Publications

2014

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

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

Holy fools: a religious phenomenon of extreme behaviour.
Poulakou-Rebelakou E, Liarmakopoulos A, Tsiamis C, Ploumpidis D.
J Relig Health Volume 53 (2014) p.95-104

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.
Angew Chem Int Ed Engl 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

Data standardization and sharing-the work of the HUPO-PSI.
Orchard S.
Biochim Biophys Acta Volume 1844 (2014) p.82-87

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 Res Volume 42 (2014) p.d749-55

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) Volume 4 (2014) p.433-445

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.
Proc Natl Acad Sci U S A Volume 111 (2014) p.6131-6138

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, Sauro HM, Stolovitzky G, Saez-Rodriguez J.
BMC Syst Biol Volume 8 (2014) p.13

The Reactome pathway knowledgebase.
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
Nucleic Acids Res Volume 42 (2014) p.d472-7

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

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.
Nat Rev Drug Discov Volume 13 (2014) p.239-240

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.
Sci Signal Volume 7 (2014) p.ra5

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

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

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.
Nat Biotechnol Volume (2014) p.

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.
Med Mycol Volume 52 (2014) p.472-481

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

Ten simple rules for running interactive workshops.
Pavelin K, Pundir S, Cham JA.
PLoS Comput Biol Volume 10 (2014) p.e1003485

Gene cooption in Mycobacteria and search for virulence attributes: Comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other mycobacteria.
Singh Y, Kohli S, Sowpati DT, Rahman SA, Tyagi AK, Hasnain SE.
Int J Med Microbiol Volume 304 (2014) p.742-748

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 Res Volume 42 (2014) p.d1001-6

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.
Nucleic Acids Res Volume 42 (2014) p.d802-9

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 Res Volume 42 (2014) p.d1083-90

The functional therapeutic chemical classification system.
Croset S, Overington JP, Rebholz-Schuhmann D.
Bioinformatics Volume 30 (2014) p.876-883

The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.
Curr Opin Struct Biol Volume 26C (2014) p.121-130

Suppression of type 1 pilus assembly in uropathogenic Escherichia coli by chemical inhibition of subunit polymerization.
Lo AW, Van de Water K, Gane PJ, Chan AW, Steadman D, Stevens K, Selwood DL, Waksman G, Remaut H.
J Antimicrob Chemother Volume 69 (2014) p.1017-1026

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.
Mol Ther Nucleic Acids Volume 3 (2014) p.e145

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.
Eur J Hum Genet Volume 22 (2014) p.386-390

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 Res Volume 42 (2014) p.d873-8

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.
Proc Natl Acad Sci U S A Volume 111 (2014) p.2235-2240

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

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 Volume 30 (2014) p.1008-1009

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.
Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME.
Front Neuroinform Volume 8 (2014) p.62

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 Res Volume 42 (2014) p.d926-32

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.
Hum Mol Genet Volume 23 (2014) p.4420-4432

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 Genet Volume 10 (2014) p.e1004132

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

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 Genet Volume 10 (2014) p.e1004151

Efficient ring perception for the Chemistry Development Kit.
May JW, Steinbeck C.
J Cheminform Volume 6 (2014) p.3

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.
J Bone Miner Res Volume 29 (2014) p.1619-1626

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

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.
Physiol Genomics Volume 46 (2014) p.418-428

Information visualisation for science and policy: engaging users and avoiding bias.
McInerny GJ, Chen M, Freeman R, Gavaghan D, Meyer M, Rowland F, Spiegelhalter DJ, Stefaner M, Tessarolo G, Hortal J.
Trends Ecol Evol Volume 29 (2014) p.148-157

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 Res Volume 42 (2014) p.d50-2

PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA.
Nucleic Acids Res Volume 42 (2014) p.d292-6

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

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

Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
International Glossina Genome Initiative.
Science Volume 344 (2014) p.380-386

Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.
Marsh JA, Teichmann SA.
Bioessays Volume 36 (2014) p.209-218

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 Res Volume 182 (2014) p.43-49

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 Res Volume 42 (2014) p.d485-9

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.
Biol Psychiatry Volume 75 (2014) p.386-397

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 Volume 30 (2014) p.1338-1339

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.
Am J Med Genet C Semin Med Genet Volume 166C (2014) p.93-104

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

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

The Nucleic Acid Database: new features and capabilities.
Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM.
Nucleic Acids Res Volume 42 (2014) p.d114-22

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 Res Volume 42 (2014) p.d789-93

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

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 Res Volume 42 (2014) p.d546-52

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A.
Nucleic Acids Res Volume 42 (2014) p.d364-73

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.
Barrera A, Alastruey-Izquierdo A, Martín MJ, Cuesta I, Vizcaíno JA.
PLoS Comput Biol Volume 10 (2014) p.e1003733

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

A survey of molecular descriptors used in mass spectrometry based proteomics.
Audain E, Sanchez A, Vizcaíno JA, Perez-Riverol Y.
Curr Top Med Chem Volume 14 (2014) p.388-397

TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Nucleic Acids Res Volume 42 (2014) p.d922-5

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Waller M, Barrett AJ, Bateman A.
Nucleic Acids Res Volume 42 (2014) p.d503-9

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 42 (2014) p.d191-8

Functional annotation of noncoding sequence variants.
Ritchie GR, Dunham I, Zeggini E, Flicek P.
Nat Methods Volume 11 (2014) p.294-296

The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.
Nucleic Acids Res Volume 42 (2014) p.d18-25

Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M.
Nucleic Acids Res Volume 42 (2014) p.d222-30

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 Res Volume 42 (2014) p.d1193-9

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

The reference genome sequence of Saccharomyces cerevisiae: then and now.
Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM.
G3 (Bethesda) Volume 4 (2014) p.389-398

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 Res Volume 42 (2014) p.d358-63

Saccharomyces genome database provides new regulation data.
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM.
Nucleic Acids Res Volume 42 (2014) p.d717-25

A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Tamuri AU, Goldman N, dos Reis M.
Genetics Volume 197 (2014) p.257-271

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 (Oxford) Volume 2014 (2014) p.bau016

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.
Biochim Biophys Acta Volume 1844 (2014) p.98-107

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.
Biochim Biophys Acta Volume 1844 (2014) p.63-76

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR 3rd, Apweiler R, Ping P.
J Proteome Res Volume 13 (2014) p.433-446

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C.
Methods Mol Biol Volume 1079 (2014) p.59-73

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 Res Volume 42 (2014) p.d285-91

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

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G.
Nat Methods Volume (2014) p.

Assembly information services in the European Nucleotide Archive.
Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic Acids Res Volume 42 (2014) p.d38-43

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

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, Paillerets BB, 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, Soom AV, Vidaković M, Widschwendter M.
BMC Genomics Volume 15 (2014) p.487

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

InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S.
Bioinformatics Volume 30 (2014) p.1236-1240

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 Res Volume 42 (2014) p.d600-6

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

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.
Studer RA, Christin PA, Williams MA, Orengo CA.
Proc Natl Acad Sci U S A Volume 111 (2014) p.2223-2228

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 Res Volume 42 (2014) p.d917-21

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 Res Volume 42 (2014) p.d240-5

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

2013

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.
Petrov AI, Zirbel CL, Leontis NB.
RNA Volume 19 (2013) p.1327-1340

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 Volume 29 (2013) p.1919-1921

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 Rep Volume 5 (2013) p.271-282

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.
Nat Genet Volume 45 (2013) p.542-545

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.
Brief Bioinform Volume 14 (2013) p.528-537

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.
Nat Methods Volume 10 (2013) p.221-227

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 Volume 21 (2013) p.1563-1570

A ligand's-eye view of protein similarity.
van Westen GJ, Overington JP.
Nat Methods Volume 10 (2013) p.116-117

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 Volume 342 (2013) p.1516-1517

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

Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data.
van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.
PLoS Comput Biol Volume 9 (2013) p.e1002899

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets.
van Westen GJ, Swier RF, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.
J Cheminform Volume 5 (2013) p.41

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.
Nat Methods Volume 10 (2013) p.676-682

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

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

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

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 Syst Biol Volume 7 (2013) p.135

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A.
J Cheminform Volume 5 (2013) p.42

Metingear: a development environment for annotating genome-scale metabolic models.
May JW, James AG, Steinbeck C.
Bioinformatics Volume 29 (2013) p.2213-2215

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic Acids Res Volume 41 (2013) p.w15-21

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 Volume 21 (2013) p.875-881

Molecular fields in ligand discovery.
Gane PJ, Chan AW.
Methods Mol Biol Volume 1008 (2013) p.479-499

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.
Bioorg Med Chem Volume 21 (2013) p.4904-4913

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 Biol Volume 14 (2013) p.r148

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 Res Volume 41 (2013) p.d483-9

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 Metab Lett Volume 7 (2013) p.68-77

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

Controlled annotations for systems biology.
Juty N, Laibe C, Le Novère N.
Methods Mol Biol Volume 1021 (2013) p.227-245

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

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

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.
Nat Genet Volume 45 (2013) p.701-706

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 Res Volume 23 (2013) p.2066-2077

A guide to best practices for Gene Ontology (GO) manual annotation.
Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM.
Database (Oxford) Volume 2013 (2013) p.bat054

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 Res Volume 41 (2013) p.d773-80

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.
J Comput Aided Mol Des Volume 27 (2013) p.859-871

The Amborella genome and the evolution of flowering plants.
Amborella Genome Project.
Science Volume 342 (2013) p.1241089

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.
Am J Hum Genet Volume 92 (2013) p.460-467

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

BioModels Database: a repository of mathematical models of biological processes.
Chelliah V, Laibe C, Le Novère N.
Methods Mol Biol Volume 1021 (2013) p.189-199

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.
J Struct Biol Volume 184 (2013) p.173-181

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

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.
Nat Methods Volume 10 (2013) p.723-729

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A.
Database (Oxford) Volume 2013 (2013) p.bat062

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

Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan.
Carss KJ, Stevens E, Foley AR, Cirak S, Riemersma M, Torelli S, Hoischen A, Willer T, van Scherpenzeel M, Moore SA, Messina S, Bertini E, Bönnemann CG, Abdenur JE, Grosmann CM, Kesari A, Punetha J, Quinlivan R, Waddell LB, Young HK, Wraige E, Yau S, Brodd L, Feng L, Sewry C, MacArthur DG, North KN, Hoffman E, Stemple DL, Hurles ME, van Bokhoven H, Campbell KP, Lefeber DJ, UK10K Consortium, Lin YY, Muntoni F.
Am J Hum Genet Volume 93 (2013) p.29-41

Structure-based identification of OATP1B1/3 inhibitors.
De Bruyn T, van Westen GJ, Ijzerman AP, Stieger B, de Witte P, Augustijns PF, Annaert PP.
Mol Pharmacol Volume 83 (2013) p.1257-1267

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 Crystallogr D Biol Crystallogr Volume 69 (2013) p.2296

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

Visualization and analysis of biological networks.
Millán PP.
Methods Mol Biol Volume 1021 (2013) p.63-88

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 Res Volume 41 (2013) p.1496-1507

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 Genet Volume 9 (2013) p.e1003398

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

The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O.
Pac Symp Biocomput Volume (2013) p.456-458

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 Genet Volume 9 (2013) p.e1004023

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.
J Intern Med Volume 274 (2013) p.67-76

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 Genet Volume 9 (2013) p.e1003803

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

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

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 Med Genomics Volume 6 (2013) p.22

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

Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner.
Stricker SH, Feber A, Engström PG, Carén H, Kurian KM, Takashima Y, Watts C, Way M, Dirks P, Bertone P, Smith A, Beck S, Pollard SM.
Genes Dev Volume 27 (2013) p.654-669

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.
Nat Genet Volume 45 (2013) p.912-917

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 Volume 342 (2013) p.1235587

Genetic and archaeological perspectives on the initial modern human colonization of southern Asia.
Mellars P, Gori KC, Carr M, Soares PA, Richards MB.
Proc Natl Acad Sci U S A Volume 110 (2013) p.10699-10704

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells.
Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T.
Genome Biol Volume 14 (2013) p.r98

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

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor.
Martello G, Bertone P, Smith A.
EMBO J Volume 32 (2013) p.2561-2574

A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1.
Danovi D, Folarin A, Gogolok S, Ender C, Elbatsh AM, Engström PG, Stricker SH, Gagrica S, Georgian A, Yu D, U KP, Harvey KJ, Ferretti P, Paddison PJ, Preston JE, Abbott NJ, Bertone P, Smith A, Pollard SM.
PLoS One Volume 8 (2013) p.e77053

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

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

Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium.
Nucleic Acids Res Volume 41 (2013) p.d43-7

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

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 Res Volume 41 (2013) p.d584-9

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.
Nat Biotechnol Volume 31 (2013) p.419-425

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 (Oxford) Volume 2013 (2013) p.bas062

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.
Br J Cancer Volume 108 (2013) p.450-460

Non-coding transcription and large-scale nuclear organisation of immunoglobulin recombination.
Stubbington MJ, Corcoran AE.
Curr Opin Genet Dev Volume 23 (2013) p.81-88

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.
Nat Genet Volume 45 (2013) p.415-21, 421e1-2

Genomicus: five genome browsers for comparative genomics in eukaryota.
Louis A, Muffato M, Roest Crollius H.
Nucleic Acids Res Volume 41 (2013) p.d700-5

Change-point detection in time-series data by relative density-ratio estimation.
Liu S, Yamada M, Collier N, Sugiyama M.
Neural Netw Volume 43 (2013) p.72-83

Evaluation of epidemic intelligence systems integrated in the early alerting and reporting project for the detection of A/H5N1 influenza events.
Barboza P, Vaillant L, Mawudeku A, Nelson NP, Hartley DM, Madoff LC, Linge JP, Collier N, Brownstein JS, Yangarber R, Astagneau P, Early Alerting Reporting Project Of The Global Health Security Initiative.
PLoS One Volume 8 (2013) p.e57252

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.
J Exp Bot Volume 64 (2013) p.2423-2434

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

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

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 Res Volume 23 (2013) p.749-761

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 Biol Evol Volume 5 (2013) p.661-679

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

Global mapping of infectious disease.
Hay SI, Battle KE, Pigott DM, Smith DL, Moyes CL, Bhatt S, Brownstein JS, Collier N, Myers MF, George DB, Gething PW.
Philos Trans R Soc Lond B Biol Sci Volume 368 (2013) p.20120250

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 Discov Today Volume 18 (2013) p.1014-1024

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 Discov Today Volume 18 (2013) p.843-852

SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.
Wong ES, Hardy MC, Wood D, Bailey T, King GF.
PLoS One Volume 8 (2013) p.e66279

Identification of natural killer cell receptor genes in the genome of the marsupial Tasmanian devil (Sarcophilus harrisii).
van der Kraan LE, Wong ES, Lo N, Ujvari B, Belov K.
Immunogenetics Volume 65 (2013) p.25-35

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) Volume 3 (2013) p.2031-2047

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

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

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 Res Volume 41 (2013) p.d781-6

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Saez-Rodriguez J.
F1000Res Volume 2 (2013) p.192

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 Volume 29 (2013) p.2320-2326

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.
Brief Bioinform Volume 14 (2013) p.548-555

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 Volume 29 (2013) p.1325-1332

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

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 Biol Volume 14 (2013) p.r88

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.
Int J Parasitol Volume 43 (2013) p.465-475

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

Dissemination of metabolomics results: role of MetaboLights and COSMOS.
Salek RM, Haug K, Steinbeck C.
Gigascience Volume 2 (2013) p.8

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

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

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 Volume 29 (2013) p.2955-2957

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 Res Volume 41 (2013) p.d456-63

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 Biol Volume 14 (2013) p.r37

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 (Oxford) Volume 2013 (2013) p.bat029

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

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

The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.
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J Hered Volume 104 (2013) p.595-600

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 Res Volume 41 (2013) p.d936-41

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.
Mol Cell Volume 49 (2013) p.262-272

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

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.
Mol Biosyst Volume 9 (2013) p.70-76

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 Res Volume 41 (2013) p.3600-3618

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 Volume 29 (2013) p.132-134

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

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.
Mol Biosyst Volume 9 (2013) p.1576-1583

CySBGN: a Cytoscape plug-in to integrate SBGN maps.
Gonçalves E, van Iersel M, Saez-Rodriguez J.
BMC Bioinformatics Volume 14 (2013) p.17

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

Do first-time breeding females imprint on their own eggs?
Soler M, Ruiz-Castellano C, Carra LG, Ontanilla J, Martín-Galvez D.
Proc Biol Sci Volume 280 (2013) p.20122518

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 Res Volume 41 (2013) p.d171-6

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 Res Volume 41 (2013) p.827-841

The evolution of the Anopheles 16 genomes project.
Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ.
G3 (Bethesda) Volume 3 (2013) p.1191-1194

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 Biotechnol Volume 13 (2013) p.1

HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Hickey G, Paten B, Earl D, Zerbino D, Haussler D.
Bioinformatics Volume 29 (2013) p.1341-1342

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.
J Anim Ecol Volume 82 (2013) p.389-398

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

Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P.
Nat Methods Volume 10 (2013) p.1177-1184

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 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

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.
Am J Hum Genet Volume 93 (2013) p.236-248

Abstracting knowledge from the protein data bank.
Furnham N, Laskowski RA, Thornton JM.
Biopolymers Volume 99 (2013) p.183-188

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.
Nat Genet Volume 45 (2013) p.25-33

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.
Nat Genet Volume 45 (2013) p.1353-1360

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

Reuse of public genome-wide gene expression data.
Rung J, Brazma A.
Nat Rev Genet Volume 14 (2013) p.89-99

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
Lawler K, Hammond-Kosack K, Brazma A, Coulson RM.
BMC Syst Biol Volume 7 (2013) p.52

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.
J Pathol Volume 230 (2013) p.270-276

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

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.
Nat Genet Volume 45 (2013) p.501-512

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 Res Volume 41 (2013) p.d226-32

Structural, evolutionary, and assembly principles of protein oligomerization.
Levy ED, Teichmann S.
Prog Mol Biol Transl Sci Volume 117 (2013) p.25-51

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 Biol Volume 14 (2013) p.r11

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.
Biosens Bioelectron Volume 41 (2013) p.282-288

Supporting SBML as a model exchange format in software applications.
Keating SM, Le Novère N.
Methods Mol Biol Volume 1021 (2013) p.201-225

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 Res Volume 41 (2013) p.d490-8

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 Crystallogr D Biol Crystallogr Volume 69 (2013) p.2395-2402

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 Comput Biol Volume 9 (2013) p.e1003382

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 Res Volume 41 (2013) p.4549-4564

Exploiting disjointness axioms to improve semantic similarity measures.
Ferreira JD, Hastings J, Couto FM.
Bioinformatics Volume 29 (2013) p.2781-2787

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

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.
Circ Res Volume 113 (2013) p.1043-1053

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 Res Volume 41 (2013) p.d987-90

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

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 Res Volume 41 (2013) p.d530-5

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.
Nat Genet Volume 45 (2013) p.208-213

The ChEMBL database as linked open data.
Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ.
J Cheminform Volume 5 (2013) p.23

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.

