Publications for 2013


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

World Health Organization International Standard to harmonize assays for detection of hepatitis E virus RNA.
Baylis SA, Blümel J, Mizusawa S, Matsubayashi K, Sakata H, Okada Y, Nübling CM, Hanschmann KM, HEV Collaborative Study Group.
Emerging Infectious Diseases Volume 19 (2013) p.729-735

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

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

Hepatitis E virus infection in Ghanaian blood donors - the importance of immunoassay selection and confirmation.
Meldal BH, Sarkodie F, Owusu-Ofori S, Allain JP.
Vox sanguinis Volume 104 (2013) p.30-36

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.
Sanseverino W, Hermoso A, D'Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR.
Nucleic Acids Research Volume 41 (2013) p.D1167-71

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D773-80

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

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

LifeTrain: towards a European framework for continuing professional development in biomedical sciences
Brooksbank C.
Nature reviews. Drug discovery Volume (2013) p.

JBioWH: an open-source Java framework for bioinformatics data integration.
Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat051

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

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

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

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

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

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

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

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

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

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2395-2402

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM.
PLoS computational biology Volume 9 (2013) p.e1003382

Abstracting knowledge from the Protein Data Bank.
Furnham N, Laskowski RA, Thornton JM.
Biopolymers Volume 99 (2013) p.183-188

Epimutation profiling in Beckwith-Wiedemann syndrome: relationship with assisted reproductive technology.
Tee L, Lim DH, Dias RP, Baudement MO, Slater AA, Kirby G, Hancocks T, Stewart H, Hardy C, Macdonald F, Maher ER.
Clinical epigenetics Volume 5 (2013) p.23

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

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

Noncanonical expression of caudal during early embryogenesis in the pea aphid Acyrthosiphon pisum: maternal cad-driven posterior development is not conserved.
Chang CC, Hsiao YM, Huang TY, Cook CE, Shigenobu S, Chang TH.
Insect molecular biology Volume 22 (2013) p.442-455

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, Apweiler R, Ge J, Hermjakob H, Ping P.
Circulation research Volume 113 (2013) p.1043-1053

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

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

Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.
Paul DS, Albers CA, Rendon A, Voss K, Stephens J, HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P.
Genome research Volume 23 (2013) p.1130-1141

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

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

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

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

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

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

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.
Science (New York, N.Y.) Volume 342 (2013) p.1516-1517

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

Ontology based molecular signatures for immune cell types via gene expression analysis.
Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD.
BMC Bioinformatics Volume 14 (2013) p.263

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

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

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

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

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

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

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

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

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

The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat029

Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling.
Invergo BM, Montanucci L, Koch KW, Bertranpetit J, Dell'orco D.
Cell communication and signaling : CCS Volume 11 (2013) p.36

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

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

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

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

A system-level, molecular evolutionary analysis of mammalian phototransduction.
Invergo BM, Montanucci L, Laayouni H, Bertranpetit J.
BMC evolutionary biology Volume 13 (2013) p.52

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

A large-scale evaluation of computational protein function prediction.
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.
Nature methods Volume 10 (2013) p.221-227

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D781-6

Best practices in bioinformatics training for life scientists.
Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.
Briefings in bioinformatics Volume 14 (2013) p.528-537

Association of gut microbiota with post-operative clinical course in Crohn's disease.
Dey N, Soergel DA, Repo S, Brenner SE.
BMC gastroenterology Volume 13 (2013) p.131

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

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

iAnn: an event sharing platform for the life sciences.
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1919-1921

UniChem: a unified chemical structure cross-referencing and identifier tracking system.
Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP.
Journal of Cheminformatics Volume 5 (2013) p.3

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

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM.
Current opinion in structural biology Volume 23 (2013) p.443-450

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

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

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

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

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

Filling out the structural map of the NTF2-like superfamily.
Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L.
BMC Bioinformatics Volume 14 (2013) p.327

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

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

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

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

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

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

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

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

Skirting the pitfalls: a clear-cut nomenclature for H3K4 methyltransferases.
Bögershausen N, Bruford E, Wollnik B.
Clinical genetics Volume 83 (2013) p.212-214

