zuffardi O.
European journal of human genetics : EJHG Volume 17 (2009) p.426-433

DASMI: exchanging, annotating and assessing molecular interaction data.
Blankenburg H, Finn RD, Prlić A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M.
Bioinformatics (Oxford, England) Volume 25 (2009) p.1321-1328

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients.
Holden MTG, Seth-Smith HMB, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EPC, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J.
Journal of bacteriology Volume 191 (2009) p.2907-2907

Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.
Motallebipour M, Enroth S, Punga T, Ameur A, Koch C, Dunham I, Komorowski J, Ericsson J, Wadelius C.
The FEBS journal Volume 276 (2009) p.1878-1890

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation.
Tarpey PS, Smith R, Pleasance E, Whibley A, Edkins S, Hardy C, O'Meara S, Latimer C, Dicks E, Menzies A, Stephens P, Blow M, Greenman C, Xue Y, Tyler-Smith C, Thompson D, Gray K, Andrews J, Barthorpe S, Buck G, Cole J, Dunmore R, Jones D, Maddison M, Mironenko T, Turner R, Turrell K, Varian J, West S, Widaa S, Wray P, Teague J, Butler A, Jenkinson A, Jia M, Richardson D, Shepherd R, Wooster R, Tejada MI, Martinez F, Carvill G, Goliath R, de Brouwer AP, van Bokhoven H, Van Esch H, Chelly J, Raynaud M, Ropers HH, Abidi FE, Srivastava AK, Cox J, Luo Y, Mallya U, Moon J, Parnau J, Mohammed S, Tolmie JL, Shoubridge C, Corbett M, Gardner A, Haan E, Rujirabanjerd S, Shaw M, Vandeleur L, Fullston T, Easton DF, Boyle J, Partington M, Hackett A, Field M, Skinner C, Stevenson RE, Bobrow M, Turner G, Schwartz CE, Gecz J, Raymond FL, Futreal PA, Stratton MR.
Nature genetics Volume 41 (2009) p.535-543

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R.
Journal of proteome research Volume 8 (2009) p.3689-3692

Petabyte-scale innovations at the European Nucleotide Archive.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E.
Nucleic acids research Volume 37 (2009) p.D19-25

ENFIN--A European network for integrative systems biology.
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E.
Comptes rendus biologies Volume 332 (2009) p.1050-1058

Ensembl 2009.
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P.
Nucleic acids research Volume 37 (2009) p.D690-7

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.
Manakov SA, Grant SG, Enright AJ.
BMC genomics Volume 10 (2009) p.419

The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM.
FEBS letters Volume 583 (2009) p.1692-1698

Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P.
Nucleic acids research Volume 37 (2009) p.D619-22

The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R.
Nucleic acids research Volume 37 (2009) p.D396-403

Annual spring meeting of the Proteomics Standards Initiative.
Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H.
Proteomics Volume 9 (2009) p.4429-4432

Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E.
Nature methods Volume 6 (2009) p.S6-S12

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic acids research Volume 37 (2009) p.D169-74

Protein promiscuity and its implications for biotechnology.
Nobeli I, Favia AD, Thornton JM.
Nature biotechnology Volume 27 (2009) p.157-167

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.
Bioinformatics (Oxford, England) Volume 25 (2009) p.3045-3046

QuickGO: a user tutorial for the web-based Gene Ontology browser.
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R.
Database : the journal of biological databases and curation Volume 2009 (2009) p.bap010

Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M, Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, Thomas G, Carling D, Okkenhaug K, Thornton JM, Partridge L, Gems D, Withers DJ.
Science (New York, N.Y.) Volume 326 (2009) p.140-144

Recurated protein interaction datasets.
Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.
Nature methods Volume 6 (2009) p.860-861

VectorBase: a data resource for invertebrate vector genomics.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.
Nucleic acids research Volume 37 (2009) p.D583-7

Guidelines for the nomenclature of the human heat shock proteins.
Kampinga HH, Hageman J, Vos MJ, Kubota H, Tanguay RM, Bruford EA, Cheetham ME, Chen B, Hightower LE.
Cell stress & chaperones Volume 14 (2009) p.105-111

DNA methylation-histone modification relationships across the desmin locus in human primary cells.
Lindahl Allen M, Koch CM, Clelland GK, Dunham I, Antoniou M.
BMC molecular biology Volume 10 (2009) p.51

Protein function annotation by homology-based inference.
Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A.
Genome biology Volume 10 (2009) p.207

Applications of high-throughput sequencing to chromatin structure and function in mammals.
Dunham I.
F1000 biology reports Volume 1 (2009) p.32

Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network.
Genome biology Volume 10 (2009) p.401

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva R, Thornton JM, Pellegrini-Calace M.
Bioinformatics (Oxford, England) Volume 25 (2009) p.3183-3184

New open drug activity data at EBI
Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J.
Chemistry Central Journal Volume 3 (2009) p.O3

Enhanced DNA binding capacity on up-regulated epidermal wild-type p53 in vitiligo by H2O2-mediated oxidation: a possible repair mechanism for DNA damage.
Salem MM, Shalbaf M, Gibbons NC, Chavan B, Thornton JM, Schallreuter KU.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 23 (2009) p.3790-3807

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM.
Journal of molecular biology Volume 388 (2009) p.356-380

OrChem - An open source chemistry search engine for Oracle(R).
Rijnbeek M, Steinbeck C.
Journal of cheminformatics Volume 1 (2009) p.17

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Durinck S, Spellman PT, Birney E, Huber W.
Nature protocols Volume 4 (2009) p.1184-1191

Bioclipse 2: a scriptable integration platform for the life sciences.
Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JE.
BMC bioinformatics Volume 10 (2009) p.397

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR.
Genome biology Volume 10 (2009) p.R51

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.
Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D.
Genome research Volume 19 (2009) p.994-1005

Metal-MACiE: a database of metals involved in biological catalysis.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2088-2089

Second Joint HUPO publication and Proteomics Standards Initiative workshop.
Orchard S, Binz PA, Hermjakob H.
Proteomics Volume 9 (2009) p.4426-4428

MAPU 2.0: high-accuracy proteomes mapped to genomes.
Gnad F, Oroshi M, Birney E, Mann M.
Nucleic acids research Volume 37 (2009) p.D902-6

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H.
Proteomics Volume 9 (2009) p.5112-5119

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.
Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J.
Journal of bacteriology Volume 191 (2009) p.261-277

The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, Codlin S, Brazma A, de Bruin RA, Bähler J.
PLoS genetics Volume 5 (2009) p.e1000626

The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C.
Structure (London, England : 1993) Volume 17 (2009) p.1051-1062

Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2092-2094

Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM.
Nature chemical biology Volume 5 (2009) p.521-525

Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.
Bioinformatics (Oxford, England) Volume 25 (2009) p.i145-53

Charting online OMICS resources: A navigational chart for clinical researchers.
Vizcaíno JA, Mueller M, Hermjakob H, Martens L.
Proteomics. Clinical applications Volume 3 (2009) p.18-29

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.
Nucleic acids research Volume 37 (2009) p.D868-72

Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday GL, Mitchell JB, Thornton JM.
Journal of molecular biology Volume 390 (2009) p.560-577

A System for Information Management in BioMedical Studies--SIMBioMS.
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2768-2769

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
Zerbino DR, McEwen GK, Margulies EH, Birney E.
PloS one Volume 4 (2009) p.e8407

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA.
Nucleic acids research Volume 37 (2009) p.D310-4

Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM.
Journal of the Royal Society, Interface / the Royal Society Volume 6 (2009) p.129-147

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.
Molecular oncology Volume 3 (2009) p.9-17

A guide to the Proteomics Identifications Database proteomics data repository.
Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.
Proteomics Volume 9 (2009) p.4276-4283

Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.
Megy K, Hammond M, Lawson D, Bruggner RV, Birney E, Collins FH.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Volume 9 (2009) p.308-313

WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM.
Bioinformatics (Oxford, England) Volume 25 (2009) p.1192-1194

Case-controlled structure validation.
Read RJ, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.140-147

Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.
Journal of cheminformatics Volume 1 (2009) p.12

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.
Genome research Volume 19 (2009) p.327-335

Genome watch: What a scorcher!
Cerdeño-Tárraga AM.
Nature reviews. Microbiology Volume 7 (2009) p.408-409

On vital aid: the why, what and how of validation.
Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.134-139

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D.
Genome research Volume 19 (2009) p.1316-1323

A chemogenomics view on protein-ligand spaces.
Strömbergsson H, Kleywegt GJ.
BMC bioinformatics Volume 10 Suppl 6 (2009) p.S13

The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ.
Biochemical Society transactions Volume 37 (2009) p.723-726

Integrating sequence, evolution and functional genomics in regulatory genomics.
Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E.
Genome biology Volume 10 (2009) p.202

In silico identification of genes in bacteriophage DNA.
Kropinski AM, Borodovsky M, Carver TJ, Cerdeño-Tárraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van Domselaar G, Wishart DS.
Methods in molecular biology (Clifton, N.J.) Volume 502 (2009) p.57-89

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
Brazma A.
TheScientificWorldJournal Volume 9 (2009) p.420-423

2008

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
Genome research Volume 18 (2008) p.1814-1828

GENETICS. The Human Variome Project.
Cotton RG, Auerbach AD, Axton M, Barash CI, Berkovic SF, Brookes AJ, Burn J, Cutting G, den Dunnen JT, Flicek P, Freimer N, Greenblatt MS, Howard HJ, Katz M, Macrae FA, Maglott D, Möslein G, Povey S, Ramesar RS, Richards CS, Seminara D, Smith TD, Sobrido MJ, Solbakk JH, Tanzi RE, Tavtigian SV, Taylor GR, Utsunomiya J, Watson M.
Science (New York, N.Y.) Volume 322 (2008) p.861-862

Determination and validation of principal gene products.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A.
Bioinformatics (Oxford, England) Volume 24 (2008) p.11-17

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Löytynoja A, Goldman N.
Science (New York, N.Y.) Volume 320 (2008) p.1632-1635

A model of evolution and structure for multiple sequence alignment.
Löytynoja A, Goldman N.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3913-3919

The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.
Nature biotechnology Volume 26 (2008) p.541-547

Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM.
BMC evolutionary biology Volume 8 (2008) p.247

nGASP--the nematode genome annotation assessment project.
Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium, Stein LD.
BMC bioinformatics Volume 9 (2008) p.549

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E.
Nucleic acids research Volume 36 (2008) p.D5-12

The universal protein resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 36 (2008) p.D190-5

Levers and fulcrums: progress in cis-regulatory motif models.
Birney E.
Nature methods Volume 5 (2008) p.297-298

Advanced genomic data mining.
Fernández-Suárez XM, Birney E.
PLoS computational biology Volume 4 (2008) p.e1000121

Data curation + process curation=data integration + science.
Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R.
Briefings in bioinformatics Volume 9 (2008) p.506-517

Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O.
Omics : a journal of integrative biology Volume 12 (2008) p.137-141

Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM.
Nature reviews. Genetics Volume 9 (2008) p.141-151

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J.
Bioinformatics (Oxford, England) Volume 24 (2008) p.i105-11

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Margulies EH, Birney E.
Nature reviews. Genetics Volume 9 (2008) p.303-313

Charting plant interactomes: possibilities and challenges.
Morsy M, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC.
Trends in plant science Volume 13 (2008) p.183-191

Remediation of the protein data bank archive.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM.
Nucleic acids research Volume 36 (2008) p.D426-33

The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.
Braconi Quintaje S, Orchard S.
Molecular & cellular proteomics : MCP Volume 7 (2008) p.1409-1419

Activation of the SPS amino acid-sensing pathway in Saccharomyces cerevisiae correlates with the phosphorylation state of a sensor component, Ptr3.
Liu Z, Thornton J, Spírek M, Butow RA.
Molecular and cellular biology Volume 28 (2008) p.551-563

What everybody should know about the rat genome and its online resources.
Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ.
Nature genetics Volume 40 (2008) p.523-527

Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Combinatorial chemistry & high throughput screening Volume 11 (2008) p.653-660

Genome analysis of the platypus reveals unique signatures of evolution.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.
Nature Volume 453 (2008) p.175-183

Minimum reporting guidelines for proteomics released by the Proteomics Standards Initiative.
Jones AR, Orchard S.
Molecular & cellular proteomics : MCP Volume 7 (2008) p.2067-2068

The HGNC Database in 2008: a resource for the human genome.
Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E.
Nucleic acids research Volume 36 (2008) p.D445-8

Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.
Goldman N, Yang Z.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3889-3892

Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T.
Omics : a journal of integrative biology Volume 12 (2008) p.101-108

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV.
The Plant cell Volume 20 (2008) p.1426-1436

Rapidly evolving human promoter regions.
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA.
Nature genetics Volume 40 (2008) p.1262-3; author reply 1263-4

Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.
Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L, Genomic Standards Consortium.
Omics : a journal of integrative biology Volume 12 (2008) p.109-113

PROCOGNATE: a cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
Nucleic acids research Volume 36 (2008) p.D618-22

Consensus nomenclature for the human ArfGAP domain-containing proteins.
Kahn RA, Bruford E, Inoue H, Logsdon JM Jr, Nie Z, Premont RT, Randazzo PA, Satake M, Theibert AB, Zapp ML, Cassel D.
The Journal of cell biology Volume 182 (2008) p.1039-1044

In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Molecular biotechnology Volume 38 (2008) p.165-177

Natural language processing in aid of FlyBase curators.
Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T.
BMC bioinformatics Volume 9 (2008) p.193

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.
Nature biotechnology Volume 26 (2008) p.779-785

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.
Kuhn S, Egert B, Neumann S, Steinbeck C.
BMC bioinformatics Volume 9 (2008) p.400

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.
Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H.
Proteomics Volume 8 (2008) p.4168-4172

InteroPORC: automated inference of highly conserved protein interaction networks.
Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H.
Bioinformatics (Oxford, England) Volume 24 (2008) p.1625-1631

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L.
Proteomics Volume 8 (2008) p.1138-1148

Data storage and analysis in ArrayExpress and Expression Profiler.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume Chapter 7 (2008) p.Unit 7.13

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.
Nucleic acids research Volume 36 (2008) p.W372-6

Functional site prediction selects correct protein models.
Chelliah V, Taylor WR.
BMC bioinformatics Volume 9 Suppl 1 (2008) p.S13

Prediction of protein structure from ideal forms.
Taylor WR, Bartlett GJ, Chelliah V, Klose D, Lin K, Sheldon T, Jonassen I.
Proteins Volume 70 (2008) p.1610-1619

Biological Data Resources at the EMBL-EBI
Lopez R.
Revista Colombiana de biotecnologia Volume 10 (2008) p.120–128

The BREW workshop series: a stimulating experience in PhD education.
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M.
Briefings in bioinformatics Volume 9 (2008) p.250-253

Ensembl 2008.
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.
Nucleic acids research Volume 36 (2008) p.D707-14

Analyzing large-scale proteomics projects with latent semantic indexing.
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H.
Journal of proteome research Volume 7 (2008) p.182-191