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 Biol Volume 14 (2013) p.r70

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
Lahti L, Torrente A, Elo LL, Brazma A, Rung J.
Nucleic Acids Res Volume 41 (2013) p.e110

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.
Nat Genet Volume 45 (2013) p.1150-1159

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

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M.
Nucleic Acids Res Volume 41 (2013) p.e121

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 Res Volume 41 (2013) p.w601-6

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 (Oxford) Volume 2013 (2013) p.bat009

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 Volume 29 (2013) p.1103-1104

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

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

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.
Clin 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

Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences.
Doğan T, Karaçalı B.
PLoS One Volume 8 (2013) p.e75458

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.
J Proteomics Volume 87 (2013) p.134-138

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

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.
Philos Trans R Soc Lond B Biol Sci Volume 368 (2013) p.20120361

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.
Anal Chem Volume 85 (2013) p.3515-3520

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

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 Res Volume 41 (2013) p.d1063-9

Mucosal addressin cell adhesion molecule (MAdCAM-1) expression is upregulated in the cirrhotic liver and immunolocalises to the peribiliary plexus and lymphoid aggregates.
Ala A, Brown D, Khan K, Standish R, Odin JA, Fiel MI, Schiano TD, Hillan KJ, Rahman SA, Hodgson HJ, Dhillon AP.
Dig Dis Sci Volume 58 (2013) p.2528-2541

ENCODE data in the UCSC Genome Browser: year 5 update.
Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.
Nucleic Acids Res Volume 41 (2013) p.d56-63

T-cell activation induces selective changes of cellular lipidome.
Lonnberg T, Yetukuri L, Seppanen-Laakso T, Lahesmaa R, Oresic M.
Front Biosci (Elite Ed) Volume 5 (2013) p.558-573

Nutrigenomics of high fat diet induced obesity in mice suggests relationships between susceptibility to fatty liver disease and the proteasome.
Waller-Evans H, Hue C, Fearnside J, Rothwell AR, Lockstone HE, Caldérari S, Wilder SP, Cazier JB, Scott J, Gauguier D.
PLoS One Volume 8 (2013) p.e82825

From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Lönnberg T, Chen Z, Lahesmaa R.
Brief Funct Genomics Volume 12 (2013) p.471-482

Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Chen Z, Lönnberg T, Lahesmaa R.
Scand J Immunol Volume 78 (2013) p.172-180

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

The impact of mathematical modeling on the understanding of diabetes and related complications.
Ajmera I, Swat M, Laibe C, Novère NL, Chelliah V.
CPT Pharmacometrics Syst Pharmacol Volume 2 (2013) p.e54

Evolution of protein structures and interactions from the perspective of residue contact networks.
Zhang X, Perica T, Teichmann SA.
Curr Opin Struct Biol Volume 23 (2013) p.954-963

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.
Proc Natl Acad Sci U S A Volume 110 (2013) p.20212-20217

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 Res Volume 41 (2013) p.d499-507

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

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 Volume 21 (2013) p.1325-1337

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.
Nat Biotechnol Volume 31 (2013) p.126-134

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 Syst Biol Volume 7 (2013) p.116

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

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM.
Mol Biosyst Volume 9 (2013) p.1756-1764

The Ramachandran plot and protein structure validation
Laskowski RA, Furnham N, Thornton JM.
Volume (2013) p.62-75

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.
J Biomed Semantics Volume 4 (2013) p.20

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 Volume 29 (2013) p.704-710

Immunology meets genomics.
Teichmann SA.
Brief Funct Genomics Volume 12 (2013) p.469-470

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.
Mol Biosyst Volume 9 (2013) p.1620-1626

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.
J Exp Med Volume 210 (2013) p.1137-1151

Elucidating human phosphatase-substrate networks.
Li X, Wilmanns M, Thornton J, Köhn M.
Sci Signal Volume 6 (2013) p.rs10

Nouvelle avancée dans notre connaissance des facteurs génétiques contribuant aux phénotypes complexes.
Baud A, Calderari S, Mott R, Flint J, Gauguier D, Rat Genome Sequencing and Mapping Consortium.
Med Sci (Paris) Volume 29 (2013) p.671-674

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.
Nat Biotechnol Volume 31 (2013) p.1015-1022

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 (Oxford) Volume 2013 (2013) p.bat077

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 Biol Volume 11 (2013) p.e1001638

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 Comput Biol Volume 9 (2013) p.e1003242

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.
Mol Cell Volume 50 (2013) p.601-608

The annotation-enriched non-redundant patent sequence databases.
Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R.
Database (Oxford) Volume 2013 (2013) p.bat005

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.
Nat Genet Volume 45 (2013) p.767-775

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.
J Pathol 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 Res Volume 73 (2013) p.4872-4884

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins Volume 81 (2013) p.583-591

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

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

ROCK: a resource for integrative breast cancer data analysis.
Ur-Rehman S, Gao Q, Mitsopoulos C, Zvelebil M.
Breast Cancer Res Treat Volume 139 (2013) p.907-921

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 Comput Biol Volume 9 (2013) p.e1003253

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.
J Cheminform Volume 5 (2013) p.3

The International Nucleotide Sequence Database Collaboration.
Nakamura Y, Cochrane G, Karsch-Mizrachi I, International Nucleotide Sequence Database Collaboration.
Nucleic Acids Res Volume 41 (2013) p.d21-4

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 Volume 63 (2013) p.41-49

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.
Mol Biosyst Volume 9 (2013) p.1411-1422

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 Res Volume 41 (2013) p.d30-5

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.
Infect Immun Volume 81 (2013) p.723-732

Detecting and comparing non-coding RNAs in the high-throughput era.
Bussotti G, Notredame C, Enright AJ.
Int J Mol Sci Volume 14 (2013) p.15423-15458

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 Ecol Volume 13 (2013) p.16

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.
Front Genet Volume 4 (2013) p.64

IPD--the Immuno Polymorphism Database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG.
Nucleic Acids Res Volume 41 (2013) p.d1234-40

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 Crystallogr D Biol Crystallogr Volume 69 (2013) p.710-721

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

The IMGT/HLA database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic Acids Res Volume 41 (2013) p.d1222-7

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 Genet Volume 9 (2013) p.e1003730

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

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

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.
Nat Methods Volume 10 (2013) p.1093-1095

Brain: biomedical knowledge manipulation.
Croset S, Overington JP, Rebholz-Schuhmann D.
Bioinformatics Volume 29 (2013) p.1238-1239

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.
Biochem Soc Trans Volume 41 (2013) p.1265-1271

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.
Mol Cell Biol Volume 33 (2013) p.3150-3165

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

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.
Nat Genet Volume 45 (2013) p.664-669

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 Res Volume 41 (2013) p.d48-55

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 Volume 44 (2013) p.1609-1615

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.
Mamm Genome Volume 24 (2013) p.358-375

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

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

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

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

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 Res Volume 41 (2013) p.w597-600

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.
Mol Cell Proteomics Volume 12 (2013) p.3026-3035

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.
Genet Epidemiol Volume 37 (2013) p.495-503

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.
Nat Methods Volume 10 (2013) p.228-238

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

Proteomics data exchange and storage: the need for common standards and public repositories.
Jiménez RC, Vizcaíno JA.
Methods Mol Biol Volume 1007 (2013) p.317-333

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC.
Genome Biol Volume 14 (2013) p.r7

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.
Proc Natl Acad Sci U S A Volume 110 (2013) p.4009-4014

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

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.
Curr Opin Struct Biol Volume 23 (2013) p.443-450

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

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.
Circ Cardiovasc Genet Volume 6 (2013) p.498-504

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).
Hum Mol Genet Volume 22 (2013) p.4653-4660

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 (Oxford) Volume 2013 (2013) p.bat066

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

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

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.
J Biomed Semantics Volume 4 (2013) p.28

2012

Analyzing protein-protein interaction networks.
Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE.
J Proteome Res Volume 11 (2012) p.2014-2031

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

PRIDE: quality control in a proteomics data repository.
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H.
Database (Oxford) Volume 2012 (2012) p.bas004

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.
J Pathol Volume 226 (2012) p.703-712

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

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 Volume 16 (2012) p.431-442

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.
Nat Methods Volume 9 (2012) p.345-350

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.
Am J Hum Genet Volume 91 (2012) p.1022-1032

UniProtKB amid the turmoil of plant proteomics research.
Schneider M, UniProt Consortium, Poux S.
Front Plant Sci Volume 3 (2012) p.270

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

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

graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P.
Bioinformatics Volume 28 (2012) p.1665-1667

Estimation of alternative splicing variability in human populations.
Gonzàlez-Porta M, Calvo M, Sammeth M, Guigó R.
Genome Res Volume 22 (2012) p.528-538

Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.
Emery L, Whelan S, Hirschi KD, Pittman JK.
Front Plant Sci Volume 3 (2012) p.1

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 Volume 335 (2012) p.823-828

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

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.
Roux J, Gonzàlez-Porta M, Robinson-Rechavi M.
Nucleic Acids Res Volume 40 (2012) p.5890-5900

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 Res Volume 40 (2012) p.d841-6

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

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.
Mol Cell Proteomics Volume 11 (2012) p.m111.014381

Improvements in the Protein Identifier Cross-Reference service.
Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA.
Nucleic Acids Res Volume 40 (2012) p.w276-80

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

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 (Basel) Volume 4 (2012) p.1180-1211

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 Res Volume 40 (2012) p.d735-41

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

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.
Mol Cell Proteomics Volume 11 (2012) p.1682-1689

Toward community standards in the quest for orthologs.
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J, Quest for Orthologs Consortium.
Bioinformatics Volume 28 (2012) p.900-904

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.
J Proteome Res Volume 11 (2012) p.1412-1419

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 Res Volume 40 (2012) p.d565-70

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

Paralogous annotation of disease-causing variants in long QT syndrome genes.
Ware JS, Walsh R, Cunningham F, Birney E, Cook SA.
Hum Mutat Volume 33 (2012) p.1188-1191

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 Volume 20 (2012) p.205-214

Implementing an X-ray validation pipeline for the Protein Data Bank.
Gore S, Velankar S, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 68 (2012) p.478-483

The 2010 cryo-EM modeling challenge.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W.
Biopolymers Volume 97 (2012) p.651-654

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 Volume 20 (2012) p.350-363

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 Res Volume 22 (2012) p.602-610

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.
Mamm Genome Volume 23 (2012) p.641-652

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.
Proc Natl Acad Sci U S A Volume 109 (2012) p.1204-1209

Three hybrid classifiers for the detection of emotions in suicide notes.
Liakata M, Kim JH, Saha S, Hastings J, Rebholz-Schuhmann D.
Biomed Inform Insights Volume 5 (2012) p.175-184

The Protein Data Bank at 40: reflecting on the past to prepare for the future.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure Volume 20 (2012) p.391-396

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.
Nat Struct Mol Biol Volume 19 (2012) p.1203-1207

Toxicology ontology perspectives.
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C.
ALTEX Volume 29 (2012) p.139-156

Food for thought ... A toxicology ontology roadmap.
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C.
ALTEX Volume 29 (2012) p.129-137

Requirements for semantic biobanks.
Andrade AQ, Kreuzthaler M, Hastings J, Krestyaninova M, Schulz S.
Stud Health Technol Inform Volume 180 (2012) p.569-573

Ontologies for human behavior analysis and their application to clinical data.
Hastings J, Schulz S.
Int Rev Neurobiol Volume 103 (2012) p.89-107

Process attributes in bio-ontologies.
Andrade AQ, Blondé W, Hastings J, Schulz S.
BMC Bioinformatics Volume 13 (2012) p.217

Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 40 (2012) p.d71-5

Open data for drug discovery: learning from the biological community.
Hersey A, Senger S, Overington JP.
Future Med Chem Volume 4 (2012) p.1865-1867

The International Nucleotide Sequence Database Collaboration.
Karsch-Mizrachi I, Nakamura Y, Cochrane G, International Nucleotide Sequence Database Collaboration.
Nucleic Acids Res 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 Res Volume 40 (2012) p.d54-6

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.
Stand Genomic Sci Volume 7 (2012) p.153-158

Genome-wide meta-analysis of common variant differences between men and women.
Boraska V, Jerončić A, Colonna V, Southam L, Nyholt DR, Rayner NW, Perry JR, Toniolo D, Albrecht E, Ang W, Bandinelli S, Barbalic M, Barroso I, Beckmann JS, Biffar R, Boomsma D, Campbell H, Corre T, Erdmann J, Esko T, Fischer K, Franceschini N, Frayling TM, Girotto G, Gonzalez JR, Harris TB, Heath AC, Heid IM, Hoffmann W, Hofman A, Horikoshi M, Zhao JH, Jackson AU, Hottenga JJ, Jula A, Kähönen M, Khaw KT, Kiemeney LA, Klopp N, Kutalik Z, Lagou V, Launer LJ, Lehtimäki T, Lemire M, Lokki ML, Loley C, Luan J, Mangino M, Mateo Leach I, Medland SE, Mihailov E, Montgomery GW, Navis G, Newnham J, Nieminen MS, Palotie A, Panoutsopoulou K, Peters A, Pirastu N, Polasek O, Rehnström K, Ripatti S, Ritchie GR, Rivadeneira F, Robino A, Samani NJ, Shin SY, Sinisalo J, Smit JH, Soranzo N, Stolk L, Swinkels DW, Tanaka T, Teumer A, Tönjes A, Traglia M, Tuomilehto J, Valsesia A, van Gilst WH, van Meurs JB, Smith AV, Viikari J, Vink JM, Waeber G, Warrington NM, Widen E, Willemsen G, Wright AF, Zanke BW, Zgaga L, Wellcome Trust Case Control Consortium, Boehnke M, d'Adamo AP, de Geus E, Demerath EW, den Heijer M, Eriksson JG, Ferrucci L, Gieger C, Gudnason V, Hayward C, Hengstenberg C, Hudson TJ, Järvelin MR, Kogevinas M, Loos RJ, Martin NG, Metspalu A, Pennell CE, Penninx BW, Perola M, Raitakari O, Salomaa V, Schreiber S, Schunkert H, Spector TD, Stumvoll M, Uitterlinden AG, Ulivi S, van der Harst P, Vollenweider P, Völzke H, Wareham NJ, Wichmann HE, Wilson JF, Rudan I, Xue Y, Zeggini E.
Hum Mol Genet Volume 21 (2012) p.4805-4815

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.
J Proteomics Volume 75 (2012) p.2269-2274

Revisiting the training of logic models of protein signaling networks with ASP
Videla S, Guziolowski C, Eduati F, Thiele S, Grabe N, Saez-Rodriguez J, Siegel A.
Volume (2012) p.342-361

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

Cheminformatics
Wegner JK, Sterling A, Guha R, Bender A, Faulon J-L, Hastings J, O'Boyle N, Overington J, Van Vlijmen H, Willighagen E.
Commun ACM Volume 55 (2012) p.65-75

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.
Mol Inform Volume 31 (2012) p.599-609

A novel nonribose agonist, LUF5834, engages residues that are distinct from those of adenosine-like ligands to activate the adenosine A(2a) receptor.
Lane JR, Klein Herenbrink C, van Westen GJ, Spoorendonk JA, Hoffmann C, IJzerman AP.
Mol Pharmacol Volume 81 (2012) p.475-487

Global analysis of small molecule binding to related protein targets.
Kruger FA, Overington JP.
PLoS Comput Biol Volume 8 (2012) p.e1002333

Mapping small molecule binding data to structural domains.
Kruger FA, Rostom R, Overington JP.
BMC Bioinformatics Volume 13 Suppl 17 (2012) p.s11

Toxicogenomics Investigation Under the eTOX Project
Taboureau O, Hersey A, Audouze K, Gautier L, Jacobsen UP, Akhtar R, Atkinson F, Overington JP, Brunak S.
J Pharmacogenomics Pharmacoproteomics Volume S7 (2012) p.1-5

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data.
van Westen GJ, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.
J Med Chem Volume 55 (2012) p.7010-7020

Three "hotspots" important for adenosine A(2B) receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop.
Peeters MC, Li Q, van Westen GJ, Ijzerman AP.
Purinergic Signal Volume 8 (2012) p.23-38

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.
Nat Methods Volume 9 (2012) p.245-253

Current challenges in genome annotation through structural biology and bioinformatics.
Furnham N, de Beer TA, Thornton JM.
Curr Opin Struct Biol Volume 22 (2012) p.594-601

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 Biol Volume 13 (2012) p.r53

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.
Mol Syst Biol Volume 8 (2012) p.603

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 Volume 28 (2012) p.2311-2317

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 Res Volume 22 (2012) p.1658-1667

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 Res Volume 40 (2012) p.d64-70

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 Res Volume 40 (2012) p.d776-82

ELIXIR: a distributed infrastructure for European biological data.
Crosswell LC, Thornton JM.
Trends Biotechnol Volume 30 (2012) p.241-242

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

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.
Mol Ther Volume 20 (2012) p.1737-1749

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 Res Volume 40 (2012) p.d43-7

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

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.
Mol Biosyst Volume 8 (2012) p.1571-1584

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.
Nat Biotechnol Volume 30 (2012) p.135-137

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.
Antimicrob Agents Chemother Volume 56 (2012) p.1364-1375

Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting.
Zheng-Bradley X, Flicek P.
Hum Mutat Volume 33 (2012) p.1016-1019

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 Comput Biol Volume 8 (2012) p.e1002403

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 Res Volume 22 (2012) p.1798-1812

The future of DNA sequence archiving.
Cochrane G, Cook CE, Birney E.
Gigascience Volume 1 (2012) p.2

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 Res Volume 22 (2012) p.9-24

Journey to the genetic interior. Interview by Stephen S Hall.
Birney E.
Sci Am Volume 307 (2012) p.80-2, 84

The making of ENCODE: Lessons for big-data projects.
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Nature Volume 489 (2012) p.49-51

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

A combined functional annotation score for non-synonymous variants.
Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E.
Hum Hered Volume 73 (2012) p.47-51

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E.
Bioinformatics Volume 28 (2012) p.1086-1092

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

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
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PLoS One Volume 7 (2012) p.e50881

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 Biol Volume 13 (2012) p.r48

Women in science.
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Genome Biol Volume 13 (2012) p.148

Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
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PLoS One Volume 7 (2012) p.e33101

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.
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Integr Biol (Camb) Volume 4 (2012) p.1038-1048

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
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BMC Syst Biol Volume 6 (2012) p.29

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 Biol Volume 13 (2012) p.r49

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

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium.
Nature Volume 487 (2012) p.94-98

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

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 Res Volume 40 (2012) p.d1077-81

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 Res Volume 40 (2012) p.d91-7

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 Res Volume 22 (2012) p.2376-2384

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

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.
Dev Cell Volume 23 (2012) p.265-279

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.
J Pathol Volume 228 (2012) p.274-285

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 Res Volume 40 (2012) p.d729-34

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 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 Sci Volume 21 (2012) p.769-785

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 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 Res Volume 40 (2012) p.d1313-7

Tools for mapping high-throughput sequencing data.
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Bioinformatics Volume 28 (2012) p.3169-3177

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.
Wimalaratne SM, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B.
Bioinformatics Volume 28 (2012) p.448-450

Bioinformatics meets user-centred design: a perspective.
Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C.
PLoS Comput Biol Volume 8 (2012) p.e1002554

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 Res Volume 40 (2012) p.d84-90

Large-scale analysis of microRNA evolution.
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BMC Genomics Volume 13 (2012) p.218

In vivo conditions to identify Prkci phosphorylation targets using the analog-sensitive kinase method in zebrafish.
Cibrián Uhalte E, Kirchner M, Hellwig N, Allen JJ, Donat S, Shokat KM, Selbach M, Abdelilah-Seyfried S.
PLoS One Volume 7 (2012) p.e40000