The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat023

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

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

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

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

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

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

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

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, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.
GigaScience Volume 2 (2013) p.10

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

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

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic acids research Volume 41 (2013) p.D530-5

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.
Nucleic acids research Volume 41 (2013) p.D499-507

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

Vive la différence: naming structural variants in the human reference genome.
Seal RL, Wright MW, Gray KA, Bruford EA.
Human genomics Volume 7 (2013) p.12

Facing growth in the European Nucleotide Archive.
Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V.
Nucleic Acids Research Volume 41 (2013) p.D30-5

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

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

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

The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.
PLoS Biology Volume 11 (2013) p.e1001638

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

A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2808-2809

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

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

HAMAP in 2013, new developments in the protein family classification and annotation system.
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium.
Nucleic Acids Research Volume 41 (2013) p.D584-9

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

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

Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium.
Nucleic Acids Research Volume 41 (2013) p.D43-7

ISMB/ECCB 2013 Proceedings Papers Committee.

Bioinformatics (Oxford, England) Volume 29 (2013) p.i3-i8

IPD--the Immuno Polymorphism Database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG.
Nucleic Acids Research Volume 41 (2013) p.D1234-40

OntoQuery: easy-to-use web-based OWL querying.
Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2955-2957

Characterization of a versatile organometallic pro-drug (CORM) for experimental CO based therapeutics.
Seixas JD, Mukhopadhyay A, Santos-Silva T, Otterbein LE, Gallo DJ, Rodrigues SS, Guerreiro BH, Gonçalves AM, Penacho N, Marques AR, Coelho AC, Reis PM, Romão MJ, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 42 (2013) p.5985-5998

Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
Ilsley GR, Fisher J, Apweiler R, De Pace AH, Luscombe NM.
eLife Volume 2 (2013) p.e00522

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D456-63

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

The IMGT/HLA database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic Acids Research Volume 41 (2013) p.D1222-7

The annotation-enriched non-redundant patent sequence databases.
Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat005

The role of structural bioinformatics resources in the era of integrative structural biology.
Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.710-721

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

Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.
Nucleic acids research Volume 41 (2013) p.D226-32

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP.
Nucleic acids research Volume 41 (2013) p.4549-4564

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

The ABCs of membrane transporters in health and disease (SLC series): introduction.
Hediger MA, Clémençon B, Burrier RE, Bruford EA.
Molecular aspects of medicine Volume 34 (2013) p.95-107

Response to Diaz.
Bögershausen N, Bruford E, Wollnik B.
Clinical genetics Volume 83 (2013) p.296

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.
Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ.
Genome biology Volume 14 (2013) p.R11

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

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

ISCB computational biology Wikipedia competition.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.
PLoS Computational Biology Volume 9 (2013) p.e1003242

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

Update on the Kelch-like (KLHL) gene family.
Dhanoa BS, Cogliati T, Satish AG, Bruford EA, Friedman JS.
Human genomics Volume 7 (2013) p.13

DbVar and DGVa: public archives for genomic structural variation.
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM.
Nucleic acids research Volume 41 (2013) p.D936-41

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

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

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.

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

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat077

ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.
Nucleic acids research Volume 41 (2013) p.D987-90

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

Detecting and comparing non-coding RNAs in the high-throughput era.
Bussotti G, Notredame C, Enright AJ.
International journal of molecular sciences Volume 14 (2013) p.15423-15458

Enhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice.
Clare S, John V, Walker AW, Hill JL, Abreu-Goodger C, Hale C, Goulding D, Lawley TD, Mastroeni P, Frankel G, Enright AJ, Vigorito E, Dougan G.
Infection and immunity Volume 81 (2013) p.723-732

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

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ.
Methods (San Diego, Calif.) Volume 63 (2013) p.41-49

LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.
Murray MJ, Saini HK, Siegler CA, Hanning JE, Barker EM, van Dongen S, Ward DM, Raby KL, Groves IJ, Scarpini CG, Pett MR, Thornton CM, Enright AJ, Nicholson JC, Coleman N, CCLG.
Cancer research Volume 73 (2013) p.4872-4884

Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state.
Hanning JE, Saini HK, Murray MJ, Caffarel MM, van Dongen S, Ward D, Barker EM, Scarpini CG, Groves IJ, Stanley MA, Enright AJ, Pett MR, Coleman N.
The Journal of pathology Volume 231 (2013) p.354-366

Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene.
Hanning JE, Saini HK, Murray MJ, van Dongen S, Davis MP, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR, Coleman N.
British journal of cancer Volume 108 (2013) p.450-460

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

miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs.
Lupini L, Bassi C, Ferracin M, Bartonicek N, D'Abundo L, Zagatti B, Callegari E, Musa G, Moshiri F, Gramantieri L, Corrales FJ, Enright AJ, Sabbioni S, Negrini M.
Frontiers in Genetics Volume 4 (2013) p.64

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, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.
Science (New York, N.Y.) Volume 342 (2013) p.1235587

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

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.132-134

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.
Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J.
Molecular bioSystems Volume 9 (2013) p.1576-1583

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

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

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

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

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

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D.
Molecular cell Volume 50 (2013) p.601-608

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic acids research Volume 41 (2013) p.W15-21

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

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

Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF.
Nolen LD, Boyle S, Ansari M, Pritchard E, Bickmore WA.
Human molecular genetics Volume 22 (2013) p.4180-4193

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

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ.
Journal of structural biology Volume 184 (2013) p.173-181

Cryo-electron microscopy--a primer for the non-microscopist.
Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S.
The FEBS journal Volume 280 (2013) p.28-45

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H.
Nucleic acids research Volume 41 (2013) p.D1063-9

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

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

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

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, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.
Genome biology Volume 14 (2013) p.R37

Proteins from Tuber magnatum Pico fruiting bodies naturally grown in different areas of Italy.
Vita F, Lucarotti V, Alpi E, Balestrini R, Mello A, Bachi A, Alessio M, Alpi A.
Proteome science Volume 11 (2013) p.7

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

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

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

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

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

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, Yates A, Zadissa A, Searle SM.
Nucleic acids research Volume 41 (2013) p.D48-55

Histone deacetylase 1 and 2 are essential for normal T-cell development and genomic stability in mice.
Dovey OM, Foster CT, Conte N, Edwards SA, Edwards JM, Singh R, Vassiliou G, Bradley A, Cowley SM.
Blood Volume 121 (2013) p.1335-1344

Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture.
Conte N, Varela I, Grove C, Manes N, Yusa K, Moreno T, Segonds-Pichon A, Bench A, Gudgin E, Herman B, Bolli N, Ellis P, Haddad D, Costeas P, Rad R, Scott M, Huntly B, Bradley A, Vassiliou GS.
Leukemia Volume 27 (2013) p.1820-1825

The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.
Li MA, Pettitt SJ, Eckert S, Ning Z, Rice S, Cadiñanos J, Yusa K, Conte N, Bradley A.
Molecular and cellular biology Volume 33 (2013) p.1317-1330

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

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.
Nature biotechnology Volume 31 (2013) p.1015-1022

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, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Psychosis Endophenotypes International Consortium, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Wellcome Trust Case Control Consortium 2, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CC, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CC, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF.
Nature genetics Volume 45 (2013) p.1150-1159

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

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC), Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL.
Nature genetics Volume 45 (2013) p.1353-1360

Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.
LeishGEN Consortium, Wellcome Trust Case Control Consortium 2, Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SM, Sundar S, Spencer CC, Blackwell JM, Donnelly P.
Nature genetics Volume 45 (2013) p.208-213

Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus.
Blue Mountains Eye Study (BMES), Wellcome Trust Case Control Consortium 2 (WTCCC2).
Human molecular genetics Volume 22 (2013) p.4653-4660

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson WO, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimäki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt MF, Mohlke KL, O'Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E.
Nature genetics Volume 45 (2013) p.501-512 the HGNC resources in 2013.
Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA.
Nucleic acids research Volume 41 (2013) p.D545-52