X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment.
Dibbens LM, Tarpey PS, Hynes K, Bayly MA, Scheffer IE, Smith R, Bomar J, Sutton E, Vandeleur L, Shoubridge C, Edkins S, Turner SJ, Stevens C, O'Meara S, Tofts C, Barthorpe S, Buck G, Cole J, Halliday K, Jones D, Lee R, Madison M, Mironenko T, Varian J, West S, Widaa S, Wray P, Teague J, Dicks E, Butler A, Menzies A, Jenkinson A, Shepherd R, Gusella JF, Afawi Z, Mazarib A, Neufeld MY, Kivity S, Lev D, Lerman-Sagie T, Korczyn AD, Derry CP, Sutherland GR, Friend K, Shaw M, Corbett M, Kim HG, Geschwind DH, Thomas P, Haan E, Ryan S, McKee S, Berkovic SF, Futreal PA, Stratton MR, Mulley JC, Gécz J.
Nature genetics Volume 40 (2008) p.776-781

The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells.
Garrick D, De Gobbi M, Samara V, Rugless M, Holland M, Ayyub H, Lower K, Sloane-Stanley J, Gray N, Koch C, Dunham I, Higgs DR.
Blood Volume 112 (2008) p.3889-3899

Finishing the finished human chromosome 22 sequence.
Cole CG, McCann OT, Collins JE, Oliver K, Willey D, Gribble SM, Yang F, McLaren K, Rogers J, Ning Z, Beare DM, Dunham I.
Genome biology Volume 9 (2008) p.R78

Epigenomics at the tipping point. Foreword.
Stamatoyannopoulos JA, Dunham I.
Pharmacogenomics Volume 9 (2008) p.1781-1783

EBI Proteomics Services
Hermjakob H.
Lecture notes in computer science Volume 5109 (2008) p.207

Data standards and controlled vocabularies for proteomics.
Martens L, Palazzi LM, Hermjakob H.
Methods in molecular biology (Clifton, N.J.) Volume 484 (2008) p.279-286

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S, Members of the RSBI Working Group.
Omics : a journal of integrative biology Volume 12 (2008) p.143-149

4DXpress: a database for cross-species expression pattern comparisons.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.
Nucleic acids research Volume 36 (2008) p.D847-53

Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E.
Genome research Volume 18 (2008) p.1829-1843

6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.
Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H.
Proteomics Volume 8 (2008) p.1331-1333

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.
Nature biotechnology Volume 26 (2008) p.889-896

PRIDE: new developments and new datasets.
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.
Nucleic acids research Volume 36 (2008) p.D878-83

Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H.
Bioinformatics (Oxford, England) Volume 24 (2008) p.2119-2121

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica C, Labarga A, Gould CM, López R, Gibson TJ.
BMC bioinformatics Volume 9 (2008) p.229

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
O'Neill K, Garcia A, Schwegmann A, Jimenez RC, Jacobson D, Hermjakob H.
BMC bioinformatics Volume 9 (2008) p.437

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.
Orchard S, Hermjakob H.
Briefings in bioinformatics Volume 9 (2008) p.166-173

UniProtJAPI: a remote API for accessing UniProt data.
Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R.
Bioinformatics (Oxford, England) Volume 24 (2008) p.1321-1322

Metal ions in biological catalysis: from enzyme databases to general principles.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry Volume 13 (2008) p.1205-1218

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W.
Bioinformatics (Oxford, England) Volume 24 (2008) p.1100-1101

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.
Nature biotechnology Volume 26 (2008) p.305-312

BioJava: an open-source framework for bioinformatics.
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.
Bioinformatics (Oxford, England) Volume 24 (2008) p.2096-2097

Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A.
BMC bioinformatics Volume 9 Suppl 8 (2008) p.S3

Performance validation of neural network based (13)c NMR prediction using a publicly available data source.
Blinov KA, Smurnyy YD, Elyashberg ME, Churanova TS, Kvasha M, Steinbeck C, Lefebvre BA, Williams AJ.
Journal of chemical information and modeling Volume 48 (2008) p.550-555

Evolution of binding sites for zinc and calcium ions playing structural roles.
Torrance JW, Macarthur MW, Thornton JM.
Proteins Volume 71 (2008) p.813-830

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.
Bioinformatics (Oxford, England) Volume 24 (2008) p.2767-2772

Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project.
Kuhn T, Zielesny A, Steinbeck C.
Chemistry Central Journal Volume 2 (2008) p.P27-P27

Epigenetic marking prepares the human HOXA cluster for activation during differentiation of pluripotent cells.
Atkinson SP, Koch CM, Clelland GK, Willcox S, Fowler JC, Stewart R, Lako M, Dunham I, Armstrong L.
Stem cells (Dayton, Ohio) Volume 26 (2008) p.1174-1185

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.
Genome research Volume 18 (2008) p.393-403

A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae.
Jones GM, Stalker J, Humphray S, West A, Cox T, Rogers J, Dunham I, Prelich G.
Nature methods Volume 5 (2008) p.239-241

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.
Genome research Volume 18 (2008) p.1518-1529

Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
O'Reilly PF, Birney E, Balding DJ.
Genome research Volume 18 (2008) p.1304-1313

SNP and haplotype mapping for genetic analysis in the rat.
STAR Consortium, Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, Guigo R, Guryev V, Heinig M, Hummel O, Jahn N, Klages S, Kren V, Kube M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee YA, Lopez-Bigas N, Lathrop GM, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet JA, Platzer M, Pravenec M, Reinhardt R, Sakaki Y, Schilhabel M, Schulz H, Serikawa T, Shikhagaie M, Tatsumoto S, Taudien S, Toyoda A, Voigt B, Zelenika D, Zimdahl H, Hubner N.
Nature genetics Volume 40 (2008) p.560-566

Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
Selman C, Lingard S, Choudhury AI, Batterham RL, Claret M, Clements M, Ramadani F, Okkenhaug K, Schuster E, Blanc E, Piper MD, Al-Qassab H, Speakman JR, Carmignac D, Robinson IC, Thornton JM, Gems D, Partridge L, Withers DJ.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 22 (2008) p.807-818

Evolutionary footprints of nucleosome positions in yeast.
Washietl S, Machné R, Goldman N.
Trends in genetics : TIG Volume 24 (2008) p.583-587

The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.
Nucleic acids research Volume 36 (2008) p.D1028-33

ISPIDER Central: an integrated database web-server for proteomics.
Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, Hubbard SJ.
Nucleic acids research Volume 36 (2008) p.W485-90

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T.
Nucleic acids research Volume 36 (2008) p.D793-9

The Universal Protein Resource. A Growing Online Protein Database.
O'Donovan C, Martin MJ, Apweiler R.
BIOforum Europe Volume 12 (2008) p.32-33

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD, Nobeli I, Glaser F, Thornton JM.
Journal of molecular biology Volume 375 (2008) p.855-874

The evolution of the DLK1-DIO3 imprinted domain in mammals.
Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, SAVOIR consortium, Dunham I, Renfree MB, Ferguson-Smith AC.
PLoS biology Volume 6 (2008) p.e135

miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
Nucleic acids research Volume 36 (2008) p.D154-8

A logic-based diagram of signalling pathways central to macrophage activation.
Raza S, Robertson KA, Lacaze PA, Page D, Enright AJ, Ghazal P, Freeman TC.
BMC systems biology Volume 2 (2008) p.36

Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.
Smits G, Mungall AJ, Griffiths-Jones S, Smith P, Beury D, Matthews L, Rogers J, Pask AJ, Shaw G, VandeBerg JL, McCarrey JR, SAVOIR Consortium, Renfree MB, Reik W, Dunham I.
Nature genetics Volume 40 (2008) p.971-976

Fusion and fission of genes define a metric between fungal genomes.
Durrens P, Nikolski M, Sherman D.
PLoS computational biology Volume 4 (2008) p.e1000200

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E.
Genome research Volume 18 (2008) p.821-829

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.
Genome biology Volume 9 Suppl 2 (2008) p.S5

Calling on a million minds for community annotation in WikiProteins.
Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A.
Genome biology Volume 9 (2008) p.R89

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.
Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S.
Immunogenetics Volume 60 (2008) p.1-18

Computational prediction of protein-protein interactions.
Skrabanek L, Saini HK, Bader GD, Enright AJ.
Molecular biotechnology Volume 38 (2008) p.1-17

Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ.
Nature methods Volume 5 (2008) p.1023-1025

Annotation of mammalian primary microRNAs.
Saini HK, Enright AJ, Griffiths-Jones S.
BMC genomics Volume 9 (2008) p.564

2007

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM.
Nucleic acids research Volume 35 (2007) p.D515-20

Estimating the neutral rate of nucleotide substitution using introns.
Hoffman MM, Birney E.
Molecular biology and evolution Volume 24 (2007) p.522-531

Challenges and standards in integrating surveys of structural variation.
Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L.
Nature genetics Volume 39 (2007) p.S7-15

Identification of novel peptide hormones in the human proteome by hidden Markov model screening.
Mirabeau O, Perlas E, Severini C, Audero E, Gascuel O, Possenti R, Birney E, Rosenthal N, Gross C.
Genome research Volume 17 (2007) p.320-327

The geometry of interactions between catalytic residues and their substrates.
Torrance JW, Holliday GL, Mitchell JB, Thornton JM.
Journal of molecular biology Volume 369 (2007) p.1140-1152

Web services at the European bioinformatics institute.
Labarga A, Valentin F, Anderson M, Lopez R.
Nucleic acids research Volume 35 (2007) p.W6-11

New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic acids research Volume 35 (2007) p.D224-8

Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.
Bioinformatics (Oxford, England) Volume 23 (2007) p.2947-2948

In vivo validation of a computationally predicted conserved Ath5 target gene set.
Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J.
PLoS genetics Volume 3 (2007) p.1661-1671

The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H.
Nature biotechnology Volume 25 (2007) p.887-893

IntAct--open source resource for molecular interaction data.
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H.
Nucleic acids research Volume 35 (2007) p.D561-5

Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK Jr, Hermjakob H.
Proteomics Volume 7 (2007) p.337-339

The PSI formal document process and its implementation on the PSI website.
Vizcaíno JA, Martens L, Hermjakob H, Julian RK, Paton NW.
Proteomics Volume 7 (2007) p.2355-2357

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.
Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C.
Genome research Volume 17 (2007) p.708-719

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Superieure (ENS), Lyon, France.
Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H.
Proteomics Volume 7 (2007) p.3436-3440

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
BMC Bioinformatics Volume 8 (2007) p.S1-S1

Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N.
Systematic biology Volume 56 (2007) p.431-444

The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.
Nature biotechnology Volume 25 (2007) p.894-898

Statistics of the log-det estimator.
Massingham T, Goldman N.
Molecular biology and evolution Volume 24 (2007) p.2277-2285

An empirical codon model for protein sequence evolution.
Kosiol C, Holmes I, Goldman N.
Molecular biology and evolution Volume 24 (2007) p.1464-1479

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.
Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M.
Genomics Volume 89 (2007) p.307-315

RPS6KA2, a putative tumour suppressor gene at 6q27 in sporadic epithelial ovarian cancer.
Bignone PA, Lee KY, Liu Y, Emilion G, Finch J, Soosay AE, Charnock FM, Beck S, Dunham I, Mungall AJ, Ganesan TS.
Oncogene Volume 26 (2007) p.683-700

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.
BMC bioinformatics Volume 8 (2007) p.401

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.
Proteomics Volume 7 Suppl 1 (2007) p.28-34

Proteomic data exchange and storage: the need for common standards and public repositories.
Orchard S, Jones P, Taylor C, Zhu W, Julian RK Jr, Hermjakob H, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 367 (2007) p.261-270

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia.
Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ.
Molecular psychiatry Volume 12 (2007) p.74-86

Clinical proteomics: A need to define the field and to begin to set adequate standards.
Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T.
Proteomics. Clinical applications Volume 1 (2007) p.148-156

Proteomics data validation: why all must provide data.
Martens L, Hermjakob H.
Molecular bioSystems Volume 3 (2007) p.518-522

The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.
Edwards CA, Rens W, Clarke O, Mungall AJ, Hore T, Graves JA, Dunham I, Ferguson-Smith AC, Ferguson-Smith MA.
BMC evolutionary biology Volume 7 (2007) p.157

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.
De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, Dunham I, Gibbons RJ, Wood WG, Higgs DR.
Blood Volume 110 (2007) p.4503-4510

Sequencing and association analysis of the type 1 diabetes-linked region on chromosome 10p12-q11.
Nejentsev S, Smink LJ, Smyth D, Bailey R, Lowe CE, Payne F, Masters J, Godfrey L, Lam A, Burren O, Stevens H, Nutland S, Walker NM, Smith A, Twells R, Barratt BJ, Wright C, French L, Chen Y, Deloukas P, Rogers J, Dunham I, Todd JA.
BMC genetics Volume 8 (2007) p.24

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ.
Proteome science Volume 5 (2007) p.4

Variation in evolutionary processes at different codon positions.
Bofkin L, Goldman N.
Molecular biology and evolution Volume 24 (2007) p.513-521

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Molecular & cellular proteomics : MCP Volume 6 (2007) p.1666-1667

Update of the Anopheles gambiae PEST genome assembly.
Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH.
Genome biology Volume 8 (2007) p.R5

The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 406 (2007) p.1-21

eGenomics: Cataloguing Our Complete Genome Collection III.
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Comparative and functional genomics Volume 2007 (2007) p.

EMBL Nucleotide Sequence Database in 2006.
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic acids research Volume 35 (2007) p.D16-20

Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases.
Allali-Hassani A, Pan W, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards A, Bochkarev A, Plotnikov A, Vedadi M, Arrowsmith C.
PLoS biology Volume 5 (2007) p.