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.
Nat Methods Volume 9 (2012) p.459-462

MyDas, an extensible Java DAS server.
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PLoS One Volume 7 (2012) p.e44180

Gene expression dynamics after murine pancreatitis unveils novel roles for Hnf1α in acinar cell homeostasis.
Molero X, Vaquero EC, Flández M, González AM, Ortiz MÁ, Cibrián-Uhalte E, Servitja JM, Merlos A, Juanpere N, Massumi M, Skoudy A, Macdonald R, Ferrer J, Real FX.
Gut Volume 61 (2012) p.1187-1196

Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.
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Lancet Volume 380 (2012) p.815-823

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.
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J Biol Chem Volume 287 (2012) p.29516-29528

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
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Circulation Volume 125 (2012) p.2751-2761

Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery.
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Genome Med Volume 4 (2012) p.37

The Gene Ontology: enhancements for 2011.
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Nucleic Acids Res Volume 40 (2012) p.d559-64

The Origin and Function of Anti-Fungal Peptides in C. elegans: Open Questions.
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Front Immunol Volume 3 (2012) p.237

Automatic categorization of diverse experimental information in the bioscience literature.
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BMC Bioinformatics Volume 13 (2012) p.16

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.
Eur J Pharm Sci Volume 45 (2012) p.515-520

PSI-Search: iterative HOE-reduced profile SSEARCH searching.
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Bioinformatics Volume 28 (2012) p.1650-1651

Modeling signaling networks using high-throughput phospho-proteomics.
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Adv Exp Med Biol Volume 736 (2012) p.19-57

Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study.
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BMC Genomics Volume 13 (2012) p.334

GrameneMart: the BioMart data portal for the Gramene project.
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Database (Oxford) Volume 2012 (2012) p.bar056

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
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Mol Cell Volume 47 (2012) p.183-192

MetaBase--the wiki-database of biological databases.
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Nucleic Acids Res Volume 40 (2012) p.d1250-4

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.
Nat Genet Volume 44 (2012) p.121-126

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

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.
Nat Genet Volume 44 (2012) p.981-990

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.
Nat Genet Volume 44 (2012) p.328-333

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.
Nat Genet Volume 44 (2012) p.3-5

Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells.
Hebenstreit D, Deonarine A, Babu MM, Teichmann SA.
Curr Opin Cell Biol Volume 24 (2012) p.350-358

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 Mol Biol Volume 786 (2012) p.3-19

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.
Nat Struct Mol Biol Volume 19 (2012) p.854-860

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.
Nat Genet Volume 44 (2012) p.1131-1136

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

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 Volume 28 (2012) p.246-253

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

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 Res Volume 22 (2012) p.2163-2175

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.
Nat Biotechnol Volume 30 (2012) p.224-226

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.
Nat Genet Volume 44 (2012) p.1336-1340

MageComet--web application for harmonizing existing large-scale experiment descriptions.
Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.
Bioinformatics Volume 28 (2012) p.1402-1403

Evolution of oligomeric state through geometric coupling of protein interfaces.
Perica T, Chothia C, Teichmann SA.
Proc Natl Acad Sci U S A Volume 109 (2012) p.8127-8132

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.
Biochem Soc Trans Volume 40 (2012) p.475-491

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

A database for chemical proteomics: ChEBI.
de Matos P, Adams N, Hastings J, Moreno P, Steinbeck C.
Methods Mol Biol Volume 803 (2012) p.273-296

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

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 Res Volume 40 (2012) p.d754-60

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 Volume 8 (2012) p.757-760

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

Probing the diverse landscape of protein flexibility and binding.
Marsh JA, Teichmann SA, Forman-Kay JD.
Curr Opin Struct Biol Volume 22 (2012) p.643-650

Structure-based classification and ontology in chemistry.
Hastings J, Magka D, Batchelor C, Duan L, Stevens R, Ennis M, Steinbeck C.
J Cheminform Volume 4 (2012) p.8

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.
Hum Genet Volume 131 (2012) p.665-674

Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC.
PLoS Comput Biol Volume 8 (2012) p.e1002789

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
Levy ED, De S, Teichmann SA.
Proc Natl Acad Sci U S A Volume 109 (2012) p.20461-20466

Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.
Teichmann SA, Wigge PA, Charoensawan V.
Cell Cycle Volume 11 (2012) p.4487-4488

Accessing and using chemical property databases.
Hastings J, Josephs Z, Steinbeck C.
Methods Mol Biol Volume 929 (2012) p.193-219

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

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 Genet Volume 8 (2012) p.e1002704

Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles.
Wang T, Schiffels D, Cuesta SM, Fygenson DK, Seeman NC.
J Am Chem Soc Volume 134 (2012) p.1606-1616

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 J Volume 26 (2012) p.2145-2153

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N.
Mol Biol Evol 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.
Mol Biol Evol Volume 29 (2012) p.2889-2893

Bioimage informatics: a new category in Bioinformatics.
Peng H, Bateman A, Valencia A, Wren JD.
Bioinformatics Volume 28 (2012) p.1057

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

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.
Mol Cell Volume 46 (2012) p.871-883

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 Res Volume 40 (2012) p.4725-4725

The YARHG domain: an extracellular domain in search of a function.
Coggill P, Bateman A.
PLoS One Volume 7 (2012) p.e35575

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.
J Biol Rhythms Volume 27 (2012) p.328-332

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

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Bateman A.
Nucleic Acids Res Volume 40 (2012) p.d343-50

Recognition of medication information from discharge summaries using ensembles of classifiers.
Doan S, Collier N, Xu H, Pham HD, Tu MP.
BMC Med Inform Decis Mak Volume 12 (2012) p.36

Uncovering text mining: a survey of current work on web-based epidemic intelligence.
Collier N.
Glob Public Health Volume 7 (2012) p.731-749

GENI-DB: a database of global events for epidemic intelligence.
Collier N, Doan S.
Bioinformatics Volume 28 (2012) p.1186-1188

Making your database available through Wikipedia: the pros and cons.
Finn RD, Gardner PP, Bateman A.
Nucleic Acids Res Volume 40 (2012) p.d9-12

A network-oriented perspective on cardiac calcium signaling.
George CH, Parthimos D, Silvester NC.
Am J Physiol Cell Physiol Volume 303 (2012) p.c897-910

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 (Oxford) Volume 2012 (2012) p.bar059

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 Crystallogr Sect F Struct Biol Cryst Commun Volume 68 (2012) p.253-258

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 Res Volume 40 (2012) p.d445-52

State-time spectrum of signal transduction logic models.
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.
Phys Biol Volume 9 (2012) p.045003

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 Volume 28 (2012) p.3163-3165

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 Syst Biol Volume 6 (2012) p.133

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 Res Volume 40 (2012) p.d1100-7

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 Res Volume 40 (2012) p.d695-9

In contrast to HIV, KIR3DS1 does not influence outcome in HTLV-1 retroviral infection.
O'Connor GM, Seich Al Basatena NK, Olavarria V, MacNamara A, Vine A, Ying Q, Hisada M, Galvão-Castro B, Asquith B, McVicar DW.
Hum Immunol Volume 73 (2012) p.783-787

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.
Hum Mol Genet Volume 21 (2012) p.5202-5208

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.
Proc Natl Acad Sci U S A Volume 109 (2012) p.e944-53

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Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L.
Drug Discov Today Volume 17 Suppl (2012) p.s3-15

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 Volume 20 (2012) p.227-236

LibKiSAO: a Java library for Querying KiSAO.
Zhukova A, Adams R, Laibe C, Le Novère N.
BMC Res Notes Volume 5 (2012) p.520

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A, Vilella AJ, Goldman N.
Bioinformatics Volume 28 (2012) p.1684-1691

Error-correcting properties of the SOLiD Exact Call Chemistry.
Massingham T, Goldman N.
BMC Bioinformatics Volume 13 (2012) p.145

All Your Base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.
Genome Biol 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 (Oxford) Volume 2012 (2012) p.bas003

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.
Int J Data Min Bioinform Volume 6 (2012) p.571-584

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival.
Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P.
Genome Med Volume 4 (2012) p.76

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 (Oxford) Volume 2012 (2012) p.bas019

Metagenomic analysis: the challenge of the data bonanza.
Hunter CI, Mitchell A, Jones P, McAnulla C, Pesseat S, Scheremetjew M, Hunter S.
Brief Bioinform Volume 13 (2012) p.743-746

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

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 Res Volume 40 (2012) p.d306-12

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome.
Albers CA, Paul DS, Schulze H, Freson K, Stephens JC, Smethurst PA, Jolley JD, Cvejic A, Kostadima M, Bertone P, Breuning MH, Debili N, Deloukas P, Favier R, Fiedler J, Hobbs CM, Huang N, Hurles ME, Kiddle G, Krapels I, Nurden P, Ruivenkamp CA, Sambrook JG, Smith K, Stemple DL, Strauss G, Thys C, van Geet C, Newbury-Ecob R, Ouwehand WH, Ghevaert C.
Nat Genet Volume 44 (2012) p.435-9, s1-2

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 (Oxford) Volume 2012 (2012) p.bas036

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 (Oxford) Volume 2012 (2012) p.bar068

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs.
Manakov SA, Morton A, Enright AJ, Grant SG.
Front Neurosci Volume 6 (2012) p.156

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

The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium.
Nature Volume 485 (2012) p.635-641

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.
Jupp S, Stevens R, Hoehndorf R.
J Biomed Semantics Volume 3 Suppl 1 (2012) p.s3

Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets.
Jupe S, Akkerman JW, Soranzo N, Ouwehand WH.
J Thromb Haemost Volume 10 (2012) p.2399-2402

Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression.
Gonçalves E, Pereira R, Rocha I, Rocha M.
J Comput Biol Volume 19 (2012) p.102-114

MACiE: exploring the diversity of biochemical reactions.
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.
Nucleic Acids Res Volume 40 (2012) p.d783-9

An integrated encyclopedia of DNA elements in the human genome.
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Nature Volume 489 (2012) p.57-74

NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression.
Reynolds N, Salmon-Divon M, Dvinge H, Hynes-Allen A, Balasooriya G, Leaford D, Behrens A, Bertone P, Hendrich B.
EMBO J Volume 31 (2012) p.593-605

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors.
Metzakopian E, Lin W, Salmon-Divon M, Dvinge H, Andersson E, Ericson J, Perlmann T, Whitsett JA, Bertone P, Ang SL.
Development Volume 139 (2012) p.2625-2634

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND.
PLoS Comput Biol Volume 8 (2012) p.e1002330

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.
Brief Bioinform Volume 13 (2012) p.383-389

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.
Nat Protoc Volume 7 (2012) p.500-507

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM.
Bioinformatics Volume 28 (2012) p.1001-1008

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.
Juty N, Le Novère N, Laibe C.
Nucleic Acids Res Volume 40 (2012) p.d580-6

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 (Austin) Volume 6 (2012) p.71-74

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.

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 Volume 28 (2012) p.2693-2695

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.
Plant Cell Volume 24 (2012) p.3530-3557

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 Res Volume 40 (2012) p.d290-301

NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment.
Reynolds N, Latos P, Hynes-Allen A, Loos R, Leaford D, O'Shaughnessy A, Mosaku O, Signolet J, Brennecke P, Kalkan T, Costello I, Humphreys P, Mansfield W, Nakagawa K, Strouboulis J, Behrens A, Bertone P, Hendrich B.
Cell Stem Cell Volume 10 (2012) p.583-594

Molecular interaction databases.
Orchard S.
Proteomics Volume 12 (2012) p.1656-1662

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 Mol Biol Volume 856 (2012) p.513-527

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 Genet Volume 8 (2012) p.e1002639

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

De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.
Nat Genet Volume 44 (2012) p.226-232

2011

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

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

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 Genet Volume 7 (2011) p.e1001316

Probing the links between in vitro potency, ADMET and physicochemical parameters.
Gleeson MP, Hersey A, Montanari D, Overington J.
Nat Rev Drug Discov Volume 10 (2011) p.197-208

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.
Biochem Soc Trans 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.
Nat Rev Drug Discov Volume 10 (2011) p.661-669

Omics technologies, data and bioinformatics principles.
Schneider MV, Orchard S.
Methods Mol Biol Volume 719 (2011) p.3-30

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

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.
Nat Genet Volume 43 (2011) p.948-955

Unintended consequences of existential quantifications in biomedical ontologies.
Boeker M, Tudose I, Hastings J, Schober D, Schulz S.
BMC Bioinformatics Volume 12 (2011) p.456

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 Res Volume 39 (2011) p.d800-6

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 Res Volume 39 (2011) p.d58-65

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

Cross-product extensions of the Gene Ontology.
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J.
J Biomed Inform Volume 44 (2011) p.80-86

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.
Mol Cell Proteomics Volume 10 (2011) p.r110.000133

Developing a kidney and urinary pathway knowledge base.
Jupp S, Klein J, Schanstra J, Stevens R.
J Biomed Semantics Volume 2 Suppl 2 (2011) p.s7

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

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.
Mol Syst Biol Volume 7 (2011) p.525

The Reactome BioMart.
Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.
Database (Oxford) Volume 2011 (2011) p.bar031

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

Integrating systems biology models and biomedical ontologies.
Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV.
BMC Syst Biol Volume 5 (2011) p.124

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.
J Biomed Semantics Volume 2 Suppl 5 (2011) p.s11

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 (Oxford) Volume 2011 (2011) p.bar047

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

Preparing molecular interaction data for publication.
Orchard S, Hermjakob H.
Methods Mol Biol Volume 694 (2011) p.229-236

Data standardization by the HUPO-PSI: how has the community benefitted?
Orchard S, Hermjakob H.
Methods Mol Biol Volume 696 (2011) p.149-160

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.
J Biomol NMR Volume 49 (2011) p.27-38

In vivo expression of human T-lymphotropic virus type 1 basic leucine-zipper protein generates specific CD8+ and CD4+ T-lymphocyte responses that correlate with clinical outcome.
Hilburn S, Rowan A, Demontis MA, MacNamara A, Asquith B, Bangham CR, Taylor GP.
J Infect Dis Volume 203 (2011) p.529-536

KIR2DL2 enhances protective and detrimental HLA class I-mediated immunity in chronic viral infection.
Seich Al Basatena NK, Macnamara A, Vine AM, Thio CL, Astemborski J, Usuku K, Osame M, Kirk GD, Donfield SM, Goedert JJ, Bangham CR, Carrington M, Khakoo SI, Asquith B.
PLoS Pathog Volume 7 (2011) p.e1002270

Short communication an interferon-γ ELISPOT assay with two cytotoxic T cell epitopes derived from HTLV-1 tax region 161-233 discriminates HTLV-1-associated myelopathy/tropical spastic paraparesis patients from asymptomatic HTLV-1 carriers in a Peruvian population.
Best I, López G, Talledo M, MacNamara A, Verdonck K, González E, Tipismana M, Asquith B, Gotuzzo E, Vanham G, Clark D.
AIDS Res Hum Retroviruses Volume 27 (2011) p.1207-1212

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.
Mol Cell Proteomics Volume 10 (2011) p.o111.015446

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 Res Volume 39 (2011) p.d402-10

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

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 Volume 27 (2011) p.2616-2617

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.
Mol Cell Proteomics Volume 10 (2011) p.m111.008490

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

Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts.
Malone CM, Domaschenz R, Amagase Y, Dunham I, Murai K, Jones PH.
Exp Cell Res Volume 317 (2011) p.1590-1602

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.
Analyst Volume 136 (2011) p.4013-4019

Computational biology for ageing.
Wieser D, Papatheodorou I, Ziehm M, Thornton JM.
Philos Trans R Soc Lond B Biol Sci Volume 366 (2011) p.51-63

A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium.
PLoS Biol Volume 9 (2011) p.e1001046

1,000 structures and more from the MCSG.
Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA.
BMC Struct Biol Volume 11 (2011) p.2

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.
FEBS J Volume 278 (2011) p.3835-3845

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.
Mol Syst Biol Volume 7 (2011) p.502

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 Res Volume 39 (2011) p.d420-6

A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics Volume 27 (2011) p.867-869

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 Res Volume 39 (2011) p.d1002-4

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 Genet Volume 7 (2011) p.e1002270

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

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philos Trans R Soc Lond B Biol Sci Volume 366 (2011) p.6-8

How the gene ontology evolves.
Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J.
BMC Bioinformatics Volume 12 (2011) p.325

Deciphering the colon cancer genes--report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010.
Kohonen-Corish MR, Macrae F, Genuardi M, Aretz S, Bapat B, Bernstein IT, Burn J, Cotton RG, den Dunnen JT, Frebourg T, Greenblatt MS, Hofstra R, Holinski-Feder E, Lappalainen I, Lindblom A, Maglott D, Møller P, Morreau H, Möslein G, Sijmons R, Spurdle AB, Tavtigian S, Tops CM, Weber TK, de Wind N, Woods MO, Contributors to the InSiGHT-HVP Workshop.
Hum Mutat Volume 32 (2011) p.491-494

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.
Proc Math Phys Eng Sci Volume 467 (2011) p.2084-2101

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.
J Tissue Eng Regen Med Volume 5 (2011) p.505-519

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 Volume 27 (2011) p.973-979

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 Volume 27 (2011) p.1001-1008

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.
Nat Methods Volume 8 (2011) p.528-529

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 Res Notes Volume 4 (2011) p.313

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

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 Volume 27 (2011) p.589-591

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

Chromatin and heritability: how epigenetic studies can complement genetic approaches.
Birney E.
Trends Genet Volume 27 (2011) p.172-176

Methods and strategies for gene structure curation in WormBase.
Williams GW, Davis PA, Rogers AS, Bieri T, Ozersky P, Spieth J.
Database (Oxford) Volume 2011 (2011) p.baq039

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 Biol Volume 12 (2011) p.402

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 Biol Volume 12 (2011) p.r81

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 (Oxford) Volume 2011 (2011) p.bar041

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

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 (Oxford) Volume 2011 (2011) p.bar030

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.
Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F.
BMC Microbiol Volume 11 (2011) p.105

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 Comput Biol Volume 7 (2011) p.e1001099

Crowdsourcing network inference: the DREAM predictive signaling network challenge.
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.
Sci Signal Volume 4 (2011) p.mr7

Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
Sci Signal Volume 4 (2011) p.pe10

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome.
Albers CA, Cvejic A, Favier R, Bouwmans EE, Alessi MC, Bertone P, Jordan G, Kettleborough RN, Kiddle G, Kostadima M, Read RJ, Sipos B, Sivapalaratnam S, Smethurst PA, Stephens J, Voss K, Nurden A, Rendon A, Nurden P, Ouwehand WH.
Nat Genet Volume 43 (2011) p.735-737

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

Creating a buzz about insect genomes.
Robinson GE, Hackett KJ, Purcell-Miramontes M, Brown SJ, Evans JD, Goldsmith MR, Lawson D, Okamuro J, Robertson HM, Schneider DJ.
Science Volume 331 (2011) p.1386

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

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.
J Cheminform Volume 3 (2011) p.37

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

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

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

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

The Protein Data Bank in Europe (PDBe): bringing structure to biology.
Velankar S, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 67 (2011) p.324-330

Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman HM, Chiu W.
Pac Symp Biocomput Volume (2011) p.369-373

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

Artificial neural network analysis of circulating tumor cells in metastatic breast cancer patients.
Giordano A, Giuliano M, De Laurentiis M, Eleuteri A, Iorio F, Tagliaferri R, Hortobagyi GN, Pusztai L, De Placido S, Hess K, Cristofanilli M, Reuben JM.
Breast Cancer Res Treat Volume 129 (2011) p.451-458