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

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 HHW, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA.
Nature genetics Volume 45 (2013) p.542-545

A variant in LDLR is associated with abdominal aortic aneurysm.
Bradley DT, Hughes AE, Badger SA, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Grétarsdóttir S, Burnand K, Child AH, Clough RE, Cockerill G, Hafez H, Scott DJ, Ariëns RA, Johnson A, Sohrabi S, Smith A, Thompson MM, van Bockxmeer FM, Waltham M, Matthíasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Wild JB, Edkins S, Gwilliam R, Hunt SE, Potter S, Lindholt JS, Golledge J, Norman PE, van Rij A, Powell JT, Eriksson P, Stefánsson K, Thompson JR, Humphries SE, Sayers RD, Deloukas P, Samani NJ, Bown MJ.
Circulation. Cardiovascular genetics Volume 6 (2013) p.498-504

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

Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.
Hinks A, Cobb J, Marion MC, Prahalad S, Sudman M, Bowes J, Martin P, Comeau ME, Sajuthi S, Andrews R, Brown M, Chen WM, Concannon P, Deloukas P, Edkins S, Eyre S, Gaffney PM, Guthery SL, Guthridge JM, Hunt SE, James JA, Keddache M, Moser KL, Nigrovic PA, Onengut-Gumuscu S, Onslow ML, Rosé CD, Rich SS, Steel KJ, Wakeland EK, Wallace CA, Wedderburn LR, Woo P, Boston Children's JIA Registry, British Society of Paediatric and Adolescent Rheumatology (BSPAR) Study Group, Childhood Arthritis Prospective Study (CAPS), Childhood Arthritis Response to Medication Study (CHARMS), German Society for Pediatric Rheumatology (GKJR), JIA Gene Expression Study, NIAMS JIA Genetic Registry, TREAT Study, United Kingdom Juvenile Idiopathic Arthritis Genetics Consortium (UKJIAGC), Bohnsack JF, Haas JP, Glass DN, Langefeld CD, Thomson W, Thompson SD.
Nature genetics Volume 45 (2013) p.664-669

Meta-analysis of gene-level associations for rare variants based on single-variant statistics.
Hu YJ, Berndt SI, Gustafsson S, Ganna A, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn J, North KE, Ingelsson E, Lin DY.
American Journal of Human Genetics Volume 93 (2013) p.236-248

Large-scale association analysis identifies new risk loci for coronary artery disease.
CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, DIAGRAM Consortium, CARDIOGENICS Consortium, Doney AS, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, MuTHER Consortium, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AF, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wellcome Trust Case Control Consortium, Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O'Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CN, Roberts R, Watkins H, Schunkert H, Samani NJ.
Nature genetics Volume 45 (2013) p.25-33

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

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

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

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

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, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.
Nature biotechnology Volume 31 (2013) p.419-425

Analysis Tool Web Services from the EMBL-EBI.
McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R.
Nucleic acids research Volume 41 (2013) p.W597-600

Detection and imaging the expression of the trans-membrane protein CD44 in RT112 cells by use of enzyme-labeled antibodies and SECM.
Roberts WS, Davis F, Holmes JL, Collyer SD, Larcombe LD, Morgan SL, Higson SP.
Biosensors & bioelectronics Volume 41 (2013) p.282-288

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

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.
Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R.
The Journal of pathology Volume 230 (2013) p.270-276

Diagnostic criteria and clinical guidelines standardization to automate case classification.
Courtot M, Zheng J, Stoeckert CJ, Brinkman RR, Ruttenberg A.
CEURS proceedings: International Conference on Biomedical Ontologies Volume 1060 (2013) p.101-104

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

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

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

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

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.
Genome biology Volume 14 (2013) p.R70

Reuse of public genome-wide gene expression data.
Rung J, Brazma A.
Nature reviews. Genetics Volume 14 (2013) p.89-99

Emdatabank: Unified Data Resource for 3DEM
Catherine Lawson, Ardan Patwardhan, Grigore D Pintilie, Eduardo Sanz Garcia, Ingvar Lagerstedt, Matthew L Baker, Raul Sala, Steven J Ludtke, Helen M Berman, Gerard Kleywegt, Wah Chiu.
Biophysical journal Volume 104 (2013) p.351a

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

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.
Hill AF, Pegtel DM, Lambertz U, Leonardi T, O'Driscoll L, Pluchino S, Ter-Ovanesyan D, Nolte-'t Hoen EN.
Journal of extracellular vesicles Volume 2 (2013) p.