Genome browsing with Ensembl: a practical overview.
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Briefings in functional genomics & proteomics Volume 6 (2007) p.202-219

Evolutionary genomics: come fly with us.
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Nature Volume 450 (2007) p.184-185

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.
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Nature methods Volume 4 (2007) p.563-565

ENFIN a network to enhance integrative systems biology.
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Annals of the New York Academy of Sciences Volume 1115 (2007) p.23-31

IMGT Colliers de Perles and IgSF domain standardization for T cell costimulatory activatory (CD28, ICOS) and inhibitory (CTLA4, PDCD1 and BTLA) receptors.
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Developmental and comparative immunology Volume 31 (2007) p.1050-1072

Gene prediction: compare and CONTRAST.
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Genome biology Volume 8 (2007) p.233

Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.
Mouse Phenotype Database Integration Consortium, Hancock JM, Adams NC, Aidinis V, Blake A, Bogue M, Brown SD, Chesler EJ, Davidson D, Duran C, Eppig JT, Gailus-Durner V, Gates H, Gkoutos GV, Greenaway S, Hrabé de Angelis M, Kollias G, Leblanc S, Lee K, Lengger C, Maier H, Mallon AM, Masuya H, Melvin DG, Müller W, Parkinson H, Proctor G, Reuveni E, Schofield P, Shukla A, Smith C, Toyoda T, Vasseur L, Wakana S, Walling A, White J, Wood J, Zouberakis M.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 18 (2007) p.157-163

Experimental design criteria in phylogenetics: where to add taxa.
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Systematic biology Volume 56 (2007) p.609-622

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nat Biotechnol. Volume (2007) p.1127-1133

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M.
Nature methods Volume 4 (2007) p.13-17

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.
BMC biology Volume 5 (2007) p.44

Recommendations of the 2006 Human Variome Project meeting.
Cotton RG, 2006 Human Variome Project, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, Cotton RG, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez AM, Pagon R, Ramesar R, Ravine D, Richards S, Rimoin D, Ring HZ, Scriver CR, Sherry S, Shimizu N, Stein L, Tadmouri GO, Taylor G, Watson M.
Nature genetics Volume 39 (2007) p.433-436

Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Mol Cell Proteomics Volume 6 (2007) p.1666-1667

ArrayExpress--a public database of microarray experiments and gene expression profiles.
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Nucleic acids research Volume 35 (2007) p.D747-50

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.
Oeder S, Mages J, Flicek P, Lang R.
BMC genomics Volume 8 (2007) p.200

Population genomics of human gene expression.
Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET.
Nature genetics Volume 39 (2007) p.1217-1224

Double Dutch for duplications.
Birney E.
Nature genetics Volume 39 (2007) p.1303-1304

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA.
Nucleic acids research Volume 35 (2007) p.D291-7

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.
Dicks E, Teague JW, Stephens P, Raine K, Yates A, Mattocks C, Tarpey P, Butler A, Menzies A, Richardson D, Jenkinson A, Davies H, Edkins S, Forbes S, Gray K, Greenman C, Shepherd R, Stratton MR, Futreal PA, Wooster R.
Bioinformatics (Oxford, England) Volume 23 (2007) p.1689-1691

Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.
Tarpey PS, Raymond FL, Nguyen LS, Rodriguez J, Hackett A, Vandeleur L, Smith R, Shoubridge C, Edkins S, Stevens C, O'Meara S, Tofts C, Barthorpe S, Buck G, Cole J, Halliday K, Hills K, Jones D, Mironenko T, Perry J, Varian J, West S, Widaa S, Teague J, Dicks E, Butler A, Menzies A, Richardson D, Jenkinson A, Shepherd R, Raine K, Moon J, Luo Y, Parnau J, Bhat SS, Gardner A, Corbett M, Brooks D, Thomas P, Parkinson-Lawrence E, Porteous ME, Warner JP, Sanderson T, Pearson P, Simensen RJ, Skinner C, Hoganson G, Superneau D, Wooster R, Bobrow M, Turner G, Stevenson RE, Schwartz CE, Futreal PA, Srivastava AK, Stratton MR, Gécz J.
Nature genetics Volume 39 (2007) p.1127-1133

Optimized design and assessment of whole genome tiling arrays.
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P.
Bioinformatics (Oxford, England) Volume 23 (2007) p.i195-204

Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006.
Orchard S, Heck A, Uhlen M, Ping P.
Proteomics Volume 7 (2007) p.1009-1011

Mutations in CUL4B, which encodes a ubiquitin E3 ligase subunit, cause an X-linked mental retardation syndrome associated with aggressive outbursts, seizures, relative macrocephaly, central obesity, hypogonadism, pes cavus, and tremor.
Tarpey PS, Raymond FL, O'Meara S, Edkins S, Teague J, Butler A, Dicks E, Stevens C, Tofts C, Avis T, Barthorpe S, Buck G, Cole J, Gray K, Halliday K, Harrison R, Hills K, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Varian J, West S, Widaa S, Mallya U, Moon J, Luo Y, Holder S, Smithson SF, Hurst JA, Clayton-Smith J, Kerr B, Boyle J, Shaw M, Vandeleur L, Rodriguez J, Slaugh R, Easton DF, Wooster R, Bobrow M, Srivastava AK, Stevenson RE, Schwartz CE, Turner G, Gecz J, Futreal PA, Stratton MR, Partington M.
American journal of human genetics Volume 80 (2007) p.345-352

Structural and chemical profiling of the human cytosolic sulfotransferases.
Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH.
PLoS biology Volume 5 (2007) p.e97

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA.
Bioinformatics (Oxford, England) Volume 23 (2007) p.1824-1827

PASSIM--an open source software system for managing information in biomedical studies.
Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U.
BMC bioinformatics Volume 8 (2007) p.52

VectorBase: a home for invertebrate vectors of human pathogens.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Emmert D, Hammond M, Hill CA, Kennedy RC, Lobo NF, MacCallum MR, Madey G, Megy K, Redmond S, Russo S, Severson DW, Stinson EO, Topalis P, Zdobnov EM, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.
Nucleic acids research Volume 35 (2007) p.D503-5

Classification and nomenclature of all human homeobox genes.
Holland PW, Booth HA, Bruford EA.
BMC biology Volume 5 (2007) p.47

Patterns of somatic mutation in human cancer genomes.
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Nature Volume 446 (2007) p.153-158

Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome biology Volume 8 (2007) p.R39

The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.
Proceedings of the National Academy of Sciences of the United States of America Volume 104 (2007) p.5495-5500

Mutations in the BRWD3 gene cause X-linked mental retardation associated with macrocephaly.
Field M, Tarpey PS, Smith R, Edkins S, O'Meara S, Stevens C, Tofts C, Teague J, Butler A, Dicks E, Barthorpe S, Buck G, Cole J, Gray K, Halliday K, Hills K, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Varian J, West S, Widaa S, Mallya U, Wooster R, Moon J, Luo Y, Hughes H, Shaw M, Friend KL, Corbett M, Turner G, Partington M, Mulley J, Bobrow M, Schwartz C, Stevenson R, Gecz J, Stratton MR, Futreal PA, Raymond FL.
American journal of human genetics Volume 81 (2007) p.367-374

Towards fully automated structure-based function prediction in structural genomics: a case study.
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM.
Journal of molecular biology Volume 367 (2007) p.1511-1522

Prediction of gene expression in embryonic structures of Drosophila melanogaster.
Samsonova AA, Niranjan M, Russell S, Brazma A.
PLoS computational biology Volume 3 (2007) p.e144

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.
Nature Volume 447 (2007) p.799-816

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM.
Bioinformatics (Oxford, England) Volume 23 (2007) p.e104-9

Construction, visualisation, and clustering of transcription networks from microarray expression data.
Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ.
PLoS computational biology Volume 3 (2007) p.2032-2042

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM.
PLoS computational biology Volume 3 (2007) p.1993-2002

Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome biology Volume 8 (2007) p.R126

Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A.
Genome biology Volume 8 (2007) p.R73

Correcting for sequence biases in present/absent calls.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome biology Volume 8 (2007) p.R125

Current approaches to gene regulatory network modelling.
Schlitt T, Brazma A.
BMC bioinformatics Volume 8 Suppl 6 (2007) p.S9

The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.
Orchard S, Jones AR, Stephan C, Binz PA.
Proteomics Volume 7 (2007) p.1006-1008

Cutaneous immune responses in the common carp detected using transcript analysis.
Gonzalez SF, Chatziandreou N, Nielsen ME, Li W, Rogers J, Taylor R, Santos Y, Cossins A.
Molecular immunology Volume 44 (2007) p.1664-1679

HCOP: a searchable database of human orthology predictions.
Eyre TA, Wright MW, Lush MJ, Bruford EA.
Briefings in bioinformatics Volume 8 (2007) p.2-5

Genome sequence of Aedes aegypti, a major arbovirus vector.
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW.
Science (New York, N.Y.) Volume 316 (2007) p.1718-1723

The Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 35 (2007) p.D193-7

Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol.
Vizcaíno JA, Redondo J, Suárez MB, Cardoza RE, Hermosa R, González FJ, Rey M, Monte E.
Applied microbiology and biotechnology Volume 75 (2007) p.853-862

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nature biotechnology Volume 25 (2007) p.1127-1133

Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach.
Suárez MB, Vizcaíno JA, Llobell A, Monte E.
Current genetics Volume 51 (2007) p.331-342

The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.
Journal of molecular biology Volume 372 (2007) p.1261-1277

The landscape of histone modifications across 1% of the human genome in five human cell lines.
Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I.
Genome research Volume 17 (2007) p.691-707

Partial silencing of a hydroxy-methylglutaryl-CoA reductase-encoding gene in Trichoderma harzianum CECT 2413 results in a lower level of resistance to lovastatin and lower antifungal activity.
Cardoza RE, Hermosa MR, Vizcaíno JA, González F, Llobell A, Monte E, Gutiérrez S.
Fungal genetics and biology : FG & B Volume 44 (2007) p.269-283

Evolution of enzymes and pathways for the biosynthesis of cofactors.
Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ.
Natural product reports Volume 24 (2007) p.972-987

Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
Journal of molecular biology Volume 368 (2007) p.283-301

Evolutionary conservation of regulated longevity assurance mechanisms.
McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas JH, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D.
Genome biology Volume 8 (2007) p.R132

Evolutionary and biomedical insights from the rhesus macaque genome.
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.
Science (New York, N.Y.) Volume 316 (2007) p.222-234

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Hamacher M, Stephan C, Eisenacher M, Lewczuk P, Wiltfang J, Martens L, Vizcaíno JA, Kwon KH, Yoo JS, Park YM, Beckers J, Horsch M, de Angelis MH, Cho ZH, Apweiler R, Meyer HE.
Proteomics Volume 7 (2007) p.2490-2496

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.
Genome research Volume 17 (2007) p.760-774

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T.
Genome research Volume 17 (2007) p.175-183

Ensembl 2007.
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.
Nucleic acids research Volume 35 (2007) p.D610-7

Renaming the DSCR1/Adapt78 gene family as RCAN: regulators of calcineurin.
Davies KJ, Ermak G, Rothermel BA, Pritchard M, Heitman J, Ahnn J, Henrique-Silva F, Crawford D, Canaider S, Strippoli P, Carinci P, Min KT, Fox DS, Cunningham KW, Bassel-Duby R, Olson EN, Zhang Z, Williams RS, Gerber HP, Pérez-Riba M, Seo H, Cao X, Klee CB, Redondo JM, Maltais LJ, Bruford EA, Povey S, Molkentin JD, McKeon FD, Duh EJ, Crabtree GR, Cyert MS, de la Luna S, Estivill X.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 21 (2007) p.3023-3028

Proteomics: from technology development to biomarker applications.
Orchard S.
Expert review of proteomics Volume 4 (2007) p.709-710

2006

Data standards: a call to action.
Brooksbank C, Quackenbush J.
Omics : a journal of integrative biology Volume 10 (2006) p.94-99

Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R.
Omics : a journal of integrative biology Volume 10 (2006) p.114-118

Evidence standards in experimental and inferential INSDC Third Party Annotation data.
Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M.
Omics : a journal of integrative biology Volume 10 (2006) p.105-113

SPINE bioinformatics and data-management aspects of high-throughput structural biology.
Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K.
Acta crystallographica. Section D, Biological crystallography Volume 62 (2006) p.1184-1195

EMBL Nucleotide Sequence Database: developments in 2005.
Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic acids research Volume 34 (2006) p.D10-5

Ensembl 2006.
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.
Nucleic acids research Volume 34 (2006) p.D556-61

Protein superfamily evolution and the last universal common ancestor (LUCA).
Ranea JA, Sillero A, Thornton JM, Orengo CA.
Journal of molecular evolution Volume 63 (2006) p.513-525

Databases and resources for in silico proteome analysis.
Pruess M, Kersey P, Kulikova T, Apweiler R.
Methods of biochemical analysis Volume 49 (2006) p.397-414

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nature cell biology Volume 8 (2006) p.1183-1189

HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA.
Orchard S, Ping P.
Proteomics Volume 6 (2006) p.4436-4438

MIAME/Plant - adding value to plant microarrray experiments.
Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee S, Wagner U, Hennig L.
Plant methods Volume 2 (2006) p.1

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM.
Journal of molecular biology Volume 356 (2006) p.928-944

A comparison of the phenotypic and genetic stability of recombinant Trichoderma spp. generated by protoplast- and Agrobacterium-mediated transformation.
Cardoza RE, Vizcaino JA, Hermosa MR, Monte E, Gutiérrez S.
Journal of microbiology (Seoul, Korea) Volume 44 (2006) p.383-395

Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene from T. harzianum CECT 2413.
Vizcaíno JA, Cardoza RE, Dubost L, Bodo B, Gutiérrez S, Monte E.
Folia microbiologica Volume 51 (2006) p.114-120

XRate: a fast prototyping, training and annotation tool for phylo-grammars.
Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.
BMC bioinformatics Volume 7 (2006) p.428

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R.
Expert review of proteomics Volume 3 (2006) p.1-3

A bioinformatician's view of the metabolome.
Nobeli I, Thornton JM.
BioEssays : news and reviews in molecular, cellular and developmental biology Volume 28 (2006) p.534-545

Cloning and characterization of the erg1 gene of Trichoderma harzianum: effect of the erg1 silencing on ergosterol biosynthesis and resistance to terbinafine.
Cardoza RE, Vizcaíno JA, Hermosa MR, Sousa S, González FJ, Llobell A, Monte E, Gutiérrez S.
Fungal genetics and biology : FG & B Volume 43 (2006) p.164-178

ThPTR2, a di/tri-peptide transporter gene from Trichoderma harzianum.
Vizcaíno JA, Cardoza RE, Hauser M, Hermosa R, Rey M, Llobell A, Becker JM, Gutiérrez S, Monte E.
Fungal genetics and biology : FG & B Volume 43 (2006) p.234-246

Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413.
Vizcaíno JA, González FJ, Suárez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutiérrez S, Monte E, Llobell A, Rey M.
BMC genomics Volume 7 (2006) p.193

The Universal Protein Resource (UniProt): an expanding universe of protein information.
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B.
Nucleic acids research Volume 34 (2006) p.D187-91

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N.
Nucleic acids research Volume 34 (2006) p.D327-31

Annotation of environmental OMICS data: application to the transcriptomics domain.
Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Rocca-Serra P, Stevens R, Snape J, Brass A, Field D.
Omics : a journal of integrative biology Volume 10 (2006) p.172-178

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Whamond GS, Thornton JM.
Journal of molecular biology Volume 359 (2006) p.238-247

Development of FuGO: an ontology for functional genomics investigations.
Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ Jr, Taylor C, White J, Wood A, FuGO Working Group.
Omics : a journal of integrative biology Volume 10 (2006) p.199-204

Concept of sample in OMICS technology.
Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D.
Omics : a journal of integrative biology Volume 10 (2006) p.127-137

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, Wiemann S, Hermjakob H.
Proteomics Volume 6 (2006) p.4439-4443

The MGED Ontology: a resource for semantics-based description of microarray experiments.
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.
Bioinformatics (Oxford, England) Volume 22 (2006) p.866-873

Cancer informatics in the U.K.: the NCRI informatics initiative.
Reddington F, Wilkinson JM, Clark R, Parkinson H, Kerr P, Begent R.
Cancer informatics Volume 2 (2006) p.389-394

Using ontologies to annotate microarray experiments.
Whetzel PL, Parkinson H, Stoeckert CJ Jr.
Methods in enzymology Volume 411 (2006) p.325-339

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.
Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM.
Genome biology Volume 7 (2006) p.R89

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
Flicek P, Brent MR.
Genome biology Volume 7 Suppl 1 (2006) p.S8.1-9

Introduction. Bioinformatics: from molecules to systems.
Jones DT, Sternberg MJ, Thornton JM.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 361 (2006) p.389-391