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 Biol Volume 9 (2011) p.e1001091

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.
Belcastro V, Siciliano V, Gregoretti F, Mithbaokar P, Dharmalingam G, Berlingieri S, Iorio F, Oliva G, Polishchuck R, Brunetti-Pierri N, di Bernardo D.
Nucleic Acids Res Volume 39 (2011) p.8677-8688

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 Res Volume 7 (2011) p.1-8

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 Res Notes Volume 4 (2011) p.272

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 Res Volume 21 (2011) p.1757-1767

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

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 Volume 27 (2011) p.2156-2158

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 Res Volume 39 (2011) p.d691-7

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses.
Vilella AJ, Birney E, Flicek P, Herrero J.
Genome Biol Volume 12 (2011) p.401

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.
Syst Biol Volume 60 (2011) p.161-174

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 Biol Volume 11 (2011) p.104

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory.
Splendiani A, Gündel M, Austyn JM, Cavalieri D, Scognamiglio C, Brandizi M.
Brief Bioinform Volume 12 (2011) p.562-575

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.
Kosiol C, Goldman N.
J Mol Biol Volume 411 (2011) p.910-923

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

ontoCAT: an R package for ontology traversal and search.
Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M.
Bioinformatics Volume 27 (2011) p.2468-2470

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

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 Volume 17 (2011) p.578-594

UniProt Knowledgebase: a hub of integrated protein data.
Magrane M, Consortium U.
Database (Oxford) Volume 2011 (2011) p.bar009

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited.
Hess J, Goldman N.
PLoS One Volume 6 (2011) p.e22783

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.
Int J Legal Med Volume 125 (2011) p.629-636

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 Res Volume 21 (2011) p.2224-2241

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.
Nat Genet Volume 43 (2011) p.712-714

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 Biol Volume 12 (2011) p.r84

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.
Proc Natl Acad Sci U S A Volume 108 (2011) p.11983-11988

Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.
Genome Res Volume 21 (2011) p.734-740

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 Res Volume 39 (2011) p.d28-31

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 Res Volume 21 (2011) p.456-464

Assemblies: the good, the bad, the ugly.
Birney E.
Nat Methods Volume 8 (2011) p.59-60

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.
Physiol Genomics Volume 43 (2011) p.711-725

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic Acids Res Volume 39 (2011) p.d214-9

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

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

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

New developments on the cheminformatics open workflow environment CDK-Taverna.
Truszkowski A, Jayaseelan KV, Neumann S, Willighagen EL, Zielesny A, Steinbeck C.
J Cheminform Volume 3 (2011) p.54

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 Volume 19 (2011) p.1395-1412

EST analysis pipeline: use of distributed computing resources.
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Methods Mol Biol Volume 722 (2011) p.103-120

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 Expr Patterns Volume 11 (2011) p.334-344

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

The sequence read archive.
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration.
Nucleic Acids Res Volume 39 (2011) p.d19-21

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.
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Nucleic Acids Res Volume 39 (2011) p.d1-6

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 Evol Biol 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

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 (Oxford) Volume 2011 (2011) p.baq027

Retroactivity as a Criterion to Define Modules in Signaling Networks
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Proteomic temporal profile of human brain endothelium after oxidative stress.
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Stroke Volume 42 (2011) p.37-43

PRIDE and "Database on Demand" as valuable tools for computational proteomics.
Vizcaíno JA, Reisinger F, Côté R, Martens L.
Methods Mol Biol Volume 696 (2011) p.93-105

Submitting proteomics data to PRIDE using PRIDE Converter.
Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.
Methods Mol Biol Volume 694 (2011) p.237-253

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

Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space.
van der Horst E, Peironcely JE, van Westen GJ, van den Hoven OO, Galloway WR, Spring DR, Wegner JK, van Vlijmen HW, Ijzerman AP, Overington JP, Bender A.
Curr Top Med Chem Volume 11 (2011) p.1964-1977

The IMGT/HLA database.
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Nucleic Acids Res Volume 39 (2011) p.d1171-6

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 Biol Volume 12 (2011) p.r90

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

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
J Chem Inf Model Volume 51 (2011) p.2778-2786

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.
Mol Syst Biol Volume 7 (2011) p.539

Protein structure databases.
Laskowski RA.
Mol Biotechnol Volume 48 (2011) p.183-198

The EBI Metagenomics Archive, Integration and Analysis resource
Hunter C, Cochrane G, Apweiler R, Hunter S.
Volume (2011) p.333–340

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 Biol Volume 9 (2011) p.e1001088

Rapid analysis of pharmacology for infectious diseases.
Hopkins AL, Bickerton GR, Carruthers IM, Boyer SK, Rubin H, Overington JP.
Curr Top Med Chem Volume 11 (2011) p.1292-1300

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 Volume 17 (2011) p.1941-1946

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.
ISME J Volume 5 (2011) p.1565-1567

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.
Nat Biotechnol Volume 29 (2011) p.415-420

The International Nucleotide Sequence Database Collaboration.
Cochrane G, Karsch-Mizrachi I, Nakamura Y, International Nucleotide Sequence Database Collaboration.
Nucleic Acids Res Volume 39 (2011) p.d15-8

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.
Mol Syst Biol Volume 7 (2011) p.543

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 Res Volume 39 (2011) p.d456-64

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 Res Volume 39 (2011) p.d1085-94

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

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.
Wang X, Terfve C, Rose JC, Markowetz F.
Bioinformatics Volume 27 (2011) p.879-880

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

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 Comput Biol Volume 7 (2011) p.e1001122

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 Res Volume 39 (2011) p.d7-10

2010

Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.
Genome Res Volume 20 (2010) p.180-189

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.
J Virol Volume 84 (2010) p.8732-8742

Functional comparison of innate immune signaling pathways in primates.
Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y.
PLoS Genet Volume 6 (2010) p.e1001249

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

Genomic-scale capture and sequencing of endogenous DNA from feces.
Perry GH, Marioni JC, Melsted P, Gilad Y.
Mol Ecol Volume 19 (2010) p.5332-5344

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 Genet Volume 6 (2010) p.e1001023

Heme proteins--diversity in structural characteristics, function, and folding.
Smith LJ, Kahraman A, Thornton JM.
Proteins Volume 78 (2010) p.2349-2368

BioXSD: the common data-exchange format for everyday bioinformatics web services.
Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I.
Bioinformatics Volume 26 (2010) p.i540-6

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.
BMC Bioinformatics Volume 11 (2010) p.415

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.
Mol Syst Biol Volume 6 (2010) p.399

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 Res Volume 20 (2010) p.578-588

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M.
Proc Natl Acad Sci U S A Volume 107 (2010) p.4135-4140

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 Volume 328 (2010) p.1036-1040

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.
Cavalieri D, Rivero D, Beltrame L, Buschow SI, Calura E, Rizzetto L, Gessani S, Gauzzi MC, Reith W, Baur A, Bonaiuti R, Brandizi M, De Filippo C, D'Oro U, Draghici S, Dunand-Sauthier I, Gatti E, Granucci F, Gündel M, Kramer M, Kuka M, Lanyi A, Melief CJ, van Montfoort N, Ostuni R, Pierre P, Popovici R, Rajnavolgyi E, Schierer S, Schuler G, Soumelis V, Splendiani A, Stefanini I, Torcia MG, Zanoni I, Zollinger R, Figdor CG, Austyn JM.
Immunome Res Volume 6 (2010) p.10

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA.
Bioinformatics Volume 26 (2010) p.2354-2356

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.
Mol Cell Volume 38 (2010) p.603-613

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.
Nat Methods Volume 7 (2010) p.s42-55

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 Discov Today Volume 15 (2010) p.804-811

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri AU, Laskowski RA.
Bioinformatics Volume 26 (2010) p.1260-1261

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic Acids Res Volume 38 (2010) p.d142-8

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan AW, Laskowski RA, Selwood DL.
J Med Chem Volume 53 (2010) p.3086-3094

Consistent annotation of gene expression arrays.
Ballester B, Johnson N, Proctor G, Flicek P.
BMC Genomics Volume 11 (2010) p.294

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N.
BMC Bioinformatics Volume 11 (2010) p.579

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 Res Volume 38 (2010) p.w689-94

Characterization and prediction of protein nucleolar localization sequences.
Scott MS, Boisvert FM, McDowall MD, Lamond AI, Barton GJ.
Nucleic Acids Res Volume 38 (2010) p.7388-7399

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

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.
Cell Mol Life Sci Volume 67 (2010) p.1049-1064

Visualizing chromosome mosaicism and detecting ethnic outliers by the method of "rare" heterozygotes and homozygotes (RHH).
McGinnis RE, Deloukas P, McLaren WM, Inouye M.
Hum Mol Genet Volume 19 (2010) p.2539-2553

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 Genet Volume 11 (2010) p.25

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression.
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C.
RNA Volume 16 (2010) p.991-1006

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

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

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 Res Volume 38 (2010) p.4325-4336

Protein structure databases.
Laskowski RA.
Methods Mol Biol Volume 609 (2010) p.59-82

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

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

The structures and physicochemical properties of organic cofactors in biocatalysis.
Fischer JD, Holliday GL, Rahman SA, Thornton JM.
J Mol Biol 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

Mining Unique-m Substrings from Genomes
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R.
J Proteomics Bioinform Volume 3 (2010) p.99-100

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 Biol Volume 8 (2010) p.

Ontology engineering.
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF.
Nat Biotechnol Volume 28 (2010) p.128-130

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic Acids Res Volume 38 (2010) p.d331-5

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.
Nat Genet Volume 42 (2010) p.813-814

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 Genet Volume 6 (2010) p.e1000881

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.

The (non)malignancy of cancerous amino acidic substitutions.
Talavera D, Taylor MS, Thornton JM.
Proteins Volume 78 (2010) p.518-529

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

Chromosomal mapping of pancreatic islet morphological features and regulatory hormones in the spontaneously diabetic (Type 2) Goto-Kakizaki rat.
Finlay C, Argoud K, Wilder SP, Ouali F, Ktorza A, Kaisaki PJ, Gauguier D.
Mamm Genome Volume 21 (2010) p.499-508

Molecular interactions and data standardisation.
Orchard S, Kerrien S.
Methods Mol Biol Volume 604 (2010) p.309-318

Journal club. A computational geneticist looks at mechanisms of chromosomal evolution.
Flicek P.
Nature Volume 463 (2010) p.713

The EMBRACE web service collection.
Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G.
Nucleic Acids Res Volume 38 (2010) p.w683-8

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

The CoFactor database: organic cofactors in enzyme catalysis.
Fischer JD, Holliday GL, Thornton JM.
Bioinformatics Volume 26 (2010) p.2496-2497

Domain-ligand mapping for enzymes.
Bashton M, Thornton JM.
J Mol Recognit Volume 23 (2010) p.194-208

Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.
Vizcaíno JA, Foster JM, Martens L.
J Proteomics Volume 73 (2010) p.2136-2146

Mining proteomic MS/MS data for MRM transitions.
Chem Mead JA, Bianco L, Bessant C.
Methods Mol Biol Volume 604 (2010) p.187-199

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

Free computational resources for designing selected reaction monitoring transitions.
Cham Mead JA, Bianco L, Bessant C.
Proteomics Volume 10 (2010) p.1106-1126

MRMaid-DB: a repository of published SRM transitions.
Cham JA, Bianco L, Barton C, Bessant C.
J Proteome Res Volume 9 (2010) p.620-625

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.
Clin Trials Volume 7 (2010) p.s5-s32

Unifying themes in microbial associations with animal and plant hosts described using the gene ontology.
Torto-Alalibo T, Collmer CW, Gwinn-Giglio M, Lindeberg M, Meng S, Chibucos MC, Tseng TT, Lomax J, Biehl B, Ireland A, Bird D, Dean RA, Glasner JD, Perna N, Setubal JC, Collmer A, Tyler BM.
Microbiol Mol Biol Rev Volume 74 (2010) p.479-503

CDK-Taverna: an open workflow environment for cheminformatics.
Kuhn T, Willighagen EL, Zielesny A, Steinbeck C.
BMC Bioinformatics Volume 11 (2010) p.159

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 Res Volume 38 (2010) p.d249-54

Molecular fragments chemoinformatics.
Kuhn H, Neumann S, Steinbeck C, Wittekindt C, Zielesny A.
Journal of Cheminformatics Volume 2 (2010) p.p14-p14

The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J.
Nucleic Acids Res Volume 38 (2010) p.d17-25

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.
Brief Bioinform Volume 11 (2010) p.544-551

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 Med Volume 2 (2010) p.24

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
Li C, Courtot M, Le Novère N, Laibe C.
Brief Bioinform Volume 11 (2010) p.270-277

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 Syst Biol Volume 4 (2010) p.92

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

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.
Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR.
Proc Natl Acad Sci U S A Volume 107 (2010) p.12168-12173

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 Res Volume 38 (2010) p.d563-9

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

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.
Science Volume 330 (2010) p.86-88

Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences.
Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E, Aguiar M, Viswanathan LD, Rogers YH, Strausberg RL, Saski CA, Lawson D, Collins FH, Kafatos FC, Christophides GK, Clifton SW, Kirkness EF, Besansky NJ.
Science Volume 330 (2010) p.512-514

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.
Cochrane GR, Galperin MY.
Nucleic Acids Res Volume 38 (2010) p.d1-4

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

So what have data standards ever done for us? The view from metabolomics.
Griffin JL, Steinbeck C.
Genome Med Volume 2 (2010) p.38

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.
Brief Bioinform Volume 11 (2010) p.552-562

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.
J Exp Med Volume 207 (2010) p.1351-1358

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
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BMC Bioinformatics Volume 11 (2010) p.112

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.
Nat Med Volume 16 (2010) p.586-91, 1p following 591

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 Res Volume 38 (2010) p.d557-62

A global map of human gene expression.
Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.
Nat Biotechnol Volume 28 (2010) p.322-324

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 Res Volume 38 (2010) p.d690-8

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 Volume 26 (2010) p.1112-1118

Large scale comparison of global gene expression patterns in human and mouse.
Zheng-Bradley X, Rung J, Parkinson H, Brazma A.
Genome Biol Volume 11 (2010) p.r124

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 Genet Volume 6 (2010) p.e1000976

Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L.
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Role of open chemical data in aiding drug discovery and design.
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Future Med Chem Volume 2 (2010) p.903-907

Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs.
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Proc Natl Acad Sci U S A Volume 107 (2010) p.13830-13835

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids.
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SylArray: a web server for automated detection of miRNA effects from expression data.
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Bioinformatics Volume 26 (2010) p.2900-2901

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression.
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Mol Cancer Volume 9 (2010) p.290

iMotifs: an integrated sequence motif visualization and analysis environment.
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Bioinformatics Volume 26 (2010) p.843-844

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

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 Res Volume 70 (2010) p.2911-2923

MapMi: automated mapping of microRNA loci.
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BMC Bioinformatics Volume 11 (2010) p.133

Diversity of human copy number variation and multicopy genes.
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Science Volume 330 (2010) p.641-646

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

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 Res Volume 38 (2010) p.d308-17

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 Res Volume 87 (2010) p.95-110

Safeguarding the integrity of protein archive.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley SK.
Nature Volume 463 (2010) p.425

Discovery of drug mode of action and drug repositioning from transcriptional responses.
Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A, di Bernardo D.
Proc Natl Acad Sci U S A Volume 107 (2010) p.14621-14626

Identification of small molecules enhancing autophagic function from drug network analysis.
Iorio F, Isacchi A, di Bernardo D, Brunetti-Pierri N.
Autophagy Volume 6 (2010) p.1204-1205

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 Biol Volume 11 (2010) p.r88

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.
Hum Mutat Volume 31 (2010) p.1374-1381

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 Volume 26 (2010) p.2069-2070

Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure
Cochrane G, Martin MJ, Apweiler R.
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Meeting Report: BioSharing at ISMB 2010.
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IPD--the Immuno Polymorphism Database.
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Nucleic Acids Res Volume 38 (2010) p.d863-9

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.
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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.
Stand Genomic Sci Volume 3 (2010) p.93-96

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 Res Volume 38 (2010) p.d52-6

Fast and efficient searching of biological data resources--using EB-eye.
Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R.
Brief Bioinform Volume 11 (2010) p.375-384

Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H.
Nucleic Acids Res Volume 38 (2010) p.d870-1

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.
Stand Genomic Sci Volume 2 (2010) p.357-360

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 Res Volume 38 (2010) p.w695-9

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.
Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.
Mol Cell Proteomics Volume 9 (2010) p.2642-2653

The consequence of natural selection on genetic variation in the mouse.
Reuveni E, Birney E, Gross CT.
Genomics Volume 95 (2010) p.196-202

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 Res Volume 38 (2010) p.w78-83

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 (Oxford) Volume 2010 (2010) p.baq014

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 Volume 328 (2010) p.710-722

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 Res Volume 38 (2010) p.d39-45

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 Res Volume 20 (2010) p.791-803

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.
Nat Biotechnol Volume 28 (2010) p.935-942

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 (Oxford) Volume 2010 (2010) p.baq018

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome Biol Volume 11 (2010) p.402

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium.
Plant Cell Volume 22 (2010) p.2530-2536

A database and API for variation, dense genotyping and resequencing data.
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BMC Bioinformatics Volume 11 (2010) p.238

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

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 Res Volume 20 (2010) p.249-256

Modeling Competition of Transcription Factors for DNA Binding Sites Improves Binding Site Predictions
Hestand MS, Hoffman MM, Birney E, van Ommen G-JB, den Dunnen JT, A.C. ’t Hoen P.
Volume (2010) p.45-62

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 Volume 328 (2010) p.235-239

Allele-specific and heritable chromatin signatures in humans.
Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Hum Mol Genet Volume 19 (2010) p.r204-9

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 Res Volume 38 (2010) p.d570-6

An effective model for natural selection in promoters.
Hoffman MM, Birney E.
Genome Res Volume 20 (2010) p.685-692

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 Volume 26 (2010) p.2470-2471

A large-scale protein-function database.
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Nat Chem Biol Volume 6 (2010) p.785

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

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.
Nat Biotechnol Volume 28 (2010) p.650-653

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.
Stand Genomic Sci Volume 3 (2010) p.259-266

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

HLA class I binding of HBZ determines outcome in HTLV-1 infection.
Macnamara A, Rowan A, Hilburn S, Kadolsky U, Fujiwara H, Suemori K, Yasukawa M, Taylor G, Bangham CR, Asquith B.
PLoS Pathog Volume 6 (2010) p.e1001117

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

Organelle proteomics experimental designs and analysis.
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS.
Proteomics Volume 10 (2010) p.3957-3969

The Ontology Lookup Service: bigger and better.
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.
Nucleic Acids Res Volume 38 (2010) p.w155-60

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.
Mol Cell Proteomics 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

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.
Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T.
Plant Cell Volume 22 (2010) p.997-1005

The publication and database deposition of molecular interaction data.
Orchard S, Aranda B, Hermjakob H.
Curr Protoc Protein Sci 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 Res Volume 38 (2010) p.d525-31

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.
J Biomol NMR Volume 48 (2010) p.85-92

The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.
Nucleic Acids Res Volume 38 (2010) p.d736-42

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

2009

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 Comput Biol Volume 5 (2009) p.e1000440

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 Res Volume 37 (2009) p.d19-25

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 Volume 17 (2009) p.1051-1062