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

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

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

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

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

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC.
Journal of proteomics Volume 89 (2013) p.179-182

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

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

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: Genes|Genomes|Genetics Volume 3 (2013) p.2031-2047

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV.
Briefings in bioinformatics Volume 14 (2013) p.548-555

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.
Anderson JW, Haas PA, Mathieson LA, Volynkin V, Lyngsø R, Tataru P, Hein J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.704-710

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bas062

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

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

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

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

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

Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.
Nucleic Acids Research Volume 41 (2013) p.827-841 a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z.
Nucleic acids research Volume 41 (2013) p.D171-6

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

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

Structural and functional annotation of the porcine immunome.
Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK.
BMC genomics Volume 14 (2013) p.332

The impact of mathematical modeling on the understanding of diabetes and related complications.
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V.
CPT: Pharmacometrics & Systems Pharmacology Volume 2 (2013) p.e54

The Drosophila anatomy ontology.
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D.
Journal of biomedical semantics Volume 4 (2013) p.32

SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping.
Betancourt LH, De Bock PJ, Staes A, Timmerman E, Perez-Riverol Y, Sanchez A, Besada V, Gonzalez LJ, Vandekerckhove J, Gevaert K.
Journal of proteomics Volume 91 (2013) p.164-171

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

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

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1325-1332

Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.
Auburn S, Marfurt J, Maslen G, Campino S, Ruano Rubio V, Manske M, Machunter B, Kenangalem E, Noviyanti R, Trianty L, Sebayang B, Wirjanata G, Sriprawat K, Alcock D, Macinnis B, Miotto O, Clark TG, Russell B, Anstey NM, Nosten F, Kwiatkowski DP, Price RN.
PLoS ONE Volume 8 (2013) p.e53160

Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya.
Borrmann S, Straimer J, Mwai L, Abdi A, Rippert A, Okombo J, Muriithi S, Sasi P, Kortok MM, Lowe B, Campino S, Assefa S, Auburn S, Manske M, Maslen G, Peshu N, Kwiatkowski DP, Marsh K, Nzila A, Clark TG.
Scientific reports Volume 3 (2013) p.3318

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

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 PAF, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FMK, 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 B, Trabzuni D, North American Brain Expression Consortium, UK Brain Expression Consortium, Rossin E, Lage K, Jacobs SBR, 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 AMJM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman D, Palotie A.
Nature genetics Volume 45 (2013) p.912-917

Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J, Bertone P.
Nature methods Volume 10 (2013) p.1177-1184

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

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

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

Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1343-1344

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ.
Nucleic Acids Research Volume 41 (2013) p.D483-9

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.
Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM, Duong S, Nguon C, Chuor CM, Saunders D, Se Y, Lon C, Fukuda MM, Amenga-Etego L, Hodgson AV, Asoala V, Imwong M, Takala-Harrison S, Nosten F, Su XZ, Ringwald P, Ariey F, Dolecek C, Hien TT, Boni MF, Thai CQ, Amambua-Ngwa A, Conway DJ, Djimdé AA, Doumbo OK, Zongo I, Ouedraogo JB, Alcock D, Drury E, Auburn S, Koch O, Sanders M, Hubbart C, Maslen G, Ruano-Rubio V, Jyothi D, Miles A, O'Brien J, Gamble C, Oyola SO, Rayner JC, Newbold CI, Berriman M, Spencer CC, McVean G, Day NP, White NJ, Bethell D, Dondorp AM, Plowe CV, Fairhurst RM, Kwiatkowski DP.
Nature genetics Volume 45 (2013) p.648-655