A method for localizing ligand binding pockets in protein structures.
Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.
Proteins Volume 62 (2006) p.479-488

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.
Omics : a journal of integrative biology Volume 10 (2006) p.205-208

PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R.
Nucleic acids research Volume 34 (2006) p.D659-63

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M.
Nucleic acids research Volume 34 (2006) p.D689-91

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Taylor CF, Hermjakob H, Julian RK Jr, Garavelli JS, Aebersold R, Apweiler R.
Omics : a journal of integrative biology Volume 10 (2006) p.145-151

UniSave: the UniProtKB sequence/annotation version database.
Leinonen R, Nardone F, Zhu W, Apweiler R.
Bioinformatics (Oxford, England) Volume 22 (2006) p.1284-1285

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.
BMC bioinformatics Volume 7 (2006) p.489

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.
Hermjakob H.
Proteomics Volume 6 Suppl 2 (2006) p.34-38

A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report.
Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M.
Molecular & cellular proteomics : MCP Volume 5 (2006) p.1996-2007

Structural genomics on membrane proteins: comparison of more than 100 GPCRs in 3 expression systems.
Lundstrom K, Wagner R, Reinhart C, Desmyter A, Cherouati N, Magnin T, Zeder-Lutz G, Courtot M, Prual C, André N, Hassaine G, Michel H, Cambillau C, Pattus F.
Journal of structural and functional genomics Volume 7 (2006) p.77-91

Dry work in a wet world: computation in systems biology.
Kahlem P, Birney E.
Molecular systems biology Volume 2 (2006) p.40

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
Côté RG, Jones P, Apweiler R, Hermjakob H.
BMC bioinformatics Volume 7 (2006) p.97

EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.
Genome biology Volume 7 Suppl 1 (2006) p.S2.1-31

Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.
Methods in enzymology Volume 411 (2006) p.370-386

Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U.
Nature reviews. Genetics Volume 7 (2006) p.593-605

Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.
Selman C, Kerrison ND, Cooray A, Piper MD, Lingard SJ, Barton RH, Schuster EF, Blanc E, Gems D, Nicholson JK, Thornton JM, Partridge L, Withers DJ.
Physiological genomics Volume 27 (2006) p.187-200

Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
Journal of molecular biology Volume 364 (2006) p.836-852

Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.
Zhang R, Skarina T, Evdokimova E, Edwards A, Savchenko A, Laskowski R, Cuff ME, Joachimiak A.
Acta crystallographica. Section F, Structural biology and crystallization communications Volume 62 (2006) p.335-339

Top-down standards will not serve systems biology.
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.
Nature Volume 440 (2006) p.24

Erratum to "Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans" [Mech. Ageing Dev. 127 (5) (2006) 458-472].
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D.
Mechanisms of ageing and development Volume 127 (2006) p.922-936

Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans.
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D.
Mechanisms of ageing and development Volume 127 (2006) p.458-472

TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, van der Weyden L, Bradley A, Birney E, Adams DJ.
Nature genetics Volume 38 (2006) p.853

A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy.
Hunter C, Smith R, Cahill DP, Stephens P, Stevens C, Teague J, Greenman C, Edkins S, Bignell G, Davies H, O'Meara S, Parker A, Avis T, Barthorpe S, Brackenbury L, Buck G, Butler A, Clements J, Cole J, Dicks E, Forbes S, Gorton M, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R, Raine K, Richardson D, Shepherd R, Small A, Solomon H, Tofts C, Varian J, West S, Widaa S, Yates A, Easton DF, Riggins G, Roy JE, Levine KK, Mueller W, Batchelor TT, Louis DN, Stratton MR, Futreal PA, Wooster R.
Cancer research Volume 66 (2006) p.3987-3991

Sequence analysis of the protein kinase gene family in human testicular germ-cell tumors of adolescents and adults.
Bignell G, Smith R, Hunter C, Stephens P, Davies H, Greenman C, Teague J, Butler A, Edkins S, Stevens C, O'Meara S, Parker A, Avis T, Barthorpe S, Brackenbury L, Buck G, Clements J, Cole J, Dicks E, Edwards K, Forbes S, Gorton M, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D, Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R, Raine K, Shepherd R, Small A, Solomon H, Stephens Y, Tofts C, Varian J, Webb A, West S, Widaa S, Yates A, Gillis AJ, Stoop HJ, van Gurp RJ, Oosterhuis JW, Looijenga LH, Futreal PA, Wooster R, Stratton MR.
Genes, chromosomes & cancer Volume 45 (2006) p.42-46

Integrating biological data through the genome.
Reeves GA, Thornton JM, BioSapiens Network of Excellence.
Human molecular genetics Volume 15 Spec No 1 (2006) p.R81-7

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.
Ikediobi ON, Davies H, Bignell G, Edkins S, Stevens C, O'Meara S, Santarius T, Avis T, Barthorpe S, Brackenbury L, Buck G, Butler A, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Hunter C, Jenkinson A, Jones D, Kosmidou V, Lugg R, Menzies A, Mironenko T, Parker A, Perry J, Raine K, Richardson D, Shepherd R, Small A, Smith R, Solomon H, Stephens P, Teague J, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Reinhold W, Weinstein JN, Stratton MR, Futreal PA, Wooster R.
Molecular cancer therapeutics Volume 5 (2006) p.2606-2612

Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation.
Tarpey PS, Stevens C, Teague J, Edkins S, O'Meara S, Avis T, Barthorpe S, Buck G, Butler A, Cole J, Dicks E, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, West S, Widaa S, Yates A, Catford R, Butler J, Mallya U, Moon J, Luo Y, Dorkins H, Thompson D, Easton DF, Wooster R, Bobrow M, Carpenter N, Simensen RJ, Schwartz CE, Stevenson RE, Turner G, Partington M, Gecz J, Stratton MR, Futreal PA, Raymond FL.
American journal of human genetics Volume 79 (2006) p.1119-1124

E-MSD: improving data deposition and structure quality.
Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S.
Nucleic acids research Volume 34 (2006) p.D287-90

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R.
Proteomics Volume 6 (2006) p.738-741

ArrayExpress service for reviewers/editors of DNA microarray papers.
Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.
Nature biotechnology Volume 24 (2006) p.1321-1322

Picking pyknons out of the human genome.
Meynert A, Birney E.
Cell Volume 125 (2006) p.836-838

Modelling in molecular biology: describing transcription regulatory networks at different scales.
Schlitt T, Brazma A.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 361 (2006) p.483-494

MGED standards: work in progress.
Ball CA, Brazma A.
Omics : a journal of integrative biology Volume 10 (2006) p.138-144

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
Hamacher M, Stephan C, Blüggel M, Chamrad D, Körting G, Martens L, Müller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R.
Proteomics Volume 6 (2006) p.1719-1721

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Blake J, Schwager C, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England) Volume 22 (2006) p.765-767

Wrestling with SUMO and bio-ontologies.
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.
Nature biotechnology Volume 24 (2006) p.21-2; author reply 23

2005

Species choice for comparative genomics: being greedy works.
Pardi F, Goldman N.
PLoS genetics Volume 1 (2005) p.e71

Different versions of the Dayhoff rate matrix.
Kosiol C, Goldman N.
Molecular biology and evolution Volume 22 (2005) p.193-199

PRIDE: the proteomics identifications database.
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R.
Proteomics Volume 5 (2005) p.3537-3545

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.
Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ.
Proteomics Volume 5 (2005) p.3246-3261

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K.
Proteomics Volume 5 (2005) p.3501-3505

Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.
Torrance JW, Bartlett GJ, Porter CT, Thornton JM.
Journal of molecular biology Volume 347 (2005) p.565-581

Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.
Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R.
Proteomics Volume 5 (2005) p.4651-4652

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R.
Proteomics Volume 5 (2005) p.3552-3555

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
Orchard S, Montecchi-Palazzi L, Hermjakob H, Apweiler R.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2005) p.186-196

The ArrayExpress gene expression database: a software engineering and implementation perspective.
Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.
Bioinformatics (Oxford, England) Volume 21 (2005) p.1495-1501

It's all GO for plant scientists.
Clark JI, Brooksbank C, Lomax J.
Plant physiology Volume 138 (2005) p.1268-1279

The European Bioinformatics Institute's data resources: towards systems biology.
Brooksbank C, Cameron G, Thornton J.
Nucleic acids research Volume 33 (2005) p.D46-53

Fusing microarray experiments with multivariate regression.
Gilks WR, Tom BD, Brazma A.
Bioinformatics (Oxford, England) Volume 21 Suppl 2 (2005) p.ii137-43

Reconstruction of gene regulatory networks under the finite state linear model.
Ruklisa D, Brazma A, Viksna J.
Genome informatics. International Conference on Genome Informatics Volume 16 (2005) p.225-236

Protein families and their evolution-a structural perspective.
Orengo CA, Thornton JM.
Annual review of biochemistry Volume 74 (2005) p.867-900

Progress of structural genomics initiatives: an analysis of solved target structures.
Todd AE, Marsden RL, Thornton JM, Orengo CA.
Journal of molecular biology Volume 348 (2005) p.1235-1260

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.
Orchard S, Hermjakob H, Binz PA, Hoogland C, Taylor CF, Zhu W, Julian RK Jr, Apweiler R.
Proteomics Volume 5 (2005) p.337-339

Microeconomic principles explain an optimal genome size in bacteria.
Ranea JA, Grant A, Thornton JM, Orengo CA.
Trends in genetics : TIG Volume 21 (2005) p.21-25

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
Torrente A, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England) Volume 21 (2005) p.3993-3999

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.
Nobeli I, Spriggs RV, George RA, Thornton JM.
Journal of molecular biology Volume 347 (2005) p.415-436

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W.
Bioinformatics (Oxford, England) Volume 21 (2005) p.3439-3440

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.
Plant physiology Volume 139 (2005) p.632-636

Binding Pocket Shape Analysis for Protein Function Prediction
Morris RJ, Kahraman A, Thornton JM.
Acta crystallographica Volume D61 (2005) p.C156-C157

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM.
Proteomics Volume 5 (2005) p.3226-3245

Modelling gene networks at different organisational levels.
Schlitt T, Brazma A.
FEBS letters Volume 579 (2005) p.1859-1866

Annotating the human proteome.
Orchard S, Hermjakob H, Apweiler R.
Molecular & cellular proteomics : MCP Volume 4 (2005) p.435-440

Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N.
Genetics Volume 169 (2005) p.1753-1762

Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.
Pellegrini-Calace M, Thornton JM.
Nucleic acids research Volume 33 (2005) p.2129-2140

Predicting protein function from sequence and structural data.
Watson JD, Laskowski RA, Thornton JM.
Current opinion in structural biology Volume 15 (2005) p.275-284

Conformational changes observed in enzyme crystal structures upon substrate binding.
Gutteridge A, Thornton J.
Journal of molecular biology Volume 346 (2005) p.21-28

Global analysis of uniparental disomy using high density genotyping arrays.
Bruce S, Leinonen R, Lindgren CM, Kivinen K, Dahlman-Wright K, Lipsanen-Nyman M, Hannula-Jouppi K, Kere J.
Journal of medical genetics Volume 42 (2005) p.847-851

Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004.
Birney E, Ciliberto A, Colding-Jørgensen M, Goldbeter A, Hohmann S, Kuiper M, Lehrach H, Miczka G, Mosekilde E, Westerhoff H, Wolkenhauer O.
Systems biology Volume 152 (2005) p.55-60

Protein function prediction using local 3D templates.
Laskowski RA, Watson JD, Thornton JM.
Journal of molecular biology Volume 351 (2005) p.614-626

The complement of enzymatic sets in different species.
Freilich S, Spriggs RV, George RA, Al-Lazikani B, Swindells M, Thornton JM.
Journal of molecular biology Volume 349 (2005) p.745-763

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C.
Nucleic acids research Volume 33 (2005) p.D247-51

Understanding nature's catalytic toolkit.
Gutteridge A, Thornton JM.
Trends in biochemical sciences Volume 30 (2005) p.622-629

ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM.
Nucleic acids research Volume 33 (2005) p.W89-93

Automated generation of heuristics for biological sequence comparison.
Slater GS, Birney E.
BMC bioinformatics Volume 6 (2005) p.31

Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression.
Giannattasio S, Liu Z, Thornton J, Butow RA.
The Journal of biological chemistry Volume 280 (2005) p.42528-42535

Second proteomics standards initiative spring workshop.
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R.
Expert review of proteomics Volume 2 (2005) p.287-289

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Laskowski RA, Chistyakov VV, Thornton JM.
Nucleic acids research Volume 33 (2005) p.D266-8

MACiE: a database of enzyme reaction mechanisms.
Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB.
Bioinformatics (Oxford, England) Volume 21 (2005) p.4315-4316

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, Croning MD, Boardman PE, Bonfield JK, Burnside J, Davies RM, Farrell ER, Francis MD, Griffiths-Jones S, Humphray SJ, Hyland C, Scott CE, Tang H, Taylor RG, Tickle C, Brown WR, Birney E, Rogers J, Wilson SA.
Genome research Volume 15 (2005) p.174-183

Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1.
Ryan AW, Thornton JM, Brophy K, Daly JS, McLoughlin RM, O'Morain C, Abuzakouk M, Kennedy NP, Stevens FM, Feighery C, Kelleher D, McManus R.
Tissue antigens Volume 65 (2005) p.150-155

InterProScan: protein domains identifier.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R.
Nucleic acids research Volume 33 (2005) p.W116-20

Effective function annotation through catalytic residue conservation.
George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB.
Proceedings of the National Academy of Sciences of the United States of America Volume 102 (2005) p.12299-12304

Dasty and UniProt DAS: a perfect pair for protein feature visualization.
Jones P, Vinod N, Down T, Hackmann A, Kahari A, Kretschmann E, Quinn A, Wieser D, Hermjakob H, Apweiler R.
Bioinformatics (Oxford, England) Volume 21 (2005) p.3198-3199

SOAP-based services provided by the European Bioinformatics Institute.
Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R.
Nucleic acids research Volume 33 (2005) p.W25-8

Reactome: a knowledgebase of biological pathways.
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L.
Nucleic acids research Volume 33 (2005) p.D428-32

InterPro, progress and status in 2005.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH.
Nucleic acids research Volume 33 (2005) p.D201-5

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM.
Bioinformatics (Oxford, England) Volume 21 (2005) p.2347-2355

Gene finding in the chicken genome.
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR.
BMC bioinformatics Volume 6 (2005) p.131

Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
Shanahan HP, Thornton JM.
Biopolymers Volume 78 (2005) p.318-328

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
Ferrer-Costa C, Shanahan HP, Jones S, Thornton JM.
Bioinformatics (Oxford, England) Volume 21 (2005) p.3679-3680

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates.
Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E.
Genome biology Volume 6 (2005) p.R104

Prediction of protein function from structure: insights from methods for the detection of local structural similarities.
Najmanovich RJ, Torrance JW, Thornton JM.
BioTechniques Volume 38 (2005) p.847, 849, 851

A survey of homozygous deletions in human cancer genomes.
Cox C, Bignell G, Greenman C, Stabenau A, Warren W, Stephens P, Davies H, Watt S, Teague J, Edkins S, Birney E, Easton DF, Wooster R, Futreal PA, Stratton MR.
Proceedings of the National Academy of Sciences of the United States of America Volume 102 (2005) p.4542-4547