Mapping organelle proteins and protein complexes in Drosophila melanogaster.
Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS.
J Proteome Res Volume 8 (2009) p.2667-2678

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 Biol Volume 10 (2009) p.402-402

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

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 Res Volume 37 (2009) p.d619-22

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Durinck S, Spellman PT, Birney E, Huber W.
Nat Protoc Volume 4 (2009) p.1184-1191

Evolution. Uniting alignments and trees.
Löytynoja A, Goldman N.
Science Volume 324 (2009) p.1528-1529

In defense of statistical methods for detecting positive selection.
Yang Z, Nielsen R, Goldman N.
Proc Natl Acad Sci U S A Volume 106 (2009) p.e95; author reply e96

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 Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res Volume 37 (2009) p.d169-74

Genomic DNA k-mer spectra: models and modalities.
Chor B, Horn D, Goldman N, Levy Y, Massingham T.
Genome Biol Volume 10 (2009) p.r108

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
Dvinge H, Bertone P.
Bioinformatics Volume 25 (2009) p.3325-3326

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 Res Volume 19 (2009) p.1316-1323

Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network.
Genome Biol Volume 10 (2009) p.401

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

ENFIN--A European network for integrative systems biology.
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E.
C R Biol Volume 332 (2009) p.1050-1058

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 Res Volume 37 (2009) p.d583-7

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 Volume 25 (2009) p.2768-2769

The need for speed.
Flicek P.
Genome Biol Volume 10 (2009) p.212

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.
Proc Natl Acad Sci U S A Volume 106 (2009) p.3829-3834

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

Applying the Gene Ontology in microbial annotation.
Giglio MG, Collmer CW, Lomax J, Ireland A.
Trends Microbiol Volume 17 (2009) p.262-268

Designing and encoding models for synthetic biology.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N.
J R Soc Interface Volume 6 Suppl 4 (2009) p.s405-17

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus.
Hu Y, Kaisaki PJ, Argoud K, Wilder SP, Wallace KJ, Woon PY, Blancher C, Tarnow L, Groop PH, Hadjadj S, Marre M, Parving HH, Farrall M, Cox RD, Lathrop M, Vionnet N, Bihoreau MT, Gauguier D.
BMC Med Genomics Volume 2 (2009) p.41

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 Res Volume 37 (2009) p.d868-72

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

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.
J Proteome Res Volume 8 (2009) p.3689-3692

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 Volume 25 (2009) p.279-280

Visualising the Epigenome
Flicek P, Birney E.
Volume (2009) p.55-66

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 Biol Volume 10 (2009) p.202

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.
Infect Genet Evol Volume 9 (2009) p.308-313

Probing the "dark matter" of protein fold space.
Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I.
Structure Volume 17 (2009) p.1244-1252

OrChem - An open source chemistry search engine for Oracle(R).
Rijnbeek M, Steinbeck C.
J Cheminform Volume 1 (2009) p.17

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 Res Volume 37 (2009) p.2274-2282

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.
Hum Mutat Volume 30 (2009) p.496-510

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 Res Volume 37 (2009) p.d310-4

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 Biol Volume 10 (2009) p.207

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

Second Joint HUPO publication and Proteomics Standards Initiative workshop.
Orchard S, Binz PA, Hermjakob H.
Proteomics Volume 9 (2009) p.4426-4428

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.
J Proteome Res Volume 8 (2009) p.1782-1791

Recent developments in public proteomic MS repositories and pipelines.
Mead JA, Bianco L, Bessant C.
Proteomics Volume 9 (2009) p.861-881

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.
Galperin MY, Cochrane GR.
Nucleic Acids Res Volume 37 (2009) p.d1-4

ChEBI: an open bioinformatics and cheminformatics resource.
Degtyarenko K, Hastings J, de Matos P, Ennis M.
Curr Protoc Bioinformatics Volume Chapter 14 (2009) p.unit 14.9

On vital aid: the why, what and how of validation.
Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 65 (2009) p.134-139

Case-controlled structure validation.
Read RJ, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 65 (2009) p.140-147

A chemogenomics view on protein-ligand spaces.
Strömbergsson H, Kleywegt GJ.
BMC Bioinformatics Volume 10 Suppl 6 (2009) p.s13

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.
Mol Cell Proteomics Volume 8 (2009) p.696-705

Finding query suggestions for PubMed.
Lu Z, Wilbur WJ, McEntyre JR, Iskhakov A, Szilagyi L.
AMIA Annu Symp Proc Volume 2009 (2009) p.396-400

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr.
Overington J.
J Comput Aided Mol Des Volume 23 (2009) p.195-198

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 Res 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 Res Volume 37 (2009) p.d1013-7

The genome of the blood fluke Schistosoma mansoni.
Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM.
Nature Volume 460 (2009) p.352-358

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 Microbiol Volume 9 (2009) p.217

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.
Nat Methods Volume 6 (2009) p.860-861

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.
Stand Genomic Sci Volume 1 (2009) p.278-282

PRIDE Converter: making proteomics data-sharing easy.
Barsnes H, Vizcaíno JA, Eidhammer I, Martens L.
Nat Biotechnol Volume 27 (2009) p.598-599

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 Res Volume 19 (2009) p.994-1005

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 Genet Volume 5 (2009) p.e1000433

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.
Genome Res Volume 19 (2009) p.327-335

MAPU 2.0: high-accuracy proteomes mapped to genomes.
Gnad F, Oroshi M, Birney E, Mann M.
Nucleic Acids Res Volume 37 (2009) p.d902-6

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

Survey-based naming conventions for use in OBO Foundry ontology development.
Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA.
BMC Bioinformatics Volume 10 (2009) p.125

Towards interoperable reporting standards for omics data: hopes and hurdles.
Sansone SA, Rocca-Serra P, Field D, Taylor CF, Tong W, Brandizi M, Maguire E, Sklyar N.
Summit on Translat Bioinforma Volume 2009 (2009) p.112-115

Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM.
J R Soc Interface Volume 6 (2009) p.129-147

Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E.
Nat Methods Volume 6 (2009) p.s6-s12

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Paten B, Herrero J, Beal K, Birney E.
Bioinformatics Volume 25 (2009) p.295-301

Application of ESTs in microarray analysis.
Li W, Olohan L, Williams D, Hughes M, Gracey A, Cossins A.
Methods Mol Biol Volume 533 (2009) p.289-309

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 Biol Evol Volume 1 (2009) p.13-22

Charting online OMICS resources: A navigational chart for clinical researchers.
Vizcaíno JA, Mueller M, Hermjakob H, Martens L.
Proteomics Clin Appl Volume 3 (2009) p.18-29

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.
Eur J Hum Genet Volume 17 (2009) p.426-433

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.
FEBS J Volume 276 (2009) p.1878-1890

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.
Arterioscler Thromb Vasc Biol Volume 29 (2009) p.774-780

Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.
Bioinformatics Volume 25 (2009) p.2092-2094

Applications of high-throughput sequencing to chromatin structure and function in mammals.
Dunham I.
F1000 Biol Rep Volume 1 (2009) p.32

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 Mol Biol Volume 10 (2009) p.51

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.
Nat Genet Volume 41 (2009) p.703-707

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

GLOBAL ANALYSIS OF PROTEIN ACTIVITY USING PROTEOME CHIPS
SNYDER MICHAEL, ZHU HENG, BERTONE PAUL, BIDLINGMAIER SCOTT M, BILGIN METIN, CASAMAYOR ANTONIO J, GERSTEIN MARK, JANSEN RONALD, LAN NING.
Volume (2009) p.

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 Volume 326 (2009) p.140-144

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.
Nat Genet Volume 41 (2009) p.1182-1190

Integrated Servers for Structure-Informed Function Prediction
Laskowski RA.
Volume (2009) p.251-272

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 Volume 25 (2009) p.1321-1328

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 Dev Volume 23 (2009) p.619-632

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.
Mol Oncol Volume 3 (2009) p.9-17

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

Network visualization and analysis of gene expression data using BioLayout Express(3D).
Theocharidis A, van Dongen S, Enright AJ, Freeman TC.
Nat Protoc Volume 4 (2009) p.1535-1550

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.
Philos Trans A Math Phys Eng Sci Volume 367 (2009) p.1845-1867

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.
Nat Biotechnol Volume 27 (2009) p.735-741

Protein promiscuity and its implications for biotechnology.
Nobeli I, Favia AD, Thornton JM.
Nat Biotechnol Volume 27 (2009) p.157-167

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.
PLoS Comput Biol Volume 5 (2009) p.e1000585

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 Res Volume 37 (2009) p.d211-5

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.
Nat Genet Volume 41 (2009) p.614-618

Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.
Bioinformatics Volume 25 (2009) p.i145-53

Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I.
J Chem Inf Model Volume 49 (2009) p.2272-2289

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 Genet Volume 5 (2009) p.e1000626

PDBsum new things.
Laskowski RA.
Nucleic Acids Res Volume 37 (2009) p.d355-9

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.
Chem Biol Interact Volume 178 (2009) p.94-98

The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ.
Biochem Soc Trans Volume 37 (2009) p.723-726

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.
Mol Cell Biochem Volume 329 (2009) p.3-15

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.
Mol Cell Proteomics Volume 8 (2009) p.1972-1987

Ending the "publish and vanish" culture: how the data standardization process will assist in data harvesting.
Orchard S.
J Proteome Res Volume 8 (2009) p.3219

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 Res Volume 37 (2009) p.d690-7

Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Watson JD, Thornton JM.
Volume (2009) p.201-215

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.
Nat Genet Volume 41 (2009) p.535-543

Debunking minimum information myths: one hat need not fit all.
Orchard S, Taylor CF.
N Biotechnol Volume 25 (2009) p.171-172

HUPO World Congress Publication Committee meeting. August 2008, Amsterdam, The Netherlands.
Orchard S, Ping P.
Proteomics Volume 9 (2009) p.502-503

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.
Exp Physiol Volume 94 (2009) p.472-485

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.
J Mol Biol Volume 388 (2009) p.356-380

Drug target central.
Harland L, Gaulton A.
Expert Opin Drug Discov Volume 4 (2009) p.857-872

Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.
J Cheminform Volume 1 (2009) p.12

Biophysical annotation and representation of CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF.
Bioinformatics Volume 25 (2009) p.2263-2270

WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM.
Bioinformatics Volume 25 (2009) p.1192-1194

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

Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday GL, Mitchell JB, Thornton JM.
J Mol Biol Volume 390 (2009) p.560-577

A method for visualizing CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.
Bioinformatics Volume 25 (2009) p.3012-3019

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.
Bioinformatics Volume 25 (2009) p.3045-3046

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 J Volume 23 (2009) p.3790-3807

Metal-MACiE: a database of metals involved in biological catalysis.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
Bioinformatics Volume 25 (2009) p.2088-2089

Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc.
de Jager SM, Scofield S, Huntley RP, Robinson AS, den Boer BG, Murray JA.
Plant Mol Biol Volume 71 (2009) p.345-365

AmiGO: online access to ontology and annotation data.
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group.
Bioinformatics Volume 25 (2009) p.288-289

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes.
Wilder SP, Kaisaki PJ, Argoud K, Salhan A, Ragoussis J, Bihoreau MT, Gauguier D.
BMC Genomics Volume 10 (2009) p.63

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva R, Thornton JM, Pellegrini-Calace M.
Bioinformatics Volume 25 (2009) p.3183-3184

The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM.
FEBS Lett Volume 583 (2009) p.1692-1698

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 (Oxford) Volume 2009 (2009) p.bap010

Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM.
Nat Chem Biol Volume 5 (2009) p.521-525

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
Reference Genome Group of the Gene Ontology Consortium.
PLoS Comput Biol Volume 5 (2009) p.e1000431

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 Res Volume 37 (2009) p.d396-403

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
Brazma A.
ScientificWorldJournal Volume 9 (2009) p.420-423

2008

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

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 Res Volume 36 (2008) p.d847-53

Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
O'Reilly PF, Birney E, Balding DJ.
Genome Res Volume 18 (2008) p.1304-1313

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 Volume 12 (2008) p.143-149

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

PROCOGNATE: a cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
Nucleic Acids Res Volume 36 (2008) p.d618-22

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 Res Volume 36 (2008) p.d426-33

Levers and fulcrums: progress in cis-regulatory motif models.
Birney E.
Nat Methods Volume 5 (2008) p.297-298

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

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 Res Volume 36 (2008) p.w485-90

Rapidly evolving human promoter regions.
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA.
Nat Genet Volume 40 (2008) p.1262-3; author reply 1263-4

Data standards and controlled vocabularies for proteomics.
Martens L, Palazzi LM, Hermjakob H.
Methods Mol Biol Volume 484 (2008) p.279-286

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 Res Volume 36 (2008) p.w372-6

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 Biol Volume 9 (2008) p.r89

Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H.
Bioinformatics Volume 24 (2008) p.2119-2121

Advanced genomic data mining.
Fernández-Suárez XM, Birney E.
PLoS Comput Biol Volume 4 (2008) p.e1000121

Pathophysiological, genetic and gene expression features of a novel rodent model of the cardio-metabolic syndrome.
Wallis RH, Collins SC, Kaisaki PJ, Argoud K, Wilder SP, Wallace KJ, Ria M, Ktorza A, Rorsman P, Bihoreau MT, Gauguier D.
PLoS One Volume 3 (2008) p.e2962

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.
J Chem Inf Model Volume 48 (2008) p.550-555

Functional site prediction selects correct protein models.
Chelliah V, Taylor WR.
BMC Bioinformatics Volume 9 Suppl 1 (2008) p.s13

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.
Mol Cell Proteomics Volume 7 (2008) p.1409-1419

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 Biol Volume 6 (2008) p.e135

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.
Orchard S, Hermjakob H.
Brief Bioinform Volume 9 (2008) p.166-173

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

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J.
Bioinformatics Volume 24 (2008) p.i105-11

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.
J Proteome Res Volume 7 (2008) p.182-191

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.
Nat Genet Volume 40 (2008) p.971-976

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

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 Biol Volume 9 Suppl 2 (2008) p.s5

Phylometabonomic patterns of adaptation to high fat diet feeding in inbred mice.
Fearnside JF, Dumas ME, Rothwell AR, Wilder SP, Cloarec O, Toye A, Blancher C, Holmes E, Tatoud R, Barton RH, Scott J, Nicholson JK, Gauguier D.
PLoS One Volume 3 (2008) p.e1668

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.
Nat Genet Volume 40 (2008) p.776-781

ChEBI: a database and ontology for chemical entities of biological interest.
Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M.
Nucleic Acids Res Volume 36 (2008) p.d344-50

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 Biol Volume 9 (2008) p.r78

Epigenomics at the tipping point. Foreword.
Stamatoyannopoulos JA, Dunham I.
Pharmacogenomics Volume 9 (2008) p.1781-1783

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 Res Volume 18 (2008) p.393-403

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 Res Volume 36 (2008) p.d707-14

Metal ions in biological catalysis: from enzyme databases to general principles.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
J Biol Inorg Chem Volume 13 (2008) p.1205-1218

In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Mol Biotechnol Volume 38 (2008) p.165-177

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.
Nat Genet Volume 40 (2008) p.523-527

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Margulies EH, Birney E.
Nat Rev Genet Volume 9 (2008) p.303-313

Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM.
Nat Rev Genet Volume 9 (2008) p.141-151

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

Charting plant interactomes: possibilities and challenges.
Morsy M, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC.
Trends Plant Sci Volume 13 (2008) p.183-191

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 Volume 24 (2008) p.1100-1101

Minimum reporting guidelines for proteomics released by the Proteomics Standards Initiative.
Jones AR, Orchard S.
Mol Cell Proteomics Volume 7 (2008) p.2067-2068

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.
Nat Methods Volume 5 (2008) p.239-241

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 Volume 26 (2008) p.1174-1185

Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Comb Chem High Throughput Screen Volume 11 (2008) p.653-660

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

Fusion and fission of genes define a metric between fungal genomes.
Durrens P, Nikolski M, Sherman D.
PLoS Comput Biol Volume 4 (2008) p.e1000200

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

ENFIN - An Integrative Structure for Systems Biology
Reisinger F, Corpas M, Hancock J, Hermjakob H, Birney E, Kahlem P.
Volume (2008) p.132-143

Data curation + process curation=data integration + science.
Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R.
Brief Bioinform Volume 9 (2008) p.506-517

Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells.
Kirstetter P, Schuster MB, Bereshchenko O, Moore S, Dvinge H, Kurz E, Theilgaard-Mönch K, Månsson R, Pedersen TA, Pabst T, Schrock E, Porse BT, Jacobsen SE, Bertone P, Tenen DG, Nerlov C.
Cancer Cell Volume 13 (2008) p.299-310

Genomic-scale prioritization of drug targets: the TDR Targets database.
Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL.
Nat Rev Drug Discov Volume 7 (2008) p.900-907

Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain.
Lappalainen I, Hurley MG, Clarke J.
J Mol Biol Volume 375 (2008) p.547-559

Annotation of mammalian primary microRNAs.
Saini HK, Enright AJ, Griffiths-Jones S.
BMC Genomics Volume 9 (2008) p.564

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.
Nat Biotechnol Volume 26 (2008) p.305-312

Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.
Goldman N, Yang Z.
Philos Trans R Soc Lond B Biol Sci Volume 363 (2008) p.3889-3892

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.
Nat Genet Volume 40 (2008) p.560-566

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 Volume 322 (2008) p.861-862

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.
Nat Biotechnol Volume 26 (2008) p.889-896

Genome wide analysis of pathogenic SH2 domain mutations.
Lappalainen I, Thusberg J, Shen B, Vihinen M.
Proteins Volume 72 (2008) p.779-792

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.
Plant Cell Volume 20 (2008) p.1426-1436

Computational prediction of protein-protein interactions.
Skrabanek L, Saini HK, Bader GD, Enright AJ.
Mol Biotechnol Volume 38 (2008) p.1-17

Infrastructure for distributed protein annotation
Reeves GA, Prlic A, Jimenez RC, Kulesha E, Hermjakob H.
Volume (2008) p.413-426

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A.
Cell Volume 133 (2008) p.813-828

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

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

miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
Nucleic Acids Res Volume 36 (2008) p.d154-8

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 J Volume 22 (2008) p.807-818

EBI Proteomics Services
Hermjakob H.
Lect Notes Comput Sci Volume 5109 (2008) p.207

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 Res Volume 18 (2008) p.1518-1529

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.
Nat Biotechnol Volume 26 (2008) p.779-785

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 Volume 24 (2008) p.1625-1631

Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM.
BMC Evol Biol Volume 8 (2008) p.247

The BREW workshop series: a stimulating experience in PhD education.
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M.
Brief Bioinform Volume 9 (2008) p.250-253

How can ontologies help vector biology?
Topalis P, Lawson D, Collins FH, Louis C.
Trends Parasitol Volume 24 (2008) p.249-252

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 Res Volume 36 (2008) p.d5-12

Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ.
Nat Methods Volume 5 (2008) p.1023-1025

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 Volume 12 (2008) p.137-141

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 Volume 24 (2008) p.2767-2772

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
Genome Res Volume 18 (2008) p.1814-1828

PRIDE: new developments and new datasets.
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.
Nucleic Acids Res Volume 36 (2008) p.d878-83

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E.
Genome Res Volume 18 (2008) p.821-829

Data storage and analysis in ArrayExpress and Expression Profiler.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.
Curr Protoc Bioinformatics Volume Chapter 7 (2008) p.unit 7.13

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 Volume 24 (2008) p.11-17

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 Volume 12 (2008) p.109-113

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 Volume 12 (2008) p.101-108

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Löytynoja A, Goldman N.
Science Volume 320 (2008) p.1632-1635

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD, Nobeli I, Glaser F, Thornton JM.
J Mol Biol Volume 375 (2008) p.855-874

Evolutionary footprints of nucleosome positions in yeast.
Washietl S, Machné R, Goldman N.
Trends Genet Volume 24 (2008) p.583-587

A model of evolution and structure for multiple sequence alignment.
Löytynoja A, Goldman N.
Philos Trans R Soc Lond B Biol Sci Volume 363 (2008) p.3913-3919

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 Syst Biol Volume 2 (2008) p.36

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.
Mol Cell Biol Volume 28 (2008) p.551-563

Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E.
Genome Res Volume 18 (2008) p.1829-1843

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

MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects
Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J.
Volume (2008) p.