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R.
BMC bioinformatics Volume 6 Suppl 1 (2005) p.S17

Ensembl 2005.
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E.
Nucleic acids research Volume 33 (2005) p.D447-53

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G.
Nucleic acids research Volume 33 (2005) p.D141-6

The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic acids research Volume 33 (2005) p.D154-9

A novel degron-mediated degradation of the RTG pathway regulator, Mks1p, by SCFGrr1.
Liu Z, Spírek M, Thornton J, Butow RA.
Molecular biology of the cell Volume 16 (2005) p.4893-4904

The EMBL Nucleotide Sequence Database.
Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, Bates K, Browne P, van den Broek A, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Gamble J, Diez FG, Harte N, Kulikova T, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Sobhany S, Stoehr P, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic acids research Volume 33 (2005) p.D29-33

NCRI informatics initiative.
Begent RH, Kerr P, Parkinson H, Reddington F, Wilkinson JM.
Nature biotechnology Volume 23 (2005) p.1212

ArrayExpress--a public repository for microarray gene expression data at the EBI.
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.
Nucleic acids research Volume 33 (2005) p.D553-5

Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM.
Genome biology Volume 6 (2005) p.R56

An algorithm for progressive multiple alignment of sequences with insertions.
Löytynoja A, Goldman N.
Proceedings of the National Academy of Sciences of the United States of America Volume 102 (2005) p.10557-10562

The Integr8 project--a resource for genomic and proteomic data.
Pruess M, Kersey P, Apweiler R.
In silico biology Volume 5 (2005) p.179-185

Prediction of Protein Function from Structure: Insights from Methods for the Detection of Local Structural Similarities
Najmanovich RF, Torrance JW, Thornton JM.
BioTechniques Volume 38 (2005) p.847-851

E-MSD: an integrated data resource for bioinformatics.
Velankar S, McNeil P, Mittard-Runte V, Suarez A, Barrell D, Apweiler R, Henrick K.
Nucleic acids research Volume 33 (2005) p.D262-5

Morphological aspects of oligomeric protein structures.
Ponstingl H, Kabir T, Gorse D, Thornton JM.
Progress in biophysics and molecular biology Volume 89 (2005) p.9-35

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.
Nucleic acids research Volume 33 (2005) p.D297-302

2004

An open letter on microarray data from the MGED Society.
Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, Microarray Gene Expression Data (MGED) Society.
Microbiology (Reading, England) Volume 150 (2004) p.3522-3524

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
International Chicken Genome Sequencing Consortium.
Nature Volume 432 (2004) p.695-716

A common open representation of mass spectrometry data and its application to proteomics research.
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.
Nature biotechnology Volume 22 (2004) p.1459-1466

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.
Dermitzakis ET, Kirkness E, Schwarz S, Birney E, Reymond A, Antonarakis SE.
Genome research Volume 14 (2004) p.852-859

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.
Nature biotechnology Volume 22 (2004) p.177-183

EnsMart: a generic system for fast and flexible access to biological data.
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E.
Genome research Volume 14 (2004) p.160-169

Standards for microarray data: an open letter.
Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, MGED Society.
Environmental health perspectives Volume 112 (2004) p.A666-7

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
PLoS biology Volume 2 (2004) p.e162

Protein sequence database methods.
Martin MJ, O'Donovan C, Apweiler R.
Genetic engineering Volume 26 (2004) p.13-17

Common interchange standards for proteomics data: Public availability of tools and schema.
Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R.
Proteomics Volume 4 (2004) p.490-491

Funding high-throughput data sharing.
Ball CA, Sherlock G, Brazma A.
Nature biotechnology Volume 22 (2004) p.1179-1183

The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R.
Proteomics Volume 4 (2004) p.1985-1988

Proteomics and data standardisation
Orchard S, Hermjakob H, Apweiler R.
Drug discovery today. Biosilico Volume 2 (2004) p.91-93

Public web-based services from the European Bioinformatics Institute.
Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R, European Bioinformatics Institute.
Nucleic acids research Volume 32 (2004) p.W3-9

The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data.
Parkinson H, Aitken S, Baldock RA, Bard JB, Burger A, Hayamizu TF, Rector A, Ringwald M, Rogers J, Rosse C, Stoeckert CJ Jr, Davidson D.
Comparative and functional genomics Volume 5 (2004) p.521-527

X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.
Savchenko A, Skarina T, Evdokimova E, Watson JD, Laskowski R, Arrowsmith CH, Edwards AM, Joachimiak A, Zhang RG.
Proteins Volume 54 (2004) p.162-165

The Ensembl core software libraries.
Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E.
Genome research Volume 14 (2004) p.929-933

IntAct: an open source molecular interaction database.
Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R.
Nucleic acids research Volume 32 (2004) p.D452-5

GeneWise and Genomewise.
Birney E, Clamp M, Durbin R.
Genome research Volume 14 (2004) p.988-995

Unconventional interactions between water and heterocyclic nitrogens in protein structures.
Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M, Luisi BF.
Proteins Volume 57 (2004) p.1-8

Sockeye: a 3D environment for comparative genomics.
Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ.
Genome research Volume 14 (2004) p.956-962

Genome information resources - developments at Ensembl.
Hammond MP, Birney E.
Trends in genetics : TIG Volume 20 (2004) p.268-272

A SNP map of the rat genome generated from cDNA sequences.
Zimdahl H, Nyakatura G, Brandt P, Schulz H, Hummel O, Fartmann B, Brett D, Droege M, Monti J, Lee YA, Sun Y, Zhao S, Winter EE, Ponting CP, Chen Y, Kasprzyk A, Birney E, Ganten D, Hubner N.
Science (New York, N.Y.) Volume 303 (2004) p.807

The Anopheles gambiae genome: an update.
Mongin E, Louis C, Holt RA, Birney E, Collins FH.
Trends in parasitology Volume 20 (2004) p.49-52

Biological database design and implementation.
Birney E, Clamp M.
Briefings in bioinformatics Volume 5 (2004) p.31-38

UniProt archive.
Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R.
Bioinformatics (Oxford, England) Volume 20 (2004) p.3236-3237

The EMBL Nucleotide Sequence Database.
Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, van den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic acids research Volume 32 (2004) p.D27-30

Standards and ontologies for functional genomics 2.
Harris MA, Parkinson H.
Comparative and functional genomics Volume 5 (2004) p.618-622

Expression Profiler: next generation--an online platform for analysis of microarray data.
Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.
Nucleic acids research Volume 32 (2004) p.W465-70

Periodic gene expression program of the fission yeast cell cycle.
Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bähler J.
Nature genetics Volume 36 (2004) p.809-817

E-MSD: an integrated data resource for bioinformatics.
Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K.
Nucleic acids research Volume 32 (2004) p.D211-6

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium.
Nature Volume 428 (2004) p.493-521

An overview of Ensembl.
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M.
Genome research Volume 14 (2004) p.925-928

Submission of microarray data to public repositories.
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N.
PLoS biology Volume 2 (2004) p.E317

Ensembl 2004.
Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T.
Nucleic acids research Volume 32 (2004) p.D468-70

ISMB/ECCB 2004

Bioinformatics (Oxford, England) Volume 20 (2004) p.i1-i2

Advances in the development of common interchange standards for proteomic data.
Orchard S, Taylor CF, Hermjakob H, Weimin-Zhu, Julian RK Jr, Apweiler R.
Proteomics Volume 4 (2004) p.2363-2365

Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
Shanahan HP, Garcia MA, Jones S, Thornton JM.
Nucleic acids research Volume 32 (2004) p.4732-4741

A new criterion and method for amino acid classification.
Kosiol C, Goldman N, Buttimore NH.
Journal of theoretical biology Volume 228 (2004) p.97-106

Estimating the frequency of events that cause multiple-nucleotide changes.
Whelan S, Goldman N.
Genetics Volume 167 (2004) p.2027-2043

Ligand selectivity and competition between enzymes in silico.
Macchiarulo A, Nobeli I, Thornton JM.
Nature biotechnology Volume 22 (2004) p.1039-1045

SCOPEC: a database of protein catalytic domains.
George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB.
Bioinformatics (Oxford, England) Volume 20 Suppl 1 (2004) p.i130-6

Conformational change in substrate binding, catalysis and product release: an open and shut case?
Gutteridge A, Thornton J.
FEBS letters Volume 567 (2004) p.67-73

Haplotype variation at the IBD5/SLC22A4 locus (5q31) in coeliac disease in the Irish population.
Ryan AW, Thornton JM, Brophy K, Daly JS, O'Morain C, McLoughlin RM, Kennedy NP, Abuzakouk M, Stevens FM, Feighery C, Kelleher D, McManus R.
Tissue antigens Volume 64 (2004) p.195-198

UniProt: the Universal Protein knowledgebase.
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic acids research Volume 32 (2004) p.D115-9

Software Engineering Challenges in Bioinformatics
Barker J, Thornton JM.
ICSE Volume (2004) p.12-16

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.
Wong WS, Yang Z, Goldman N, Nielsen R.
Genetics Volume 168 (2004) p.1041-1051

Conformational Change in Substrate Binding, Catalysis and Product Release: An Open and Shut Case?
Gutteridge A, Thornton JM.
FEBS letters Volume 567 (2004) p.67-73

The European dimension for the mouse genome mutagenesis program.
Auwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M, Berns A, Bradley A, Brown S, Carmeliet P, Chambon P, Cox R, Davidson D, Davies K, Duboule D, Forejt J, Granucci F, Hastie N, de Angelis MH, Jackson I, Kioussis D, Kollias G, Lathrop M, Lendahl U, Malumbres M, von Melchner H, Müller W, Partanen J, Ricciardi-Castagnoli P, Rigby P, Rosen B, Rosenthal N, Skarnes B, Stewart AF, Thornton J, Tocchini-Valentini G, Wagner E, Wahli W, Wurst W.
Nature genetics Volume 36 (2004) p.925-927

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.
Nucleic acids research Volume 32 (2004) p.D262-6

Phylogenomics and bioinformatics of SARS-CoV.
Liò P, Goldman N.
Trends in microbiology Volume 12 (2004) p.106-111

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
Porter CT, Bartlett GJ, Thornton JM.
Nucleic acids research Volume 32 (2004) p.D129-33

An examination of the conservation of surface patch polarity for proteins.
Shanahan HP, Thornton JM.
Bioinformatics (Oxford, England) Volume 20 (2004) p.2197-2204

The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'.
Binz PA, Hermjakob H, van der Vet P.
Comparative and functional genomics Volume 5 (2004) p.148-155

Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
Eyre TA, Partridge L, Thornton JM.
Protein engineering, design & selection : PEDS Volume 17 (2004) p.613-624

Searching for functional sites in protein structures.
Jones S, Thornton JM.
Current opinion in chemical biology Volume 8 (2004) p.3-7

Evolution of protein superfamilies and bacterial genome size.
Ranea JA, Buchan DW, Thornton JM, Orengo CA.
Journal of molecular biology Volume 336 (2004) p.871-887

Current status of proteomic standards development.
Orchard S, Taylor C, Hermjakob H, Zhu W, Julian R, Apweiler R.
Expert review of proteomics Volume 1 (2004) p.179-183

A practical and robust sequence search strategy for structural genomics target selection.
Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA.
Bioinformatics (Oxford, England) Volume 20 (2004) p.2288-2295

Toward the detection and validation of repeats in protein structure.
Murray KB, Taylor WR, Thornton JM.
Proteins Volume 57 (2004) p.365-380

2003

From gene networks to gene function.
Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A.
Genome research Volume 13 (2003) p.2568-2576

Ensembl: a genome infrastructure.
Birney E, Ensembl Team.
Cold Spring Harbor symposia on quantitative biology Volume 68 (2003) p.213-215

[Standardization of microarray experiment data].
Brazma A, Ikeo K, Tateno Y.
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme Volume 48 (2003) p.280-285

The EMBL sequence version archive.
Leinonen R, Nardone F, Oyewole O, Redaschi N, Stoehr P.
Bioinformatics (Oxford, England) Volume 19 (2003) p.1861-1862

Structural characterisation and functional significance of transient protein-protein interactions.
Nooren IM, Thornton JM.
Journal of molecular biology Volume 325 (2003) p.991-1018

The EMBL Nucleotide Sequence Database: major new developments.
Stoesser G, Baker W, van den Broek A, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, Nardone F, Stoehr P, Tuli MA, Tzouvara K, Vaughan R.
Nucleic acids research Volume 31 (2003) p.17-22

The CATH domain structure database.
Orengo CA, Pearl FM, Thornton JM.
Methods of biochemical analysis Volume 44 (2003) p.249-271

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Barker JA, Thornton JM.
Bioinformatics (Oxford, England) Volume 19 (2003) p.1644-1649

Molecular basis of inherited diseases: a structural perspective.
Steward RE, MacArthur MW, Laskowski RA, Thornton JM.
Trends in genetics : TIG Volume 19 (2003) p.505-513

The InterPro Database, 2003 brings increased coverage and new features.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM.
Nucleic acids research Volume 31 (2003) p.315-318

Sequences and topology.
Gerstein M, Thornton JM.
Current opinion in structural biology Volume 13 (2003) p.341-343

Mouse proteome analysis.
Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schönbach C, Teasdale RD, Yuan Z, RIKEN GER Group, GSL Members.
Genome research Volume 13 (2003) p.1335-1344

Proteomics: The Protein Complement of the Genome
Ponstingl H, Thornton JM.
The biochemist Volume 25 (2003) p.7-9

Gene3D: structural assignments for the biologist and bioinformaticist alike.
Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA.
Nucleic acids research Volume 31 (2003) p.469-473

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Nucleic acids research Volume 31 (2003) p.414-417

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D.
Genome research Volume 13 (2003) p.13-26

ArrayExpress: a public database of gene expression data at EBI.
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.
Comptes rendus biologies Volume 326 (2003) p.1075-1078

Global transcriptional responses of fission yeast to environmental stress.
Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J.
Molecular biology of the cell Volume 14 (2003) p.214-229

The Proteome and the Metabolome
Thornton JM, Nobeli I.
Biopolymers Volume 71 (2003) p.281

Automated annotation of microbial proteomes in SWISS-PROT.
Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A.
Computational biology and chemistry Volume 27 (2003) p.49-58

Comparing bacterial genomes through conservation profiles.
Martin MJ, Herrero J, Mateos A, Dopazo J.
Genome research Volume 13 (2003) p.991-998

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.
Genome research Volume 13 (2003) p.662-672

Discovering novel cis-regulatory motifs using functional networks.
Ettwiller LM, Rung J, Birney E.
Genome research Volume 13 (2003) p.883-895

Comparative genomics: genome-wide analysis in metazoan eukaryotes.
Ureta-Vidal A, Ettwiller L, Birney E.
Nature reviews. Genetics Volume 4 (2003) p.251-262

A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks.
Shepherd AJ, Gorse D, Thornton JM.
Proteins Volume 50 (2003) p.290-302

MCB-mediated regulation of cell cycle-specific cdc22+ transcription in fission yeast.
Maqbool Z, Kersey PJ, Fantes PA, McInerny CJ.
Molecular genetics and genomics : MGG Volume 269 (2003) p.765-775