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

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 Res Volume 36 (2008) p.d445-8

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.
Nat Biotechnol Volume 26 (2008) p.541-547

2007

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

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.
Am J Hum Genet Volume 81 (2007) p.367-374

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 Genet Biol Volume 44 (2007) p.269-283

Current approaches to gene regulatory network modelling.
Schlitt T, Brazma A.
BMC Bioinformatics Volume 8 Suppl 6 (2007) p.s9

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.
Curr Genet Volume 51 (2007) p.331-342

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 Biol Volume 8 (2007) p.r73

eGenomics: Cataloguing Our Complete Genome Collection III.
Field D, Garrity G, Gray T, Selengut J, Sterk P, Thomson N, Tatusova T, Cochrane G, Glöckner FO, Kottmann R, Lister AL, Tateno Y, Vaughan R.
Comp Funct Genomics Volume 2007 (2007) p.

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.
Am J Hum Genet Volume 80 (2007) p.345-352

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.
Appl Microbiol Biotechnol Volume 75 (2007) p.853-862

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 Res Volume 35 (2007) p.d16-20

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 Volume 23 (2007) p.1689-1691

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

An empirical codon model for protein sequence evolution.
Kosiol C, Holmes I, Goldman N.
Mol Biol Evol Volume 24 (2007) p.1464-1479

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

Web services at the European bioinformatics institute.
Labarga A, Valentin F, Anderson M, Lopez R.
Nucleic Acids Res 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 Res Volume 35 (2007) p.d224-8

Integrating sequence and structural biology with DAS.
Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ.
BMC Bioinformatics Volume 8 (2007) p.333

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 Volume 316 (2007) p.222-234

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.
Proc Natl Acad Sci U S A Volume 104 (2007) p.5495-5500

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 Biol Volume 8 (2007) p.r39

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 Res Volume 17 (2007) p.691-707

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 Res Volume 17 (2007) p.760-774

ProServer: a simple, extensible Perl DAS server.
Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J, Pettett R.
Bioinformatics Volume 23 (2007) p.1568-1570

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 Res Volume 35 (2007) p.d610-7

Gene prediction: compare and CONTRAST.
Flicek P.
Genome Biol Volume 8 (2007) p.233

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 25 (2007) p.1127-1133

The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R.
Methods Mol Biol Volume 406 (2007) p.1-21

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.
Laibe C, Le Novère N.
BMC Syst Biol Volume 1 (2007) p.58

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

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.
Nat Genet Volume 39 (2007) p.433-436

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 Res Volume 35 (2007) p.d503-5

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 Volume 316 (2007) p.1718-1723

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.
Nat Genet Volume 39 (2007) p.1217-1224

Estimating the neutral rate of nucleotide substitution using introns.
Hoffman MM, Birney E.
Mol Biol Evol Volume 24 (2007) p.522-531

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J.
Nat Methods Volume 4 (2007) p.563-565

The genopolis microarray database.
Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P.
BMC Bioinformatics Volume 8 Suppl 1 (2007) p.s21

Proteomics: from technology development to biomarker applications.
Orchard S.
Expert Rev Proteomics Volume 4 (2007) p.709-710

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.
Nat Genet 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 Res Volume 17 (2007) p.320-327

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

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

Patterns of somatic mutation in human cancer genomes.
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR.
Nature Volume 446 (2007) p.153-158

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 Biol Volume 8 (2007) p.r5

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.
Mol Immunol Volume 44 (2007) p.1664-1679

Prediction of gene expression in embryonic structures of Drosophila melanogaster.
Samsonova AA, Niranjan M, Russell S, Brazma A.
PLoS Comput Biol Volume 3 (2007) p.e144

Evolutionary genomics: come fly with us.
Birney E.
Nature Volume 450 (2007) p.184-185

Experimental design criteria in phylogenetics: where to add taxa.
Geuten K, Massingham T, Darius P, Smets E, Goldman N.
Syst Biol Volume 56 (2007) p.609-622

Variation in evolutionary processes at different codon positions.
Bofkin L, Goldman N.
Mol Biol Evol Volume 24 (2007) p.513-521

ENFIN a network to enhance integrative systems biology.
Kahlem P, Birney E.
Ann N Y Acad Sci Volume 1115 (2007) p.23-31

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 Genet Volume 3 (2007) p.1661-1671

Statistics of the log-det estimator.
Massingham T, Goldman N.
Mol Biol Evol Volume 24 (2007) p.2277-2285

Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N.
Syst Biol Volume 56 (2007) p.431-444

Double Dutch for duplications.
Birney E.
Nat Genet Volume 39 (2007) p.1303-1304

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA.
Bioinformatics Volume 23 (2007) p.1824-1827

Optimized design and assessment of whole genome tiling arrays.
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P.
Bioinformatics Volume 23 (2007) p.i195-204

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.
Nat Genet Volume 39 (2007) p.1127-1133

Genome browsing with Ensembl: a practical overview.
Spudich G, Fernández-Suárez XM, Birney E.
Brief Funct Genomic Proteomic Volume 6 (2007) p.202-219

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

The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.
J Mol Biol Volume 372 (2007) p.1261-1277

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 Clin Appl Volume 1 (2007) p.148-156

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 Res Volume 35 (2007) p.d515-20

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.
J Mol Biol Volume 367 (2007) p.1511-1522

Correcting for sequence biases in present/absent calls.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome Biol Volume 8 (2007) p.r125

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.
Nat Methods Volume 4 (2007) p.13-17

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

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 Supérieure (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

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 Res Volume 35 (2007) p.d561-5

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.
Nat Biotechnol Volume 25 (2007) p.887-893

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 Biol Volume 5 (2007) p.44

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 Mol Biol Volume 367 (2007) p.261-270

Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome Biol Volume 8 (2007) p.r126

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 Biol Volume 5 (2007) p.e97

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 Res Volume 35 (2007) p.d291-7

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 Volume 23 (2007) p.e104-9

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 Volume 23 (2007) p.2947-2948

Proteomics data validation: why all must provide data.
Martens L, Hermjakob H.
Mol Biosyst Volume 3 (2007) p.518-522

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.
Nat Prod Rep Volume 24 (2007) p.972-987

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 Comput Biol Volume 3 (2007) p.2032-2042

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 Biol Volume 8 (2007) p.r132

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

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM.
PLoS Comput Biol Volume 3 (2007) p.1993-2002

The geometry of interactions between catalytic residues and their substrates.
Torrance JW, Holliday GL, Mitchell JB, Thornton JM.
J Mol Biol Volume 369 (2007) p.1140-1152

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

Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
J Mol Biol Volume 368 (2007) p.283-301

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 Genet Volume 8 (2007) p.24

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

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

ArrayExpress--a public database of microarray experiments and gene expression profiles.
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.
Nucleic Acids Res Volume 35 (2007) p.d747-50

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 Sci Volume 5 (2007) p.4

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

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.
Nat Biotechnol Volume 25 (2007) p.894-898

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 Res Volume 17 (2007) p.708-719

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 Evol Biol Volume 7 (2007) p.157

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

2006

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 Res Volume 66 (2006) p.3987-3991

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.
Mol Cancer Ther Volume 5 (2006) p.2606-2612

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 Biol Volume 7 (2006) p.r89

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM.
J Mol Biol Volume 356 (2006) p.928-944

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Whamond GS, Thornton JM.
J Mol Biol Volume 359 (2006) p.238-247

Concept of sample in OMICS technology.
Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D.
OMICS Volume 10 (2006) p.127-137

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

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

Guilt by association: using protein interactions and expression patterns to predict protein function
Orchard S, Hermjakob H.
Volume (2006) p.79-88

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

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.
Am J Hum Genet Volume 79 (2006) p.1119-1124

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 Res Volume 34 (2006) p.d327-31

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.
Mech Ageing Dev Volume 127 (2006) p.922-936

Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
J Mol Biol Volume 364 (2006) p.836-852

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 Res Volume 34 (2006) p.d659-63

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.
Hermjakob H.
Proteomics Volume 6 Suppl 2 (2006) p.34-38

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

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nat Cell Biol Volume 8 (2006) p.1183-1189

Transcriptional regulatory networks in bacteria: from input signals to output responses.
Seshasayee AS, Bertone P, Fraser GM, Luscombe NM.
Curr Opin Microbiol Volume 9 (2006) p.511-519

Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R.
OMICS Volume 10 (2006) p.114-118

Databases and resources for in silico proteome analysis.
Pruess M, Kersey P, Kulikova T, Apweiler R.
Methods Biochem Anal Volume 49 (2006) p.397-414

Integr8: Navigating Genome Reviews and the Proteome Analysis Database
Kersey P, Kulikova T, Pruess M.
Volume (2006) p.201-217

Sequence clustering as a method of protein functional annotation
Petryszak R, Kersey P.
Volume (2006) p.11-23

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
Flicek P, Brent MR.
Genome Biol Volume 7 Suppl 1 (2006) p.s8.1-9

WormBase: better software, richer content.
Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW.
Nucleic Acids Res Volume 34 (2006) p.d475-8

Design optimization methods for genomic DNA tiling arrays.
Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M.
Genome Res Volume 16 (2006) p.271-281

Target hub proteins serve as master regulators of development in yeast.
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M.
Genes Dev Volume 20 (2006) p.435-448

Data standards: a call to action.
Brooksbank C, Quackenbush J.
OMICS Volume 10 (2006) p.94-99

Curator driven protein sequence analysis and annotation
Magrane M, O'Donovan C.
Volume (2006) p.55-70

HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA.
Orchard S, Ping P.
Proteomics Volume 6 (2006) p.4436-4438

Integrating biological data through the genome.
Reeves GA, Thornton JM, BioSapiens Network of Excellence.
Hum Mol Genet Volume 15 Spec No 1 (2006) p.r81-7

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.
Mech Ageing Dev Volume 127 (2006) p.458-472

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.
Mol Cell Proteomics Volume 5 (2006) p.1996-2007

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 Res Volume 34 (2006) p.d187-91

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 Crystallogr D Biol Crystallogr Volume 62 (2006) p.1184-1195

UniSave: the UniProtKB sequence/annotation version database.
Leinonen R, Nardone F, Zhu W, Apweiler R.
Bioinformatics Volume 22 (2006) p.1284-1285

Protein superfamily evolution and the last universal common ancestor (LUCA).
Ranea JA, Sillero A, Thornton JM, Orengo CA.
J Mol Evol Volume 63 (2006) p.513-525

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

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 Res Volume 34 (2006) p.d556-61

Introduction. Bioinformatics: from molecules to systems.
Jones DT, Sternberg MJ, Thornton JM.
Philos Trans R Soc Lond B Biol Sci 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

Picking pyknons out of the human genome.
Meynert A, Birney E.
Cell Volume 125 (2006) p.836-838

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

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

A bioinformatician's view of the metabolome.
Nobeli I, Thornton JM.
Bioessays Volume 28 (2006) p.534-545

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 Res Volume 34 (2006) p.d10-5

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 Volume 10 (2006) p.205-208

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

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 Biol Volume 7 Suppl 1 (2006) p.s2.1-31

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 Microbiol (Praha) Volume 51 (2006) p.114-120

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 Volume 10 (2006) p.145-151

Proteomic Data Standardization, Deposition and Exchange
Orchard S, Hermjakob H, Pruess M, Apweiler R.
Volume (2006) p.19–30

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 Genet Biol Volume 43 (2006) p.234-246

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.
Nat Biotechnol Volume 24 (2006) p.21-2; author reply 23

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

Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.
Methods Enzymol Volume 411 (2006) p.370-386

Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U.
Nat Rev Genet Volume 7 (2006) p.593-605

Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks.
Rahman SA, Schomburg D.
Bioinformatics Volume 22 (2006) p.1767-1774

Overview of gene structure.
Spieth J, Lawson D.
WormBook Volume (2006) p.1-10

Modelling in molecular biology: describing transcription regulatory networks at different scales.
Schlitt T, Brazma A.
Philos Trans R Soc Lond B Biol Sci Volume 361 (2006) p.483-494

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.
Nat Genet Volume 38 (2006) p.853

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.
Devi SM, Ahmed I, Khan AA, Rahman SA, Alvi A, Sechi LA, Ahmed N.
BMC Genomics Volume 7 (2006) p.191

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 Volume 10 (2006) p.105-113

MGED standards: work in progress.
Ball CA, Brazma A.
OMICS Volume 10 (2006) p.138-144

Ensembl’s annotation pipeline and its use in eukaryotic genomes
Fernandez XM, Searle S, Birney E.
Volume (2006) p.109-203

Dry work in a wet world: computation in systems biology.
Kahlem P, Birney E.
Mol Syst Biol Volume 2 (2006) p.40

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R.
Expert Rev Proteomics Volume 3 (2006) p.1-3

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.
Physiol Genomics Volume 27 (2006) p.187-200

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 Genet Biol Volume 43 (2006) p.164-178

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Blake J, Schwager C, Kapushesky M, Brazma A.
Bioinformatics Volume 22 (2006) p.765-767

ArrayExpress service for reviewers/editors of DNA microarray papers.
Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.
Nat Biotechnol Volume 24 (2006) p.1321-1322

2005

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M.
Trends Genet Volume 21 (2005) p.466-475

Global changes in STAT target selection and transcription regulation upon interferon treatments.
Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M.
Genes Dev Volume 19 (2005) p.2953-2968

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 Res Volume 33 (2005) p.d247-51

Different versions of the Dayhoff rate matrix.
Kosiol C, Goldman N.
Mol Biol Evol Volume 22 (2005) p.193-199

Progress of structural genomics initiatives: an analysis of solved target structures.
Todd AE, Marsden RL, Thornton JM, Orengo CA.
J Mol Biol Volume 348 (2005) p.1235-1260

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.
Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD.
Nucleic Acids Res Volume 33 (2005) p.d383-9

Morphological aspects of oligomeric protein structures.
Ponstingl H, Kabir T, Gorse D, Thornton JM.
Prog Biophys Mol Biol Volume 89 (2005) p.9-35

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 Res Volume 33 (2005) p.d447-53

Global analysis of protein activities using proteome chips
SNYDER MICHAEL, ZHU HENGZHU, BERTONE PAUL, BIDLINGMAIER SCOTT M, BILGIN METIN, CASAMAYOR ANTONIO, GERSTEIN MARK, JANSEN RONALD, LAN NING.
Volume (2005) p.

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 Volume 21 (2005) p.3679-3680

Prospects and challenges in proteomics.
Bertone P, Snyder M.
Plant Physiol Volume 138 (2005) p.560-562

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

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 Res Volume 33 (2005) p.2129-2140

Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.
Bertone P, Gerstein M, Snyder M.
Chromosome Res Volume 13 (2005) p.259-274

Advances in functional protein microarray technology.
Bertone P, Snyder M.
FEBS J Volume 272 (2005) p.5400-5411

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

The complement of enzymatic sets in different species.
Freilich S, Spriggs RV, George RA, Al-Lazikani B, Swindells M, Thornton JM.
J Mol Biol Volume 349 (2005) p.745-763

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 Biol Volume 6 (2005) p.r104

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

Protein function prediction using local 3D templates.
Laskowski RA, Watson JD, Thornton JM.
J Mol Biol Volume 351 (2005) p.614-626

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.
Proc Natl Acad Sci U S A Volume 102 (2005) p.12299-12304

ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.w89-93

Fusing microarray experiments with multivariate regression.
Gilks WR, Tom BD, Brazma A.
Bioinformatics Volume 21 Suppl 2 (2005) p.ii137-43

Modelling gene networks at different organisational levels.
Schlitt T, Brazma A.
FEBS Lett Volume 579 (2005) p.1859-1866

Conformational changes observed in enzyme crystal structures upon substrate binding.
Gutteridge A, Thornton J.
J Mol Biol Volume 346 (2005) p.21-28

Predicting protein function from sequence and structural data.
Watson JD, Laskowski RA, Thornton JM.
Curr Opin Struct Biol Volume 15 (2005) p.275-284

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

Understanding nature's catalytic toolkit.
Gutteridge A, Thornton JM.
Trends Biochem Sci Volume 30 (2005) p.622-629

Reconstruction of gene regulatory networks under the finite state linear model.
Ruklisa D, Brazma A, Viksna J.
Genome Inform Volume 16 (2005) p.225-236

MACiE: a database of enzyme reaction mechanisms.
Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB.
Bioinformatics Volume 21 (2005) p.4315-4316

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 Physiol Volume 139 (2005) p.632-636

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 Volume 21 (2005) p.3198-3199

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 Volume 21 (2005) p.1495-1501

Get ready to GO! A biologist's guide to the Gene Ontology.
Lomax J.
Brief Bioinform Volume 6 (2005) p.298-304

Relations in biomedical ontologies.
Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C.
Genome Biol Volume 6 (2005) p.r46

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 Volume 21 (2005) p.3439-3440

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
Torrente A, Kapushesky M, Brazma A.
Bioinformatics Volume 21 (2005) p.3993-3999

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

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Laskowski RA, Chistyakov VV, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.d266-8

Species choice for comparative genomics: being greedy works.
Pardi F, Goldman N.
PLoS Genet Volume 1 (2005) p.e71

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 Res Volume 33 (2005) p.d297-302

Biological Databases: Infrastructure, Content and Integration
Williams AL, Kersey PJ, Pruess M, Apweiler R.
Volume (2005) p.11–28

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 Biol Volume 6 (2005) p.r56

The Integr8 project--a resource for genomic and proteomic data.
Pruess M, Kersey P, Apweiler R.
In Silico Biol Volume 5 (2005) p.179-185

It's all GO for plant scientists.
Clark JI, Brooksbank C, Lomax J.
Plant Physiol Volume 138 (2005) p.1268-1279

Protein families and their evolution-a structural perspective.
Orengo CA, Thornton JM.
Annu Rev Biochem Volume 74 (2005) p.867-900

A Quick Guide to the EMBL Bank Nucleotide Sequence Database
Cochrane G, Brooksbank C.
Volume (2005) p.34-35

The European Bioinformatics Institute's data resources: towards systems biology.
Brooksbank C, Cameron G, Thornton J.
Nucleic Acids Res Volume 33 (2005) p.d46-53

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 Res Volume 33 (2005) p.d141-6

D-type cyclins activate division in the root apex to promote seed germination in Arabidopsis.
Masubelele NH, Dewitte W, Menges M, Maughan S, Collins C, Huntley R, Nieuwland J, Scofield S, Murray JA.
Proc Natl Acad Sci U S A Volume 102 (2005) p.15694-15699

A novel degron-mediated degradation of the RTG pathway regulator, Mks1p, by SCFGrr1.
Liu Z, Spírek M, Thornton J, Butow RA.
Mol Biol Cell Volume 16 (2005) p.4893-4904