Catalysing new reactions during evolution: economy of residues and mechanism.
Bartlett GJ, Borkakoti N, Thornton JM.
Journal of molecular biology Volume 331 (2003) p.829-860

From protein structure to biochemical function?
Laskowski RA, Watson JD, Thornton JM.
Journal of structural and functional genomics Volume 4 (2003) p.167-177

Managing core resources for genomics and proteomics.
Apweiler R, Martin MJ, O'Donovan C, Pruess M.
Pharmacogenomics Volume 4 (2003) p.343-350

Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Gutteridge A, Bartlett GJ, Thornton JM.
Journal of molecular biology Volume 330 (2003) p.719-734

A structure-based anatomy of the E.coli metabolome.
Nobeli I, Ponstingl H, Krissinel EB, Thornton JM.
Journal of molecular biology Volume 334 (2003) p.697-719

Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor.
Wu RY, Zhang RG, Zagnitko O, Dementieva I, Maltzev N, Watson JD, Laskowski R, Gornicki P, Joachimiak A.
The Journal of biological chemistry Volume 278 (2003) p.20240-20244

Recognizing the fold of a protein structure.
Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C.
Bioinformatics (Oxford, England) Volume 19 (2003) p.1748-1759

Target selection and determination of function in structural genomics.
Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM.
IUBMB life Volume 55 (2003) p.249-255

The Genome Knowledgebase: a resource for biologists and bioinformaticists.
Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D'Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L.
Cold Spring Harbor symposia on quantitative biology Volume 68 (2003) p.237-243

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.
Boutselakis H, Dimitropoulos D, Fillon J, Golovin A, Henrick K, Hussain A, Ionides J, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Oldfield T, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan J, Tagari M, Tate J, Tromm S, Velankar S, Vranken W.
Nucleic acids research Volume 31 (2003) p.458-462

Diversity of protein-protein interactions.
Nooren IM, Thornton JM.
The EMBO journal Volume 22 (2003) p.3486-3492

Using structural motif templates to identify proteins with DNA binding function.
Jones S, Barker JA, Nobeli I, Thornton JM.
Nucleic acids research Volume 31 (2003) p.2811-2823

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M.
Nucleic acids research Volume 31 (2003) p.365-370

Analysis of metabolic networks using a pathway distance metric through linear programming.
Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG.
Metabolic engineering Volume 5 (2003) p.211-219

The CATH database: an extended protein family resource for structural and functional genomics.
Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA.
Nucleic acids research Volume 31 (2003) p.452-455

Estimation of weights and validation: a marginal likelihood approach.
Lebedev AA, Tickle IJ, Laskowski RA, Moss DS.
Acta crystallographica. Section D, Biological crystallography Volume 59 (2003) p.1557-1566

Ensembl 2002: accommodating comparative genomics.
Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E.
Nucleic acids research Volume 31 (2003) p.38-42

Public services from the European Bioinformatics Institute.
Lopez R, Duggan K, Harte N, Kibria A.
Briefings in bioinformatics Volume 4 (2003) p.332-340

[Initial analysis of complete genome sequences of SARS coronavirus].
Chen YJ, Gao G, Bao YM, Lopez R, Wu JM, Cai T, Ye ZQ, Gu XC, Luo JC.
Yi chuan xue bao = Acta genetica Sinica Volume 30 (2003) p.493-500

WU-Blast2 server at the European Bioinformatics Institute.
Lopez R, Silventoinen V, Robinson S, Kibria A, Gish W.
Nucleic acids research Volume 31 (2003) p.3795-3798

The European Bioinformatics Institute web site: a new view.
Lopez R, Robinson S, Kibria A, Harte N, Patel G, Harper R, Quevillon E, Silventoinen V, Kallio K, Jokinen P.
Bioinformatics (Oxford, England) Volume 19 (2003) p.546-547

A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
Dawe JH, Porter CT, Thornton JM, Tabor AB.
Proteins Volume 52 (2003) p.427-435

Towards reconstruction of gene networks from expression data by supervised learning.
Soinov LA, Krestyaninova MA, Brazma A.
Genome biology Volume 4 (2003) p.R6

Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.
Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM.
The Journal of biological chemistry Volume 278 (2003) p.26039-26045

Protein-DNA interactions: the story so far and a new method for prediction.
Jones S, Thornton JM.
Comparative and functional genomics Volume 4 (2003) p.428-431

Unrestricted free access works and must continue.
Salzberg S, Birney E, Eddy S, White O.
Nature Volume 422 (2003) p.801

Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases.
Zhang RG, Duke N, Laskowski R, Evdokimova E, Skarina T, Edwards A, Joachimiak A, Savchenko A.
Proteins Volume 51 (2003) p.311-314

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
Jones S, Shanahan HP, Berman HM, Thornton JM.
Nucleic acids research Volume 31 (2003) p.7189-7198

ArrayExpress--a public repository for microarray gene expression data at the EBI.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.
Nucleic acids research Volume 31 (2003) p.68-71

Multiple sequence alignment with the Clustal series of programs.
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD.
Nucleic acids research Volume 31 (2003) p.3497-3500

Inferring protein function from structure.
Bartlett GJ, Todd AE, Thornton JM.
Methods of biochemical analysis Volume 44 (2003) p.387-407

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R.
Comparative and functional genomics Volume 4 (2003) p.203-206

Pandit: a database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Goldman N.
Bioinformatics (Oxford, England) Volume 19 (2003) p.1556-1563

Integr8: enhanced inter-operability of European molecular biology databases.
Kersey PJ, Morris L, Hermjakob H, Apweiler R.
Methods of information in medicine Volume 42 (2003) p.154-160

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Orchard S, Kersey P, Hermjakob H, Apweiler R.
Comparative and functional genomics Volume 4 (2003) p.16-19

The proteomics standards initiative.
Orchard S, Hermjakob H, Apweiler R.
Proteomics Volume 3 (2003) p.1374-1376

The MGED ontology: a framework for describing functional genomics experiments.
Stoeckert CJ Jr, Parkinson H.
Comparative and functional genomics Volume 4 (2003) p.127-132

The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro.
Camon E, Barrell D, Brooksbank C, Magrane M, Apweiler R.
Comparative and functional genomics Volume 4 (2003) p.71-74

Further advances in the development of a data interchange standard for proteomics data.
Orchard S, Zhu W, Julian RK Jr, Hermjakob H, Apweiler R.
Proteomics Volume 3 (2003) p.2065-2066

Protein evolution with dependence among codons due to tertiary structure.
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL.
Molecular biology and evolution Volume 20 (2003) p.1692-1704

Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine.
Harris MA, Parkinson H.
Comparative and functional genomics Volume 4 (2003) p.116-120

The European Bioinformatics Institute's data resources.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.
Nucleic acids research Volume 31 (2003) p.43-50

2002

The EMBL Nucleotide Sequence Database.
Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Redaschi N, Stoehr P, Tuli MA, Tzouvara K, Vaughan R.
Nucleic acids research Volume 30 (2002) p.21-26

Microarray data representation, annotation and storage.
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K.
Advances in biochemical engineering/biotechnology Volume 77 (2002) p.113-139

The Ensembl genome database project.
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M.
Nucleic acids research Volume 30 (2002) p.38-41

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P.
Science (New York, N.Y.) Volume 298 (2002) p.149-159

Bioinformatics and protein design.
Laskowski RA, Chan AW.
Current pharmaceutical biotechnology Volume 3 (2002) p.317-327

Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
Zhang RG, Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Edwards A, Joachimiak A, Savchenko A.
The Journal of biological chemistry Volume 277 (2002) p.19183-19190

Correlating gene promoters and expression in gene disruption experiments.
Palin K, Ukkonen E, Brazma A, Vilo J.
Bioinformatics (Oxford, England) Volume 18 Suppl 2 (2002) p.S172-80

The EBI SRS server--recent developments.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics (Oxford, England) Volume 18 (2002) p.368-373

The genome sequence of the malaria mosquito Anopheles gambiae.
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL.
Science (New York, N.Y.) Volume 298 (2002) p.129-149

Organisation and standardisation of information in SWISS-PROT and TrEMBL.
Magrane M, Apweiler R.
Data Science Journal Volume 1 (2002) p.13-18

Metastasis: Bad company
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.153-153

Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein.
Martin AC, Facchiano AM, Cuff AL, Hernandez-Boussard T, Olivier M, Hainaut P, Thornton JM.
Human mutation Volume 19 (2002) p.149-164

Apollo: a sequence annotation editor.
Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME.
Genome biology Volume 3 (2002) p.RESEARCH0082

TEMBLOR - Perspectives of EBI Database Services.
Hermjakob H, Apweiler R.
Comparative and functional genomics Volume 3 (2002) p.47-50

The CATH protein family database: a resource for structural and functional annotation of genomes.
Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM.
Proteomics Volume 2 (2002) p.11-21

The underlying principles of scientific publication.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data.
Bioinformatics (Oxford, England) Volume 18 (2002) p.1409

RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast prion [URE3].
Sekito T, Liu Z, Thornton J, Butow RA.
Molecular biology of the cell Volume 13 (2002) p.795-804

Web Watch: Microarray mania
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.405-405

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.
Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC.
Molecular cell Volume 9 (2002) p.1133-1143

The Bioperl toolkit: Perl modules for the life sciences.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E.
Genome research Volume 12 (2002) p.1611-1618

Toward predicting protein topology: an approach to identifying beta hairpins.
de la Cruz X, Hutchinson EG, Shepherd A, Thornton JM.
Proceedings of the National Academy of Sciences of the United States of America Volume 99 (2002) p.11157-11162

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.
Rison SC, Teichmann SA, Thornton JM.
Journal of molecular biology Volume 318 (2002) p.911-932

P53 regulation: Hitting the G spot
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.405-405

Tumour–stroma interactions:: The causes of crime
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.404-404

A physical map of the mouse genome.
Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR.
Nature Volume 418 (2002) p.743-750

Oncogenes: Dancing the two-step
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.156-156

Web Watch: Realistic goals
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.326-326

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA.
Genome research Volume 12 (2002) p.503-514

InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium.
Briefings in bioinformatics Volume 3 (2002) p.225-235

Databases and tools for browsing genomes.
Birney E, Clamp M, Hubbard T.
Annual review of genomics and human genetics Volume 3 (2002) p.293-310

The CCPN project: an interim report on a data model for the NMR community.
Fogh R, Ionides J, Ulrich E, Boucher W, Vranken W, Linge JP, Habeck M, Rieping W, Bhat TN, Westbrook J, Henrick K, Gilliland G, Berman H, Thornton J, Nilges M, Markley J, Laue E.
Nature structural biology Volume 9 (2002) p.416-418

The EBI SRS server-new features.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics (Oxford, England) Volume 18 (2002) p.1149-1150

Learning about gene regulatory networks from gene deletion experiments.
Schlitt T, Brazma A.
Comparative and functional genomics Volume 3 (2002) p.499-503

A novel use of equilibrium frequencies in models of sequence evolution.
Goldman N, Whelan S.
Molecular biology and evolution Volume 19 (2002) p.1821-1831

Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.
Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Joachimiak A, Edwards A, Savchenko A.
Proteins Volume 48 (2002) p.427-430

Kinases as targets: prospects for chronic therapy.
Orchard S.
Current opinion in drug discovery & development Volume 5 (2002) p.713-717

The Pfam protein families database.
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL.
Nucleic acids research Volume 30 (2002) p.276-280

Genome annotation techniques: new approaches and challenges.
Rust AG, Mongin E, Birney E.
Drug discovery today Volume 7 (2002) p.S70-6

Quantifying the similarities within fold space.
Harrison A, Pearl F, Mott R, Thornton J, Orengo C.
Journal of molecular biology Volume 323 (2002) p.909-926

Analysis of catalytic residues in enzyme active sites.
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM.
Journal of molecular biology Volume 324 (2002) p.105-121

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R.
Briefings in bioinformatics Volume 3 (2002) p.275-284

Applications of InterPro in protein annotation and genome analysis.
Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Briefings in bioinformatics Volume 3 (2002) p.285-295

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.
Lombard V, Camon EB, Parkinson HE, Hingamp P, Stoesser G, Redaschi N.
Bioinformatics (Oxford, England) Volume 18 (2002) p.763-764

Sequence and structural differences between enzyme and nonenzyme homologs.
Todd AE, Orengo CA, Thornton JM.
Structure (London, England : 1993) Volume 10 (2002) p.1435-1451

Automatic Interence of Protein Quatenary Structure from Crystals
Ponstingl H, Kabir T, Thornton JM.
Journal of applied crystallography Volume 36 (2002) p.1116-1122

Web Watch: Buried treasure
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.154-154

Standards for microarray data.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data (MGED) Society.
Science (New York, N.Y.) Volume 298 (2002) p.539

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
Nagano N, Orengo CA, Thornton JM.
Journal of molecular biology Volume 321 (2002) p.741-765

Drifting downstream.
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.79

Molecular basis of amplification in Drosophila phototransduction: roles for G protein, phospholipase C, and diacylglycerol kinase.
Hardie RC, Martin F, Cochrane GW, Juusola M, Georgiev P, Raghu P.
Neuron Volume 36 (2002) p.689-701

Top scorer.
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.81

One size fits all.
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.78-79

RAS, the magician.
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.249

Plasticity of enzyme active sites.
Todd AE, Orengo CA, Thornton JM.
Trends in biochemical sciences Volume 27 (2002) p.419-426

Unable to resist.
Brooksbank C.
Nature reviews. Cancer Volume 2 (2002) p.248

Design and implementation of microarray gene expression markup language (MAGE-ML).
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A.
Genome biology Volume 3 (2002) p.RESEARCH0046

Pathway evolution, structurally speaking.
Rison SC, Thornton JM.
Current opinion in structural biology Volume 12 (2002) p.374-382

Interactive InterPro-based comparisons of proteins in whole genomes.
Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.
Bioinformatics (Oxford, England) Volume 18 (2002) p.374-375

Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
Steward RE, Thornton JM.
Proteins Volume 48 (2002) p.178-191

Modeling mitochondrial protein evolution using structural information.
Liò P, Goldman N.
Journal of molecular evolution Volume 54 (2002) p.519-529

Wavelet transforms for the characterization and detection of repeating motifs.
Murray KB, Gorse D, Thornton JM.
Journal of molecular biology Volume 316 (2002) p.341-363

Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES.
Nature Volume 420 (2002) p.520-562

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Luscombe NM, Thornton JM.
Journal of molecular biology Volume 320 (2002) p.991-1009

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team.
Nature Volume 420 (2002) p.563-573

Immunity-related genes and gene families in Anopheles gambiae.
Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Müller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC.
Science (New York, N.Y.) Volume 298 (2002) p.159-165

2001

Evaluation of a Knowledge-Based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes
Nobeli I, Mitchell JM, Alex A, Thornton JM.
Journal of computational chemistry Volume 22 (2001) p.673-688

Small-molecule metabolism: an enzyme mosaic.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C.
Trends in biotechnology Volume 19 (2001) p.482-486

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
Whelan S, Goldman N.
Molecular biology and evolution Volume 18 (2001) p.691-699

Conservation helps to identify biologically relevant crystal contacts.
Valdar WS, Thornton JM.
Journal of molecular biology Volume 313 (2001) p.399-416

Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses.
Núñez JI, Martín MJ, Piccone ME, Carrillo E, Palma EL, Dopazo J, Sobrino F.
Veterinary research Volume 32 (2001) p.31-45

On the molecular discrimination between adenine and guanine by proteins.
Nobeli I, Laskowski RA, Valdar WS, Thornton JM.
Nucleic acids research Volume 29 (2001) p.4294-4309

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.
Nucleic acids research Volume 29 (2001) p.37-40

Evolution of function in protein superfamilies, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
Journal of molecular biology Volume 307 (2001) p.1113-1143

The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
Nagano N, Porter CT, Thornton JM.
Protein engineering Volume 14 (2001) p.845-855

Molecular phylogenetics: state-of-the-art methods for looking into the past.
Whelan S, Liò P, Goldman N.
Trends in genetics : TIG Volume 17 (2001) p.262-272

Protein-protein interfaces: analysis of amino acid conservation in homodimers.
Valdar WS, Thornton JM.
Proteins Volume 42 (2001) p.108-124

The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution.
Thornton JM.
Protein science : a publication of the Protein Society Volume 10 (2001) p.3-11

Integration of cytogenetic landmarks into the draft sequence of the human genome.
Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ, BAC Resource Consortium.
Nature Volume 409 (2001) p.953-958

Structural genomics takes off.
Thornton J.
Trends in biochemical sciences Volume 26 (2001) p.88-89

Progress in sequencing the mouse genome.
Lindblad-Toh K, Lander ES, McPherson JD, Waterston RH, Rodgers J, Birney E.
Genesis (New York, N.Y. : 2000) Volume 31 (2001) p.137-141

Mining the draft human genome.
Birney E, Bateman A, Clamp ME, Hubbard TJ.
Nature Volume 409 (2001) p.827-828

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C.
Journal of molecular biology Volume 311 (2001) p.693-708

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.
Nature genetics Volume 29 (2001) p.365-371

Hidden Markov models in biological sequence analysis
Birney E.
IBM Journal of Research and Development Volume 45 (2001) p.449-454

The EMBL nucleotide sequence database.
Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Lombard V, Lopez R, Parkinson H, Redaschi N, Sterk P, Stoehr P, Tuli MA.
Nucleic acids research Volume 29 (2001) p.17-21

From genome to function.
Thornton JM.
Science (New York, N.Y.) Volume 292 (2001) p.2095-2097

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
Luscombe NM, Laskowski RA, Thornton JM.
Nucleic acids research Volume 29 (2001) p.2860-2874

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E.
Nucleic acids research Volume 29 (2001) p.44-48

Cancer and genomics.
Futreal PA, Kasprzyk A, Birney E, Mullikin JC, Wooster R, Stratton MR.
Nature Volume 409 (2001) p.850-852

The human proteomics initiative (HPI).
O'Donovan C, Apweiler R, Bairoch A.
Trends in biotechnology Volume 19 (2001) p.178-181

Protein-RNA interactions: a structural analysis.
Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM.
Nucleic acids research Volume 29 (2001) p.943-954

Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium.
Nature Volume 409 (2001) p.860-921

A rapid classification protocol for the CATH Domain Database to support structural genomics.
Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA.
Nucleic acids research Volume 29 (2001) p.223-227

2000

The Bioperl project: motivation and usage
Stajich J, Birney E.
ACM SIGBIO Newsletter Volume 20 (2000) p.13-14

The EMBL nucleotide sequence database.
Baker W, van den Broek A, Camon E, Hingamp P, Sterk P, Stoesser G, Tuli MA.
Nucleic acids research Volume 28 (2000) p.19-23

Codon-substitution models for heterogeneous selection pressure at amino acid sites.
Yang Z, Nielsen R, Goldman N, Pedersen AM.
Genetics Volume 155 (2000) p.431-449

Identification of domains from protein sequences.
Ponting CP, Birney E.
Methods in molecular biology (Clifton, N.J.) Volume 143 (2000) p.53-69

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Kersey P, Hermjakob H, Apweiler R.
Bioinformatics (Oxford, England) Volume 16 (2000) p.1048-1049

Comparative genomics of the eukaryotes.
Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S.
Science (New York, N.Y.) Volume 287 (2000) p.2204-2215

A comparison of signal sequence prediction methods using a test set of signal peptides.
Menne KM, Hermjakob H, Apweiler R.
Bioinformatics (Oxford, England) Volume 16 (2000) p.741-742

The role SWISS-PROT and TrEMBL play in the genome research environment.
Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O'Donovan C, Apweiler R.
Journal of biotechnology Volume 78 (2000) p.221-234

Likelihood-based tests of topologies in phylogenetics.
Goldman N, Anderson JP, Rodrigo AG.
Systematic biology Volume 49 (2000) p.652-670

The Pfam protein families database.
Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL.
Nucleic acids research Volume 28 (2000) p.263-266

Assigning genomic sequences to CATH.
Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA.
Nucleic acids research Volume 28 (2000) p.277-282

Using the CATH domain database to assign structures and functions to the genome sequences.
Pearl F, Todd AE, Bray JE, Martin AC, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA.
Biochemical Society transactions Volume 28 (2000) p.269-275

An overview of the structures of protein-DNA complexes.
Luscombe NM, Austin SE, Berman HM, Thornton JM.
Genome biology Volume 1 (2000) p.REVIEWS001

InterPro--an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM, InterPro Consortium.
Bioinformatics (Oxford, England) Volume 16 (2000) p.1145-1150

From structure to function: approaches and limitations.
Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA.
Nature structural biology Volume 7 Suppl (2000) p.991-994

Comparison of functional annotation schemes for genomes.
Rison SC, Hodgman TC, Thornton JM.
Functional & integrative genomics Volume 1 (2000) p.56-69

Open annotation offers a democratic solution to genome sequencing.
Hubbard T, Birney E.
Nature Volume 403 (2000) p.825

Using GeneWise in the Drosophila annotation experiment.
Birney E, Durbin R.
Genome research Volume 10 (2000) p.547-548

ProtEST: protein multiple sequence alignments from expressed sequence tags.
Cuff JA, Birney E, Clamp ME, Barton GJ.
Bioinformatics (Oxford, England) Volume 16 (2000) p.111-116

Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.
Jones S, Marin A, Thornton JM.
Protein engineering Volume 13 (2000) p.77-82

Heterozygous germline mutations in BMPR2, encoding a TGF-beta receptor, cause familial primary pulmonary hypertension.
International PPH Consortium, Lane KB, Machado RD, Pauciulo MW, Thomson JR, Phillips JA 3rd, Loyd JE, Nichols WC, Trembath RC.
Nature genetics Volume 26 (2000) p.81-84

Searching databases to find protein domain organization.
Bateman A, Birney E.
Advances in protein chemistry Volume 54 (2000) p.137-157

EDIBLE: experimental design and information calculations in phylogenetics.
Massingham T, Goldman N.
Bioinformatics (Oxford, England) Volume 16 (2000) p.294-295

Evidence for mitochondrial DNA recombination in a human population of island Melanesia: correction.
Hagelberg E, Goldman N, Liò P, Whelan S, Schiefenhövel W, Clegg JB, Bowden DK.
Proceedings. Biological sciences / The Royal Society Volume 267 (2000) p.1595-1596

Mus musculus in the SWISS-PROT database: its relevance to developmental research.
Magrane M, Apweiler R.
Genesis (New York, N.Y. : 2000) Volume 26 (2000) p.1-4

Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics.
Goldman N, Whelan S.
Molecular biology and evolution Volume 17 (2000) p.975-978

Analysis and prediction of carbohydrate binding sites.
Taroni C, Jones S, Thornton JM.
Protein engineering Volume 13 (2000) p.89-98

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.
Bray JE, Todd AE, Pearl FM, Thornton JM, Orengo CA.
Protein engineering Volume 13 (2000) p.153-165

Discriminating between homodimeric and monomeric proteins in the crystalline state.
Ponstingl H, Henrick K, Thornton JM.
Proteins Volume 41 (2000) p.47-57

1999

Coevolving protein residues: maximum likelihood identification and relationship to structure.
Pollock DD, Taylor WR, Goldman N.
Journal of molecular biology Volume 287 (1999) p.187-198

COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.
Harding SE, Horton JC, Jones S, Thornton JM, Winzor DJ.
Biophysical journal Volume 76 (1999) p.2432-2438

Swissknife - 'lazy parsing' of SWISS-PROT entries.
Hermjakob H, Fleischmann W, Apweiler R.
Bioinformatics (Oxford, England) Volume 15 (1999) p.771-772

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Apweiler R, Hermjakob H, Sharon N.
Biochimica et biophysica acta Volume 1473 (1999) p.4-8

Prediction of the location and type of beta-turns in proteins using neural networks.
Shepherd AJ, Gorse D, Thornton JM.
Protein science : a publication of the Protein Society Volume 8 (1999) p.1045-1055

Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?
MacArthur MW, Thornton JM.
Acta crystallographica. Section D, Biological crystallography Volume 55 (1999) p.994-1004

Using protein structural information in evolutionary inference: transmembrane proteins.
Liò P, Goldman N.
Molecular biology and evolution Volume 16 (1999) p.1696-1710

DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.
Todd AE, Orengo CA, Thornton JM.
Protein engineering Volume 12 (1999) p.375-379

Motif-based searching in TOPS protein topology databases.
Gilbert D, Westhead D, Nagano N, Thornton J.
Bioinformatics (Oxford, England) Volume 15 (1999) p.317-326

Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
Whelan S, Goldman N.
Molecular biology and evolution Volume 16 (1999) p.1292-1299

Evidence for mitochondrial DNA recombination in a human population of island Melanesia.
Hagelberg E, Goldman N, Lió P, Whelan S, Schiefenhövel W, Clegg JB, Bowden DK.
Proceedings. Biological sciences / The Royal Society Volume 266 (1999) p.485-492

BLEEP - A Potential of Mean Force Describing Protein-Ligan Interactions: Generating the Potential
Mitchell JBO, Laskowski RA, Alex A, Thornton JM.
Journal of computational chemistry Volume 20 (1999) p.11

Three-dimensional structure analysis of PROSITE patterns.
Kasuya A, Thornton JM.
Journal of molecular biology Volume 286 (1999) p.1673-1691

From protein structure to function.
Orengo CA, Todd AE, Thornton JM.
Current opinion in structural biology Volume 9 (1999) p.374-382

Small subunit rRNA gene sequences of Aeromonas salmonicida subsp. smithia and Haemophilus piscium reveal pronounced similarities with A. salmonicida subsp. salmonicida.
Thornton JM, Austin DA, Austin B, Powell R.
Diseases of aquatic organisms Volume 35 (1999) p.155-158

Protein-DNA interactions: A structural analysis.
Jones S, van Heyningen P, Berman HM, Thornton JM.
Journal of molecular biology Volume 287 (1999) p.877-896

Removing redundancy in SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Glemet E, Codani JJ, Apweiler R.
Bioinformatics (Oxford, England) Volume 15 (1999) p.258-259

Evolution of protein function, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
Current opinion in chemical biology Volume 3 (1999) p.548-556

Correlation of observed fold frequency with the occurrence of local structural motifs.
Salem GM, Hutchinson EG, Orengo CA, Thornton JM.
Journal of molecular biology Volume 287 (1999) p.969-981

Factors limiting the performance of prediction-based fold recognition methods.
de la Cruz X, Thornton JM.
Protein science : a publication of the Protein Society Volume 8 (1999) p.750-759

The CATH Database provides insights into protein structure/function relationships.
Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM.
Nucleic acids research Volume 27 (1999) p.275-279

The EMBL Nucleotide Sequence Database.
Stoesser G, Tuli MA, Lopez R, Sterk P.
Nucleic acids research Volume 27 (1999) p.18-24

Protein structural topology: Automated analysis and diagrammatic representation.
Westhead DR, Slidel TW, Flores TP, Thornton JM.
Protein science : a publication of the Protein Society Volume 8 (1999) p.897-904

Polymerase chain reaction (PCR)-based typing analysis of atypical isolates of the fish pathogen Aeromonas salmonicida.
Høie S, Dalsgaard I, Aase IL, Heum M, Thornton JM, Powell R.
Systematic and applied microbiology Volume 22 (1999) p.403-411

Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
Nagano N, Hutchinson EG, Thornton JM.
Protein science : a publication of the Protein Society Volume 8 (1999) p.2072-2084

Protein folds, functions and evolution.
Thornton JM, Orengo CA, Todd AE, Pearl FM.
Journal of molecular biology Volume 293 (1999) p.333-342

1998

A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine.
Núñez JI, Blanco E, Hernández T, Gómez-Tejedor C, Martín MJ, Dopazo J, Sobrino F.
Journal of virological methods Volume 72 (1998) p.227-235

Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.
Zuccotto F, Martin AC, Laskowski RA, Thornton JM, Gilbert IH.
Journal of computer-aided molecular design Volume 12 (1998) p.241-257

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).
Patel SU, Osborn R, Rees S, Thornton JM.
Biochemistry Volume 37 (1998) p.983-990

Validation of protein models derived from experiment.
Laskowski RA, MacArthur MW, Thornton JM.
Current opinion in structural biology Volume 8 (1998) p.631-639

New tools and resources for analysing protein structures and their interactions.
Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou M, Thornton JM.
Acta crystallographica. Section D, Biological crystallography Volume 54 (1998) p.1132-1138

Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
Hubbard SJ, Beynon RJ, Thornton JM.
Protein engineering Volume 11 (1998) p.349-359

Models of molecular evolution and phylogeny.
Liò P, Goldman N.
Genome research Volume 8 (1998) p.1233-1244

Glycosyltransferases in SWISS-PROT.
O'Donovan C, Mitaritonna N.
Glycoconjugate journal Volume 15 (1998) p.507-509

Contemporary approaches to protein structure classification.
Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM.
BioEssays : news and reviews in molecular, cellular and developmental biology Volume 20 (1998) p.884-891

Determinants of strand register in antiparallel beta-sheets of proteins.
Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN.
Protein science : a publication of the Protein Society Volume 7 (1998) p.2287-2300

Characterization of atypical Aeromonas salmonicida by different methods.
Austin B, Austin DA, Dalsgaard I, Gudmundsdóttir BK, Høie S, Thornton JM, Larsen JL, O'Hici B, Powell R.
Systematic and applied microbiology Volume 21 (1998) p.50-64

Pattern Search over the TOPS Protein Topology Database
Gilbert DR, Westhead DR, Hatton DC, Thornton JM.
Protein Data Bank Quarterly Newsletter Volume 85 (1998) p.7-9

Protein folds and functions.
Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM.
Structure (London, England : 1993) Volume 6 (1998) p.875-884

A procedure for detecting selection in highly variable viral genomes: evidence of positive selection in antigenic regions of capsid protein VP1 of foot-and-mouth disease virus.
Martín MJ, Núñez JI, Sobrino F, Dopazo J.
Journal of virological methods Volume 74 (1998) p.215-221

Evolution of the androgen receptor: structure-function implications.
Thornton JW, Kelley DB.
BioEssays : news and reviews in molecular, cellular and developmental biology Volume 20 (1998) p.860-869

SPTR - A comprehensive, non-redundant and up-to-date view of the protein sequence world.
Hermjakob H, Lang F, Apweiler R,.
CCP11 Newsletter Volume 2.3 (1998) p.