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 Volume 21 (2005) p.2347-2355

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 Res Volume 33 (2005) p.d262-5

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 Res Volume 33 (2005) p.d201-5

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 Res Volume 33 (2005) p.w25-8

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.
J Med Genet Volume 42 (2005) p.847-851

Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression.
Giannattasio S, Liu Z, Thornton J, Butow RA.
J Biol Chem Volume 280 (2005) p.42528-42535

InterProScan: protein domains identifier.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R.
Nucleic Acids Res Volume 33 (2005) p.w116-20

Microeconomic principles explain an optimal genome size in bacteria.
Ranea JA, Grant A, Thornton JM, Orengo CA.
Trends Genet Volume 21 (2005) p.21-25

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP.
Genome Res Volume 15 (2005) p.674-680

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 Res Volume 15 (2005) p.174-183

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.
J Mol Biol Volume 347 (2005) p.565-581

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 Res Volume 33 (2005) p.d428-32

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.
Proc Natl Acad Sci U S A Volume 102 (2005) p.4542-4547

Automated generation of heuristics for biological sequence comparison.
Slater GS, Birney E.
BMC Bioinformatics Volume 6 (2005) p.31

Protein Sequence Analysis and Domain Identification
Ponting CP, Birney E.
Volume (2005) p.527-541

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.
Syst Biol (Stevenage) Volume 152 (2005) p.55-60

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.
Nobeli I, Spriggs RV, George RA, Thornton JM.
J Mol Biol Volume 347 (2005) p.415-436

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

Protein Sequence Databases
Magrane M, Martin MJ, O’Donovan C, Apweiler R.
Volume (2005) p.609-618

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

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

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

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 Res Volume 33 (2005) p.d553-5

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

Automatic generation and evaluation of sparse protein signatures for families of protein structural domains.
Blades MJ, Ison JC, Ranasinghe R, Findlay JB.
Protein Sci Volume 14 (2005) p.13-23

ROCPLOT: a generic software tool for ROC analysis and the validation of predictive methods.
Ison JC, Blades MJ.
Appl Bioinformatics Volume 4 (2005) p.131-135

Survey of the geometric association of domain-domain interfaces.
Kim WK, Ison JC.
Proteins Volume 61 (2005) p.1075-1088

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 Res Volume 33 (2005) p.d29-33

Second proteomics standards initiative spring workshop.
Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R.
Expert Rev Proteomics Volume 2 (2005) p.287-289

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

Annotating the human proteome.
Orchard S, Hermjakob H, Apweiler R.
Mol Cell Proteomics Volume 4 (2005) p.435-440

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.
Pac Symp Biocomput Volume (2005) p.186-196

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

An algorithm for progressive multiple alignment of sequences with insertions.
Löytynoja A, Goldman N.
Proc Natl Acad Sci U S A Volume 102 (2005) p.10557-10562

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 Res Volume 33 (2005) p.d154-9

2004

The Ensembl core software libraries.
Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E.
Genome Res Volume 14 (2004) p.929-933

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

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

Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
Shanahan HP, Garcia MA, Jones S, Thornton JM.
Nucleic Acids Res Volume 32 (2004) p.4732-4741

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 Res Volume 14 (2004) p.956-962

Genome information resources - developments at Ensembl.
Hammond MP, Birney E.
Trends Genet Volume 20 (2004) p.268-272

The Anopheles gambiae genome: an update.
Mongin E, Louis C, Holt RA, Birney E, Collins FH.
Trends Parasitol Volume 20 (2004) p.49-52

Biological database design and implementation.
Birney E, Clamp M.
Brief Bioinform Volume 5 (2004) p.31-38

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 Res Volume 14 (2004) p.160-169

Toward the detection and validation of repeats in protein structure.
Murray KB, Taylor WR, Thornton JM.
Proteins Volume 57 (2004) p.365-380

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 Volume 303 (2004) p.807

ISMB/ECCB 2004

Bioinformatics Volume 20 (2004) p.i1-i2

Searching for functional sites in protein structures.
Jones S, Thornton JM.
Curr Opin Chem Biol Volume 8 (2004) p.3-7

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 Res Volume 32 (2004) p.d129-33

Phylogenomics and bioinformatics of SARS-CoV.
Liò P, Goldman N.
Trends Microbiol Volume 12 (2004) p.106-111

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 Biol Volume 2 (2004) p.e162

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 Res Volume 32 (2004) p.d115-9

SCOPEC: a database of protein catalytic domains.
George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB.
Bioinformatics Volume 20 Suppl 1 (2004) p.i130-6

Evolution of protein superfamilies and bacterial genome size.
Ranea JA, Buchan DW, Thornton JM, Orengo CA.
J Mol Biol Volume 336 (2004) p.871-887

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 Res Volume 32 (2004) p.d262-6

Conformational change in substrate binding, catalysis and product release: an open and shut case?
Gutteridge A, Thornton J.
FEBS Lett Volume 567 (2004) p.67-73

Ligand selectivity and competition between enzymes in silico.
Macchiarulo A, Nobeli I, Thornton JM.
Nat Biotechnol Volume 22 (2004) p.1039-1045

The Gene Ontology (GO) database and informatics resource.
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R, Gene Ontology Consortium.
Nucleic Acids Res Volume 32 (2004) p.d258-61

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.
Nat Biotechnol Volume 22 (2004) p.177-183

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.
Nat Biotechnol Volume 22 (2004) p.1459-1466

Funding high-throughput data sharing.
Ball CA, Sherlock G, Brazma A.
Nat Biotechnol Volume 22 (2004) p.1179-1183

Proteomics and data standardisation
Orchard S, Hermjakob H, Apweiler R.
Drug Discov Today Biosilico Volume 2 (2004) p.91-93

Mapping the gene ontology into the unified medical language system.
Lomax J, McCray AT.
Comp Funct Genomics Volume 5 (2004) p.354-361

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 Res Volume 32 (2004) p.d27-30

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 Res Volume 32 (2004) p.w465-70

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.
Comp Funct Genomics Volume 5 (2004) p.148-155

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 Volume 150 (2004) p.3522-3524

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.
Environ Health Perspect Volume 112 (2004) p.a666-7

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

Current status of proteomic standards development.
Orchard S, Taylor C, Hermjakob H, Zhu W, Julian R, Apweiler R.
Expert Rev Proteomics Volume 1 (2004) p.179-183

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

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.
Nat Genet Volume 36 (2004) p.809-817

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 Res Volume 14 (2004) p.852-859

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 Biol Volume 2 (2004) p.e317

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 Res Volume 32 (2004) p.d452-5

GeneWise and Genomewise.
Birney E, Clamp M, Durbin R.
Genome Res Volume 14 (2004) p.988-995

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

UniProt archive.
Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R.
Bioinformatics Volume 20 (2004) p.3236-3237

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

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 examination of the conservation of surface patch polarity for proteins.
Shanahan HP, Thornton JM.
Bioinformatics Volume 20 (2004) p.2197-2204

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

Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
Eyre TA, Partridge L, Thornton JM.
Protein Eng Des Sel Volume 17 (2004) p.613-624

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 Res Volume 32 (2004) p.d468-70

A new criterion and method for amino acid classification.
Kosiol C, Goldman N, Buttimore NH.
J Theor Biol Volume 228 (2004) p.97-106

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 Res Volume 14 (2004) p.925-928

Estimating the frequency of events that cause multiple-nucleotide changes.
Whelan S, Goldman N.
Genetics Volume 167 (2004) p.2027-2043

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 Volume 20 (2004) p.2288-2295

2003

A structure-based anatomy of the E.coli metabolome.
Nobeli I, Ponstingl H, Krissinel EB, Thornton JM.
J Mol Biol Volume 334 (2003) p.697-719

Protein-DNA interactions: the story so far and a new method for prediction.
Jones S, Thornton JM.
Comp Funct Genomics Volume 4 (2003) p.428-431

Using structural motif templates to identify proteins with DNA binding function.
Jones S, Barker JA, Nobeli I, Thornton JM.
Nucleic Acids Res Volume 31 (2003) p.2811-2823

Unravelling dispersal patterns in an expanding population of a highly mobile seabird, the northern fulmar (Fulmarus glacialis).
Burg TM, Lomax J, Almond R, Brooke Mde L, Amos W.
Proc Biol Sci Volume 270 (2003) p.979-984

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Orchard S, Kersey P, Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 4 (2003) p.16-19

Towards reconstruction of gene networks from expression data by supervised learning.
Soinov LA, Krestyaninova MA, Brazma A.
Genome Biol Volume 4 (2003) p.r6

Discovering novel cis-regulatory motifs using functional networks.
Ettwiller LM, Rung J, Birney E.
Genome Res Volume 13 (2003) p.883-895

Sequences and topology.
Gerstein M, Thornton JM.
Curr Opin Struct Biol Volume 13 (2003) p.341-343

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.
Comp Funct Genomics Volume 4 (2003) p.203-206

Diversity of protein-protein interactions.
Nooren IM, Thornton JM.
EMBO J Volume 22 (2003) p.3486-3492

Recognizing the fold of a protein structure.
Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C.
Bioinformatics Volume 19 (2003) p.1748-1759

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 Res Volume 31 (2003) p.469-473

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 Res Volume 31 (2003) p.43-50

Pandit: a database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Goldman N.
Bioinformatics Volume 19 (2003) p.1556-1563

MCB-mediated regulation of cell cycle-specific cdc22+ transcription in fission yeast.
Maqbool Z, Kersey PJ, Fantes PA, McInerny CJ.
Mol Genet Genomics Volume 269 (2003) p.765-775

Probabilistic models for the study of protein evolution
Thorne JL, Goldman N.
Volume (2003) p.209-226

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 Volume 19 (2003) p.546-547

WU-Blast2 server at the European Bioinformatics Institute.
Lopez R, Silventoinen V, Robinson S, Kibria A, Gish W.
Nucleic Acids Res Volume 31 (2003) p.3795-3798

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

Catalysing new reactions during evolution: economy of residues and mechanism.
Bartlett GJ, Borkakoti N, Thornton JM.
J Mol Biol Volume 331 (2003) p.829-860

From gene networks to gene function.
Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A.
Genome Res Volume 13 (2003) p.2568-2576

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

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.
Comput Biol Chem Volume 27 (2003) p.49-58

Ensembl: a genome infrastructure.
Birney E, Ensembl Team.
Cold Spring Harb Symp Quant Biol Volume 68 (2003) p.213-215

Structural characterisation and functional significance of transient protein-protein interactions.
Nooren IM, Thornton JM.
J Mol Biol Volume 325 (2003) p.991-1018

Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Gutteridge A, Bartlett GJ, Thornton JM.
J Mol Biol Volume 330 (2003) p.719-734

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 Res Volume 31 (2003) p.38-42

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.
Mol Biol Cell Volume 14 (2003) p.214-229

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

Estimation of weights and validation: a marginal likelihood approach.
Lebedev AA, Tickle IJ, Laskowski RA, Moss DS.
Acta Crystallogr D Biol Crystallogr Volume 59 (2003) p.1557-1566

Comparative genomics: genome-wide analysis in metazoan eukaryotes.
Ureta-Vidal A, Ettwiller L, Birney E.
Nat Rev Genet Volume 4 (2003) p.251-262

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 Res Volume 31 (2003) p.17-22

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

Integr8: enhanced inter-operability of European molecular biology databases.
Kersey PJ, Morris L, Hermjakob H, Apweiler R.
Methods Inf Med Volume 42 (2003) p.154-160

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
Jones S, Shanahan HP, Berman HM, Thornton JM.
Nucleic Acids Res Volume 31 (2003) p.7189-7198

Standardization of microarray experiment data].
Brazma A, Ikeo K, Tateno Y.
Tanpakushitsu Kakusan Koso Volume 48 (2003) p.280-285

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 Res Volume 31 (2003) p.458-462

Molecular basis of inherited diseases: a structural perspective.
Steward RE, MacArthur MW, Laskowski RA, Thornton JM.
Trends Genet Volume 19 (2003) p.505-513

The proteomics standards initiative.
Orchard S, Hermjakob H, Apweiler R.
Proteomics Volume 3 (2003) p.1374-1376

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Barker JA, Thornton JM.
Bioinformatics Volume 19 (2003) p.1644-1649

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 Res Volume 31 (2003) p.315-318

Unrestricted free access works and must continue.
Salzberg S, Birney E, Eddy S, White O.
Nature Volume 422 (2003) p.801

Analysis of metabolic networks using a pathway distance metric through linear programming.
Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG.
Metab Eng Volume 5 (2003) p.211-219

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 Harb Symp Quant Biol Volume 68 (2003) p.237-243

The EMBL sequence version archive.
Leinonen R, Nardone F, Oyewole O, Redaschi N, Stoehr P.
Bioinformatics Volume 19 (2003) p.1861-1862

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 Res Volume 13 (2003) p.662-672

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.
Comp Funct Genomics Volume 4 (2003) p.71-74

From protein structure to biochemical function?
Laskowski RA, Watson JD, Thornton JM.
J Struct Funct Genomics Volume 4 (2003) p.167-177

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 Res Volume 13 (2003) p.13-26

Inferring protein function from structure.
Bartlett GJ, Todd AE, Thornton JM.
Methods Biochem Anal Volume 44 (2003) p.387-407

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.
J Biol Chem Volume 278 (2003) p.26039-26045

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 Res Volume 31 (2003) p.414-417

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

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 Res Volume 13 (2003) p.1335-1344

The CATH domain structure database.
Orengo CA, Pearl FM, Thornton JM.
Methods Biochem Anal Volume 44 (2003) p.249-271

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 Res Volume 31 (2003) p.68-71

Protein evolution with dependence among codons due to tertiary structure.
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL.
Mol Biol Evol Volume 20 (2003) p.1692-1704

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.
C R Biol Volume 326 (2003) p.1075-1078

2002

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 Volume 18 (2002) p.374-375

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.
Brief Bioinform Volume 3 (2002) p.285-295

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 Volume 298 (2002) p.149-159

Quantifying the similarities within fold space.
Harrison A, Pearl F, Mott R, Thornton J, Orengo C.
J Mol Biol Volume 323 (2002) p.909-926

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Luscombe NM, Thornton JM.
J Mol Biol Volume 320 (2002) p.991-1009

Modeling mitochondrial protein evolution using structural information.
Liò P, Goldman N.
J Mol Evol Volume 54 (2002) p.519-529

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 Res Volume 30 (2002) p.21-26

The EBI SRS server-new features.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics Volume 18 (2002) p.1149-1150

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 Volume 298 (2002) p.129-149

Toward predicting protein topology: an approach to identifying beta hairpins.
de la Cruz X, Hutchinson EG, Shepherd A, Thornton JM.
Proc Natl Acad Sci U S A Volume 99 (2002) p.11157-11162

Analysis of catalytic residues in enzyme active sites.
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM.
J Mol Biol Volume 324 (2002) p.105-121

Wavelet transforms for the characterization and detection of repeating motifs.
Murray KB, Gorse D, Thornton JM.
J Mol Biol Volume 316 (2002) p.341-363

Top scorer.
Brooksbank C.
Nat Rev Cancer Volume 2 (2002) p.81

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.
Brief Bioinform Volume 3 (2002) p.225-235

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 Volume 298 (2002) p.159-165

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 Res Volume 12 (2002) p.503-514

The EBI SRS server--recent developments.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics Volume 18 (2002) p.368-373

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

Bioinformatics and protein design.
Laskowski RA, Chan AW.
Curr Pharm Biotechnol Volume 3 (2002) p.317-327

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 Res Volume 30 (2002) p.38-41

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.
Rison SC, Teichmann SA, Thornton JM.
J Mol Biol Volume 318 (2002) p.911-932

Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
Steward RE, Thornton JM.
Proteins Volume 48 (2002) p.178-191

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

TEMBLOR - Perspectives of EBI Database Services.
Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 3 (2002) p.47-50

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.
Hum Mutat Volume 19 (2002) p.149-164

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.
Nat Struct Biol Volume 9 (2002) p.416-418

Correlating gene promoters and expression in gene disruption experiments.
Palin K, Ukkonen E, Brazma A, Vilo J.
Bioinformatics Volume 18 Suppl 2 (2002) p.s172-80

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 Res Volume 12 (2002) p.1611-1618

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

Databases and tools for browsing genomes.
Birney E, Clamp M, Hubbard T.
Annu Rev Genomics Hum Genet Volume 3 (2002) p.293-310

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

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 Volume 18 (2002) p.763-764

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

Microarray data representation, annotation and storage.
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K.
Adv Biochem Eng Biotechnol Volume 77 (2002) p.113-139

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 Biol Volume 3 (2002) p.research0046

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 Res Volume 30 (2002) p.276-280

A novel use of equilibrium frequencies in models of sequence evolution.
Goldman N, Whelan S.
Mol Biol Evol Volume 19 (2002) p.1821-1831

Pathway evolution, structurally speaking.
Rison SC, Thornton JM.
Curr Opin Struct Biol Volume 12 (2002) p.374-382

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.
Mol Biol Cell Volume 13 (2002) p.795-804

RAS, the magician.
Brooksbank C.
Nat Rev Cancer Volume 2 (2002) p.249

Unable to resist.
Brooksbank C.
Nat Rev Cancer Volume 2 (2002) p.248

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 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.
J Mol Biol Volume 321 (2002) p.741-765

One size fits all.
Brooksbank C.
Nat Rev Cancer Volume 2 (2002) p.78-79

Drifting downstream.
Brooksbank C.
Nat Rev Cancer Volume 2 (2002) p.79

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

Plasticity of enzyme active sites.
Todd AE, Orengo CA, Thornton JM.
Trends Biochem Sci Volume 27 (2002) p.419-426

Computational Methods and Bioinformatic Tools
Cullen P, Lorkowski S, Hennig S, Poustka A, Panopoulou G, Lehrach H, Korsching E, Pickeral O, Herwig R, Kel A, Tchekmenev D, Wingender E, Streicher J, Müller GB, Kawashima T, Makabe KW, Dubchak I, Ji H, Okubo K, Kawamoto S, Fricke E, Karas D, Haubrock M, Land S, Rotert S, Chen X, Pontius J, Eveno E, Auffray C, Decraene C, Chelala C, Piétu G, Devignes M-D, Mariage-Samson R, Imbeaud S, Bortoli S, Amit A, Ringwald M, de Veer MJ, Williams BRG, Walker EM, Davies JA, Grunau C, Baldock R, Davidson DR, Stoeckert CJ Jr., Pizarro A, Manduchi E, Grant GR, Crabtree J, Liu J, Le PV, McWeeney SK, Welle S, Ball CA, Botstein D, Binkley G, Sherlock GJ, Cherry JM, Dolinski K, Issel-Tarver L, Schroeder M, Dwight SS, Wenig S, Matese JC, Jin H, Gollub J, Hebert J, Kaloper M, Brown PO, Hernandez-Boussard T, Kumar A, Cheung K, Marenco L, Snyder M, Tosches N, Bertone P, Miller P, Masiar P, Liu Y, Pesole G, Marc P, Biswas M, Kersey P, Apweiler R, Hoogland C.
Volume (2002) p.769–904

Kinases as targets: prospects for chronic therapy.
Orchard S.
Curr Opin Drug Discov Devel Volume 5 (2002) p.713-717

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 Volume 18 (2002) p.1409

Learning about gene regulatory networks from gene deletion experiments.
Schlitt T, Brazma A.
Comp Funct Genomics Volume 3 (2002) p.499-503

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.
Mol Cell Volume 9 (2002) p.1133-1143

Apollo: a sequence annotation editor.
Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME.
Genome Biol Volume 3 (2002) p.research0082

Sequence and structural differences between enzyme and nonenzyme homologs.
Todd AE, Orengo CA, Thornton JM.
Structure Volume 10 (2002) p.1435-1451

Genome annotation techniques: new approaches and challenges.
Rust AG, Mongin E, Birney E.
Drug Discov Today Volume 7 (2002) p.s70-6

2001

Hidden Markov models in biological sequence analysis
Birney E.
IBM J. Res. Dev. Volume 45 (2001) p.449-454

Conservation helps to identify biologically relevant crystal contacts.
Valdar WS, Thornton JM.
J Mol Biol Volume 313 (2001) p.399-416

From genome to function.
Thornton JM.
Science Volume 292 (2001) p.2095-2097

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 Res Volume 29 (2001) p.37-40

Progress in sequencing the mouse genome.
Lindblad-Toh K, Lander ES, McPherson JD, Waterston RH, Rodgers J, Birney E.
Genesis Volume 31 (2001) p.137-141

The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution.
Thornton JM.
Protein Sci 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

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.
J Mol Biol Volume 311 (2001) p.693-708

On the molecular discrimination between adenine and guanine by proteins.
Nobeli I, Laskowski RA, Valdar WS, Thornton JM.
Nucleic Acids Res Volume 29 (2001) p.4294-4309

Mining the draft human genome.
Birney E, Bateman A, Clamp ME, Hubbard TJ.
Nature Volume 409 (2001) p.827-828

The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
Nagano N, Porter CT, Thornton JM.
Protein Eng Volume 14 (2001) p.845-855

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 Res Volume 29 (2001) p.223-227

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 N, 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, Szustakowski 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, International Human Genome Sequencing Consortium.
Nature Volume 409 (2001) p.860-921

Protein-protein interfaces: analysis of amino acid conservation in homodimers.
Valdar WS, Thornton JM.
Proteins Volume 42 (2001) p.108-124

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
Whelan S, Goldman N.
Mol Biol Evol Volume 18 (2001) p.691-699

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.
Nat Genet Volume 29 (2001) p.365-371

Evolution of function in protein superfamilies, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
J Mol Biol Volume 307 (2001) p.1113-1143

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 Res Volume 29 (2001) p.17-21

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
Luscombe NM, Laskowski RA, Thornton JM.
Nucleic Acids Res 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 Res Volume 29 (2001) p.44-48

Protein-RNA interactions: a structural analysis.
Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM.
Nucleic Acids Res Volume 29 (2001) p.943-954

Cancer and genomics.
Futreal PA, Kasprzyk A, Birney E, Mullikin JC, Wooster R, Stratton MR.
Nature Volume 409 (2001) p.850-852

Small-molecule metabolism: an enzyme mosaic.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C.
Trends Biotechnol Volume 19 (2001) p.482-486

2000

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 Eng Volume 13 (2000) p.153-165

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.
Nat Genet Volume 26 (2000) p.81-84

Hidden Markov models for database similarity searches
Birney E.
Volume (2000) p.77

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

Open annotation offers a democratic solution to genome sequencing.
Hubbard T, Birney E.
Nature Volume 403 (2000) p.825

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.
Proc Biol Sci Volume 267 (2000) p.1595-1596

Comparison of functional annotation schemes for genomes.
Rison SC, Hodgman TC, Thornton JM.
Funct Integr Genomics Volume 1 (2000) p.56-69

The Pfam protein families database.
Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL.
Nucleic Acids Res 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 Res Volume 28 (2000) p.277-282

An overview of the structures of protein-DNA complexes.
Luscombe NM, Austin SE, Berman HM, Thornton JM.
Genome Biol Volume 1 (2000) p.reviews001

Identification of domains from protein sequences.
Ponting CP, Birney E.
Methods Mol Biol Volume 143 (2000) p.53-69

Likelihood-based tests of topologies in phylogenetics.
Goldman N, Anderson JP, Rodrigo AG.
Syst Biol Volume 49 (2000) p.652-670

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.
Biochem Soc Trans Volume 28 (2000) p.269-275

Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics.
Goldman N, Whelan S.
Mol Biol Evol Volume 17 (2000) p.975-978

Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.
Jones S, Marin A, Thornton JM.
Protein Eng Volume 13 (2000) p.77-82

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 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 Volume 16 (2000) p.741-742

Searching databases to find protein domain organization.
Bateman A, Birney E.
Adv Protein Chem Volume 54 (2000) p.137-157

The EMBL nucleotide sequence database.
Baker W, van den Broek A, Camon E, Hingamp P, Sterk P, Stoesser G, Tuli MA.
Nucleic Acids Res Volume 28 (2000) p.19-23

Mus musculus in the SWISS-PROT database: its relevance to developmental research.
Magrane M, Apweiler R.
Genesis Volume 26 (2000) p.1-4

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 Volume 16 (2000) p.1145-1150

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Kersey P, Hermjakob H, Apweiler R.
Bioinformatics Volume 16 (2000) p.1048-1049

EDIBLE: experimental design and information calculations in phylogenetics.
Massingham T, Goldman N.
Bioinformatics Volume 16 (2000) p.294-295

From structure to function: approaches and limitations.
Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA.
Nat Struct Biol Volume 7 Suppl (2000) p.991-994

Analysis and prediction of carbohydrate binding sites.
Taroni C, Jones S, Thornton JM.
Protein Eng Volume 13 (2000) p.89-98

ProtEST: protein multiple sequence alignments from expressed sequence tags.
Cuff JA, Birney E, Clamp ME, Barton GJ.
Bioinformatics Volume 16 (2000) p.111-116

The Bioperl project: motivation and usage
Stajich J, Birney E.
ACM SIGBIO Newsletter Volume 20 (2000) p.13-14

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.
J Biotechnol Volume 78 (2000) p.221-234

Discriminating between homodimeric and monomeric proteins in the crystalline state.
Ponstingl H, Henrick K, Thornton JM.
Proteins Volume 41 (2000) p.47-57

Using GeneWise in the Drosophila annotation experiment.
Birney E, Durbin R.
Genome Res Volume 10 (2000) p.547-548

1999

Using protein structural information in evolutionary inference: transmembrane proteins.
Liò P, Goldman N.
Mol Biol Evol Volume 16 (1999) p.1696-1710

Prediction of the location and type of beta-turns in proteins using neural networks.
Shepherd AJ, Gorse D, Thornton JM.
Protein Sci Volume 8 (1999) p.1045-1055

Protein-DNA interactions: A structural analysis.
Jones S, van Heyningen P, Berman HM, Thornton JM.
J Mol Biol Volume 287 (1999) p.877-896

Protein structural topology: Automated analysis and diagrammatic representation.
Westhead DR, Slidel TW, Flores TP, Thornton JM.
Protein Sci Volume 8 (1999) p.897-904

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 Crystallogr D Biol Crystallogr Volume 55 (1999) p.994-1004

Factors limiting the performance of prediction-based fold recognition methods.
de la Cruz X, Thornton JM.
Protein Sci Volume 8 (1999) p.750-759

Coevolving protein residues: maximum likelihood identification and relationship to structure.
Pollock DD, Taylor WR, Goldman N.
J Mol Biol Volume 287 (1999) p.187-198

Protein folds, functions and evolution.
Thornton JM, Orengo CA, Todd AE, Pearl FM.
J Mol Biol Volume 293 (1999) p.333-342

Evolution of protein function, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
Curr Opin Chem Biol Volume 3 (1999) p.548-556

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Apweiler R, Hermjakob H, Sharon N.
Biochim Biophys Acta Volume 1473 (1999) p.4-8

The EMBL Nucleotide Sequence Database.
Stoesser G, Tuli MA, Lopez R, Sterk P.
Nucleic Acids Res Volume 27 (1999) p.18-24

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 Eng Volume 12 (1999) p.375-379

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.
Dis Aquat Organ Volume 35 (1999) p.155-158

From protein structure to function.
Orengo CA, Todd AE, Thornton JM.
Curr Opin Struct Biol Volume 9 (1999) p.374-382

Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
Whelan S, Goldman N.
Mol Biol Evol Volume 16 (1999) p.1292-1299

Three-dimensional structure analysis of PROSITE patterns.
Kasuya A, Thornton JM.
J Mol Biol Volume 286 (1999) p.1673-1691

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.
Syst Appl Microbiol Volume 22 (1999) p.403-411

Swissknife - 'lazy parsing' of SWISS-PROT entries.
Hermjakob H, Fleischmann W, Apweiler R.
Bioinformatics Volume 15 (1999) p.771-772

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.
Proc Biol Sci Volume 266 (1999) p.485-492

Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
Nagano N, Hutchinson EG, Thornton JM.
Protein Sci Volume 8 (1999) p.2072-2084

Correlation of observed fold frequency with the occurrence of local structural motifs.
Salem GM, Hutchinson EG, Orengo CA, Thornton JM.
J Mol Biol Volume 287 (1999) p.969-981

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 Res Volume 27 (1999) p.275-279

1998

PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.
Bioinformatics Volume 14 (1998) p.726-733

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).
Patel SU, Osborn R, Rees S, Thornton JM.
Biochemistry Volume 37 (1998) p.983-990

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 Sci Volume 7 (1998) p.233-242

Protein folds and functions.
Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM.
Structure Volume 6 (1998) p.875-884

Models of molecular evolution and phylogeny.
Liò P, Goldman N.
Genome Res Volume 8 (1998) p.1233-1244

Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Milburn D, Laskowski RA, Thornton JM.
Protein Eng Volume 11 (1998) p.855-859

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

Contemporary approaches to protein structure classification.
Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM.
Bioessays 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 Sci Volume 7 (1998) p.2287-2300

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

Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
Hubbard SJ, Beynon RJ, Thornton JM.
Protein Eng Volume 11 (1998) p.349-359

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 Crystallogr D Biol Crystallogr Volume 54 (1998) p.1132-1138

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 Crystallogr D Biol Crystallogr Volume 54 (1998) p.1155-1167

Validation of protein models derived from experiment.
Laskowski RA, MacArthur MW, Thornton JM.
Curr Opin Struct Biol Volume 8 (1998) p.631-639

Evolution of the androgen receptor: structure-function implications.
Thornton JW, Kelley DB.
Bioessays Volume 20 (1998) p.860-869

An atlas of protein topology cartoons available on the World-Wide Web.
Westhead DR, Hatton DC, Thornton JM.
Trends Biochem Sci Volume 23 (1998) p.35-36

Phylogenetic information and experimental design in molecular systematics.
Goldman N.
Proc Biol Sci Volume 265 (1998) p.1779-1786

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.
J Mol Biol Volume 277 (1998) p.317-332

Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.
Zuccotto F, Martin AC, Laskowski RA, Thornton JM, Gilbert IH.
J Comput Aided Mol Des Volume 12 (1998) p.241-257

Protein structure prediction.
Westhead DR, Thornton JM.
Curr Opin Biotechnol Volume 9 (1998) p.383-389

PQS: a protein quaternary structure file server.
Henrick K, Thornton JM.
Trends Biochem Sci Volume 23 (1998) p.358-361

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 Res Volume 26 (1998) p.362-367

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.
Syst Appl Microbiol Volume 21 (1998) p.50-64

1997

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 Biochem Sci Volume 22 (1997) p.488-490

Are big trees indeed easy?
Yang Z, Goldman N.
Trends Ecol Evol Volume 12 (1997) p.357

Assessment of comparative modeling in CASP2.
Martin AC, MacArthur MW, Thornton JM.
Proteins Volume Suppl 1 (1997) p.14-28

Prediction of protein-protein interaction sites using patch analysis.
Jones S, Thornton JM.
J Mol Biol Volume 272 (1997) p.133-143

RIFLE: rapid identification of microorganisms by fragment length evaluation.
Hermjakob H, Giegerich R, Arnold W.
Proc Int Conf Intell Syst Mol Biol Volume 5 (1997) p.131-139

CATH--a hierarchic classification of protein domain structures.
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM.
Structure Volume 5 (1997) p.1093-1108

Phylogenetic estimation
Goldman N.
Volume (1997) p.279-312

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 Sci Volume 6 (1997) p.2308-2323

Modelling protein unfolding: hen egg-white lysozyme.
Williams MA, Thornton JM, Goodfellow JM.
Protein Eng Volume 10 (1997) p.895-903

Analysis of protein-protein interaction sites using surface patches.
Jones S, Thornton JM.
J Mol Biol 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 Res Volume 25 (1997) p.4940-4945

Structures of N-termini of helices in proteins.
Doig AJ, MacArthur MW, Stapley BJ, Thornton JM.
Protein Sci Volume 6 (1997) p.147-155

Non-randomness in side-chain packing: the distribution of interplanar angles.
Mitchell JB, Laskowski RA, Thornton JM.
Proteins Volume 29 (1997) p.370-380

Bayesian probabilities and quartet puzzling
Strimmer K, Goldman N, von Haeseler A.
Mol Biol Evol Volume 14 (1997) p.210

1996

Molecular recognition by proteins: protein-ligand interactions from a structural perspective.
Wallace AC, Laskowski RA, Singh J, Thornton JM.
Biochem Soc Trans Volume 24 (1996) p.280-284

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.
Martin AC, Thornton JM.
J Mol Biol Volume 263 (1996) p.800-815

Principles of protein-protein interactions.
Jones S, Thornton JM.
Proc Natl Acad Sci U S A Volume 93 (1996) p.13-20

Combining protein evolution and secondary structure.
Thorne JL, Goldman N, Jones DT.
Mol Biol Evol Volume 13 (1996) p.666-673

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.
Eur J Biochem Volume 242 (1996) p.352-362

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.
Mol Immunol Volume 33 (1996) p.471-483

Deviations from planarity of the peptide bond in peptides and proteins.
MacArthur MW, Thornton JM.
J Mol Biol Volume 264 (1996) p.1180-1195

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.
J Biomol NMR Volume 8 (1996) p.477-486

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 Biochem Sci Volume 21 (1996) p.251-256

Analysis of domain structural class using an automated class assignment protocol.
Michie AD, Orengo CA, Thornton JM.
J Mol Biol Volume 262 (1996) p.168-185

Protein clefts in molecular recognition and function.
Laskowski RA, Luscombe NM, Swindells MB, Thornton JM.
Protein Sci Volume 5 (1996) p.2438-2452

Protein recognition of adenylate: an example of a fuzzy recognition template.
Moodie SL, Mitchell JB, Thornton JM.
J Mol Biol Volume 263 (1996) p.486-500

Antibody-antigen interactions: contact analysis and binding site topography.
MacCallum RM, Martin AC, Thornton JM.
J Mol Biol Volume 262 (1996) p.732-745

Protein fold recognition by sequence threading: tools and assessment techniques.
Miller RT, Jones DT, Thornton JM.
FASEB J Volume 10 (1996) p.171-178

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.
J Mol Biol Volume 255 (1996) p.494-506

Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.
Goldman N, Thorne JL, Jones DT.
J Mol Biol Volume 263 (1996) p.196-208

PROMOTIF--a program to identify and analyze structural motifs in proteins.
Hutchinson EG, Thornton JM.
Protein Sci Volume 5 (1996) p.212-220

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 Sci Volume 5 (1996) p.1001-1013

Potential energy functions for threading.
Jones DT, Thornton JM.
Curr Opin Struct Biol Volume 6 (1996) p.210-216

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.
Int J Pept Protein Res Volume 47 (1996) p.427-436

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.
J Mol Biol Volume 259 (1996) p.175-201

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

1995

Combining protein secondary structure and evolution
Thorne JL, Goldman N, Jones DT.
Volume (1995) p.62-64

Protein folds: towards understanding folding from inspection of native structures.
Thornton JM, Jones DT, MacArthur MW, Orengo CM, Swindells MB.
Philos Trans R Soc Lond B Biol Sci Volume 348 (1995) p.71-79

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.
Swindells MB, MacArthur MW, Thornton JM.
Nat Struct Biol Volume 2 (1995) p.596-603

Estimation of Parameters of Evolutionary Models, with Applications in the Analysis of Large Data Sets
Goldman N.
Volume (1995) p.26-27

Long loops in proteins.
Martin AC, Toda K, Stirk HJ, Thornton JM.
Protein Eng Volume 8 (1995) p.1093-1101

Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem
Yang Z, Goldman N, Friday A.
Syst Biol Volume 44 (1995) p.384-399

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.
J Gen Virol Volume 76 ( Pt 2) (1995) p.333-345

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

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 Sci Volume 4 (1995) p.1977-1983

Protein-protein interactions: a review of protein dimer structures.
Jones S, Thornton JM.
Prog Biophys Mol Biol Volume 63 (1995) p.31-65

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Wallace AC, Laskowski RA, Thornton JM.
Protein Eng Volume 8 (1995) p.127-134

1994

Protein superfamilies and domain superfolds.
Orengo CA, Jones DT, Thornton JM.
Nature Volume 372 (1994) p.631-634

Evaluation and extension of Markov process models for the evolution of DNA].
Yang Z, Goldman N.
Yi Chuan Xue Bao Volume 21 (1994) p.17-23

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.
Mol Biol Evol Volume 11 (1994) p.725-736

Models of DNA substitution and the discrimination of evolutionary parameters
Goldman N, Yang Z.
Volume (1994) p.407-420

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Hubbard SJ, Eisenmenger F, Thornton JM.
Protein Sci Volume 3 (1994) p.757-768

NMR and crystallography--complementary approaches to structure determination.
MacArthur MW, Driscoll PC, Thornton JM.
Trends Biotechnol Volume 12 (1994) p.149-153

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
Yang Z, Goldman N, Friday A.
Mol Biol Evol Volume 11 (1994) p.316-324

A revised set of potentials for beta-turn formation in proteins.
Hutchinson EG, Thornton JM.
Protein Sci Volume 3 (1994) p.2207-2216

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.
Goldman N.
Mol Phylogenet Evol Volume 3 (1994) p.230-239

An algorithm for automatically generating protein topology cartoons.
Flores TP, Moss DS, Thornton JM.
Protein Eng Volume 7 (1994) p.31-37

Satisfying hydrogen bonding potential in proteins.
McDonald IK, Thornton JM.
J Mol Biol Volume 238 (1994) p.777-793

Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
Mitchell JB, Nandi CL, McDonald IK, Thornton JM, Price SL.
J Mol Biol Volume 239 (1994) p.315-331

The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.
Stirk HJ, Thornton JM.
Protein Eng Volume 7 (1994) p.47-56

1993

Further results on error minimization in the genetic code.
Goldman N.
J Mol Evol 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 Res Volume 21 (1993) p.2487-2491

Simple diagnostic statistical tests of models for DNA substitution.
Goldman N.
J Mol Evol Volume 37 (1993) p.650-661

1992

Human origins. Genetics and geography.
Goldman N, Barton NH.
Nature Volume 357 (1992) p.440-441

1990

Quantitative analysis of shape variation in populations of Surirella fastuosa
Goldman N, Paddock TBB, Shaw KM.
Diatom Res. Volume 5 (1990) p.25-42

Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses
Goldman N.
Syst Biol Volume 39 (1990) p.345

1989

The Empire of Chance: How probability changed science and everyday life (book review)
Goldman N.
Volume (1989) p.252-253

1988

Methods for discrete coding of morphological characters for numerical analysis
Goldman N.
Cladistics Volume 4 (1988) p.59-71