Domain assignment for protein structures using a consensus approach: characterization and analysis.
Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM.
Protein science : a publication of the Protein Society Volume 7 (1998) p.233-242

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Journal of molecular biology Volume 276 (1998) p.417-436

SPTR- A comprehensive, non-redundant and up-to-date protein sequence database.
Hermjakob H, Lang F, Apweiler R,.
The Bioinformer Volume 4 (1998) p.

Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage.
Smith GP, Patel SU, Windass JD, Thornton JM, Winter G, Griffiths AD.
Journal of molecular biology Volume 277 (1998) p.317-332

An atlas of protein topology cartoons available on the World-Wide Web.
Westhead DR, Hatton DC, Thornton JM.
Trends in biochemical sciences Volume 23 (1998) p.35-36

Protein structure prediction.
Westhead DR, Thornton JM.
Current opinion in biotechnology Volume 9 (1998) p.383-389

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel AE, Kel OV, Ignatieva EV, Ananko EA, Podkolodnaya OA, Kolpakov FA, Podkolodny NL, Kolchanov NA.
Nucleic acids research Volume 26 (1998) p.362-367

Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Milburn D, Laskowski RA, Thornton JM.
Protein engineering Volume 11 (1998) p.855-859

PQS: a protein quaternary structure file server.
Henrick K, Thornton JM.
Trends in biochemical sciences Volume 23 (1998) p.358-361

Design, synthesis and structure of a zinc finger with an artificial beta-turn.
Viles JH, Patel SU, Mitchell JB, Moody CM, Justice DE, Uppenbrink J, Doyle PM, Harris CJ, Sadler PJ, Thornton JM.
Journal of molecular biology Volume 279 (1998) p.973-986

Assessing the impact of secondary structure and solvent accessibility on protein evolution.
Goldman N, Thorne JL, Jones DT.
Genetics Volume 149 (1998) p.445-458

Classifying a protein in the CATH database of domain structures.
Orengo CA, Martin AM, Hutchinson G, Jones S, Jones DT, Michie AD, Swindells MB, Thornton JM.
Acta crystallographica. Section D, Biological crystallography Volume 54 (1998) p.1155-1167

Phylogenetic information and experimental design in molecular systematics.
Goldman N.
Proceedings. Biological sciences / The Royal Society Volume 265 (1998) p.1779-1786

Iditis: protein structure database.
Gardner S, Thornton J.
Acta crystallographica. Section D, Biological crystallography Volume 54 (1998) p.1071-1077

1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.
Bloch C Jr, Patel SU, Baud F, Zvelebil MJ, Carr MD, Sadler PJ, Thornton JM.
Proteins Volume 32 (1998) p.334-349

PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.
Bioinformatics (Oxford, England) Volume 14 (1998) p.726-733

1997

Structures of N-termini of helices in proteins.
Doig AJ, MacArthur MW, Stapley BJ, Thornton JM.
Protein science : a publication of the Protein Society Volume 6 (1997) p.147-155

Modelling protein unfolding: hen egg-white lysozyme.
Williams MA, Thornton JM, Goodfellow JM.
Protein engineering Volume 10 (1997) p.895-903

Assessment of comparative modeling in CASP2.
Martin AC, MacArthur MW, Thornton JM.
Proteins Volume Suppl 1 (1997) p.14-28

CATH--a hierarchic classification of protein domain structures.
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM.
Structure (London, England : 1993) Volume 5 (1997) p.1093-1108

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
Wallace AC, Borkakoti N, Thornton JM.
Protein science : a publication of the Protein Society Volume 6 (1997) p.2308-2323

Analysis of protein-protein interaction sites using surface patches.
Jones S, Thornton JM.
Journal of molecular biology Volume 272 (1997) p.121-132

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Luscombe NM, Laskowski RA, Thornton JM.
Nucleic acids research Volume 25 (1997) p.4940-4945

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.
Apweiler R, Gateau A, Contrino S, Martin MJ, Junker V, O'Donovan C, Lang F, Mitaritonna N, Kappus S, Bairoch A.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology Volume 5 (1997) p.33-43

Representation of mouse data in SWISS-PROT and TREMBL
Magrane M, Junker V, O'Donovan C, Lang F, Mitaritonna N, Kappus S, Apweiler R.
Mouse genome Volume 95 (1997) p.701-703

Non-randomness in side-chain packing: the distribution of interplanar angles.
Mitchell JB, Laskowski RA, Thornton JM.
Proteins Volume 29 (1997) p.370-380

Are big trees indeed easy?
Yang Z, Goldman N.
Trends in ecology & evolution Volume 12 (1997) p.357

Prediction of protein-protein interaction sites using patch analysis.
Jones S, Thornton JM.
Journal of molecular biology Volume 272 (1997) p.133-143

RIFLE: rapid identification of microorganisms by fragment length evaluation.
Hermjakob H, Giegerich R, Arnold W.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology Volume 5 (1997) p.131-139

PDBsum: a Web-based database of summaries and analyses of all PDB structures.
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM.
Trends in biochemical sciences Volume 22 (1997) p.488-490

Bayesian probabilities and quartet puzzling
Strimmer K, Goldman N, von Haeseler A.
Molecular biology and evolution Volume 14 (1997) p.210

New Developments in Biological Databases: SWISS-PROT and its Computer-annotated Supplement TREMBL.
Apweiler R, Junker V, O'Donovan C, Lang F, Mitaritonna N, Kappus S, Contrino S, Martin M.
Protein science : a publication of the Protein Society Volume 6(suppl.) (1997) p.56

1996

PROMOTIF--a program to identify and analyze structural motifs in proteins.
Hutchinson EG, Thornton JM.
Protein science : a publication of the Protein Society Volume 5 (1996) p.212-220

Potential energy functions for threading.
Jones DT, Thornton JM.
Current opinion in structural biology Volume 6 (1996) p.210-216

Protein recognition of adenylate: an example of a fuzzy recognition template.
Moodie SL, Mitchell JB, Thornton JM.
Journal of molecular biology Volume 263 (1996) p.486-500

Multiple solution conformations of the integrin-binding cyclic pentapeptide cyclo(-Ser-D-Leu-Asp-Val-Pro-). Analysis of the (phi, psi) space available to cyclic pentapeptides.
Viles JH, Mitchell JB, Gough SL, Doyle PM, Harris CJ, Sadler PJ, Thornton JM.
European journal of biochemistry / FEBS Volume 242 (1996) p.352-362

Protein clefts in molecular recognition and function.
Laskowski RA, Luscombe NM, Swindells MB, Thornton JM.
Protein science : a publication of the Protein Society Volume 5 (1996) p.2438-2452

Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM.
Journal of molecular biology Volume 255 (1996) p.494-506

Protein fold recognition by sequence threading: tools and assessment techniques.
Miller RT, Jones DT, Thornton JM.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 10 (1996) p.171-178

Analysis of domain structural class using an automated class assignment protocol.
Michie AD, Orengo CA, Thornton JM.
Journal of molecular biology Volume 262 (1996) p.168-185

Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic.
Doyle PM, Harris JC, Moody CM, Sadler PJ, Sims M, Thornton JM, Uppenbrink J, Viles JH.
International journal of peptide and protein research Volume 47 (1996) p.427-436

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.
Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J.
Trends in biochemical sciences Volume 21 (1996) p.251-256

Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.
Goldman N, Thorne JL, Jones DT.
Journal of molecular biology Volume 263 (1996) p.196-208

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.
Wallace AC, Laskowski RA, Thornton JM.
Protein science : a publication of the Protein Society Volume 5 (1996) p.1001-1013

Phylogenetic relationships of european strains of porcine reproductive and respiratory syndrome virus (PRRSV) inferred from DNA sequences of putative ORF-5 and ORF-7 genes.
Suárez P, Zardoya R, Martín MJ, Prieto C, Dopazo J, Solana A, Castro JM.
Virus research Volume 42 (1996) p.159-165

X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.
Laskowski RA, Thornton JM, Humblet C, Singh J.
Journal of molecular biology Volume 259 (1996) p.175-201

Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.
Kalsi JK, Martin AC, Hirabayashi Y, Ehrenstein M, Longhurst CM, Ravirajan C, Zvelebil M, Stollar BD, Thornton JM, Isenberg DA.
Molecular immunology Volume 33 (1996) p.471-483

Molecular recognition by proteins: protein-ligand interactions from a structural perspective.
Wallace AC, Laskowski RA, Singh J, Thornton JM.
Biochemical Society transactions Volume 24 (1996) p.280-284

Deviations from planarity of the peptide bond in peptides and proteins.
MacArthur MW, Thornton JM.
Journal of molecular biology Volume 264 (1996) p.1180-1195

Principles of protein-protein interactions.
Jones S, Thornton JM.
Proceedings of the National Academy of Sciences of the United States of America Volume 93 (1996) p.13-20

Towards meeting the Paracelsus Challenge: The design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50% sequence identity to an all-beta protein.
Jones DT, Moody CM, Uppenbrink J, Viles JH, Doyle PM, Harris CJ, Pearl LH, Sadler PJ, Thornton JM.
Proteins Volume 24 (1996) p.502-513

Combining protein evolution and secondary structure.
Thorne JL, Goldman N, Jones DT.
Molecular biology and evolution Volume 13 (1996) p.666-673

Antibody-antigen interactions: contact analysis and binding site topography.
MacCallum RM, Martin AC, Thornton JM.
Journal of molecular biology Volume 262 (1996) p.732-745

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM.
Journal of biomolecular NMR Volume 8 (1996) p.477-486

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.
Martin AC, Thornton JM.
Journal of molecular biology Volume 263 (1996) p.800-815

1995

Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity.
Orengo CA, Swindells MB, Michie AD, Zvelebil MJ, Driscoll PC, Waterfield MD, Thornton JM.
Protein science : a publication of the Protein Society Volume 4 (1995) p.1977-1983

The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains.
McDonald IK, Thornton JM.
Protein engineering Volume 8 (1995) p.217-224

Protein-protein interactions: a review of protein dimer structures.
Jones S, Thornton JM.
Progress in biophysics and molecular biology Volume 63 (1995) p.31-65

Human immunodeficiency virus type 2 (HIV-2) env gene analysis: prediction of glycoprotein epitopes important for heterotypic neutralization and evidence for three genotype clusters within the HIV-2a subtype.
Breuer J, Douglas NW, Goldman N, Daniels RS.
The Journal of general virology Volume 76 ( Pt 2) (1995) p.333-345

Long loops in proteins.
Martin AC, Toda K, Stirk HJ, Thornton JM.
Protein engineering Volume 8 (1995) p.1093-1101

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Wallace AC, Laskowski RA, Thornton JM.
Protein engineering Volume 8 (1995) p.127-134

Folding of Beta Structure in Proteins
Evans PA, Gladwin ST, Gopalakrishnan B, Tisi LC, Woolfson DN, Murracy JH, Packman LC, Trotter BW, Mackay JP, Williams DH, Thornton JM.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 9 (1995) p.A1239

Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Jones DT, Miller RT, Thornton JM.
Proteins Volume 23 (1995) p.387-397

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.
Swindells MB, MacArthur MW, Thornton JM.
Nature structural biology Volume 2 (1995) p.596-603

Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem
Yang Z, Goldman N, Friday A.
Systematic biology Volume 44 (1995) p.384-399

Protein folds: towards understanding folding from inspection of native structures.
Thornton JM, Jones DT, MacArthur MW, Orengo CM, Swindells MB.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 348 (1995) p.71-79

Protein Folds and Folding
Thornton JM, Jones DT, MacArthur M, Orengo CA, Swindells M.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 9 (1995) p.A1240

1994

[Evaluation and extension of Markov process models for the evolution of DNA].
Yang Z, Goldman N.
Yi chuan xue bao = Acta genetica Sinica Volume 21 (1994) p.17-23

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Hubbard SJ, Eisenmenger F, Thornton JM.
Protein science : a publication of the Protein Society Volume 3 (1994) p.757-768

An algorithm for automatically generating protein topology cartoons.
Flores TP, Moss DS, Thornton JM.
Protein engineering Volume 7 (1994) p.31-37

The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.
Stirk HJ, Thornton JM.
Protein engineering Volume 7 (1994) p.47-56

Protein Motifs and Folding Recognition
Thornton JM, Orengo CM, Jones DT, Taylor WR.
Biophysical journal Volume 66 (1994) p.A241

Protein superfamilies and domain superfolds.
Orengo CA, Jones DT, Thornton JM.
Nature Volume 372 (1994) p.631-634

A mutation data matrix for transmembrane proteins.
Jones DT, Taylor WR, Thornton JM.
FEBS letters Volume 339 (1994) p.269-275

Satisfying hydrogen bonding potential in proteins.
McDonald IK, Thornton JM.
Journal of molecular biology Volume 238 (1994) p.777-793

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.
Goldman N.
Molecular phylogenetics and evolution Volume 3 (1994) p.230-239

NMR and crystallography--complementary approaches to structure determination.
MacArthur MW, Driscoll PC, Thornton JM.
Trends in biotechnology Volume 12 (1994) p.149-153

Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
Mitchell JB, Nandi CL, McDonald IK, Thornton JM, Price SL.
Journal of molecular biology Volume 239 (1994) p.315-331

A revised set of potentials for beta-turn formation in proteins.
Hutchinson EG, Thornton JM.
Protein science : a publication of the Protein Society Volume 3 (1994) p.2207-2216

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
Yang Z, Goldman N, Friday A.
Molecular biology and evolution Volume 11 (1994) p.316-324

Buried waters and internal cavities in monomeric proteins.
Williams MA, Goodfellow JM, Thornton JM.
Protein science : a publication of the Protein Society Volume 3 (1994) p.1224-1235

A model recognition approach to the prediction of all-helical membrane protein structure and topology.
Jones DT, Taylor WR, Thornton JM.
Biochemistry Volume 33 (1994) p.3038-3049

A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Goldman N, Yang Z.
Molecular biology and evolution Volume 11 (1994) p.725-736

Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum.
Gardner MJ, Goldman N, Barnett P, Moore PW, Rangachari K, Strath M, Whyte A, Williamson DH, Wilson RJ.
Molecular and biochemical parasitology Volume 66 (1994) p.221-231

1993

Further results on error minimization in the genetic code.
Goldman N.
Journal of molecular evolution Volume 37 (1993) p.662-664

Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences.
Goldman N.
Nucleic acids research Volume 21 (1993) p.2487-2491

Statistical tests of models of DNA substitution.
Goldman N.
Journal of molecular evolution Volume 36 (1993) p.182-198

Simple diagnostic statistical tests of models for DNA substitution.
Goldman N.
Journal of molecular evolution Volume 37 (1993) p.650-661

1992

Human origins. Genetics and geography.
Goldman N, Barton NH.
Nature Volume 357 (1992) p.440-441

1990

Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses
Goldman N.
Systematic biology Volume 39 (1990) p.345

Quantitative analysis of shape variation in populations of Surirella fastuosa
Goldman N, Paddock TBB, Shaw KM.
Diatom research : the journal of the International Society for Diatom Research Volume 5