Publications for 2012

2012

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

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

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

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

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

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

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

Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study.
Budczies J, Denkert C, Müller BM, Brockmöller SF, Klauschen F, Györffy B, Dietel M, Richter-Ehrenstein C, Marten U, Salek RM, Griffin JL, Hilvo M, Orešič M, Wohlgemuth G, Fiehn O.
BMC Genomics Volume 13 (2012) p.334

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

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

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

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

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

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

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

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

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ, Swertz MA.
Hum Mutat Volume 33 (2012) p.867-873

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

Women in science.
Dean C, Osborn M, Oshlack A, Thornton J.
Genome Biol Volume 13 (2012) p.148

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

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA.
Mol Cell Volume 47 (2012) p.183-192

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

Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Schwarz MA, Thornton J, Xu H, Awasthi N, Schwarz RE.
PLoS One Volume 7 (2012) p.e33101

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

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

Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery.
Denkert C, Bucher E, Hilvo M, Salek R, Orešič M, Griffin J, Brockmöller S, Klauschen F, Loibl S, Barupal DK, Budczies J, Iljin K, Nekljudova V, Fiehn O.
Genome Med Volume 4 (2012) p.37

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.
arcOGEN Consortium, arcOGEN Collaborators, Zeggini E, Panoutsopoulou K, Southam L, Rayner NW, Day-Williams AG, Lopes MC, Boraska V, Esko T, Evangelou E, Hoffman A, Houwing-Duistermaat JJ, Ingvarsson T, Jonsdottir I, Jonnson H, Kerkhof HJ, Kloppenburg M, Bos SD, Mangino M, Metrustry S, Slagboom PE, Thorleifsson G, Raine EV, Ratnayake M, Ricketts M, Beazley C, Blackburn H, Bumpstead S, Elliott KS, Hunt SE, Potter SC, Shin SY, Yadav VK, Zhai G, Sherburn K, Dixon K, Arden E, Aslam N, Battley PK, Carluke I, Doherty S, Gordon A, Joseph J, Keen R, Koller NC, Mitchell S, O'Neill F, Paling E, Reed MR, Rivadeneira F, Swift D, Walker K, Watkins B, Wheeler M, Birrell F, Ioannidis JP, Meulenbelt I, Metspalu A, Rai A, Salter D, Stefansson K, Stykarsdottir U, Uitterlinden AG, van Meurs JB, Chapman K, Deloukas P, Ollier WE, Wallis GA, Arden N, Carr A, Doherty M, McCaskie A, Willkinson JM, Ralston SH, Valdes AM, Spector TD, Loughlin J.
Lancet Volume 380 (2012) p.815-823

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

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

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

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

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

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.
Birney E.
Nature Volume 489 (2012) p.49-51

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Large-scale analysis of microRNA evolution.
Guerra-Assunção JA, Enright AJ.
BMC Genomics Volume 13 (2012) p.218

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

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ Jr, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A.
Circulation Volume 125 (2012) p.2751-2761

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

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

Foreword
Goldman N, Yang Z.
Volume (2012) p.ix-x

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

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

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

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

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

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

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

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

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

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

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

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

WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW.
Worm Volume 1 (2012) p.15-21

WormBase: 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

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

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

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

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

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

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

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

Modeling signaling networks using high-throughput phospho-proteomics.
Terfve C, Saez-Rodriguez J.
Adv Exp Med Biol Volume 736 (2012) p.19-57

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

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

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

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

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

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.
Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C.
J Biol Chem Volume 287 (2012) p.29516-29528

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

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

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

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

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

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

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
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Nat Protoc Volume 7 (2012) p.500-507

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

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

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

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

Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics Volume 28 (2012) p.3169-3177

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

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

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

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

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

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

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

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

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

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

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

PSI-Search: iterative HOE-reduced profile SSEARCH searching.
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR.
Bioinformatics Volume 28 (2012) p.1650-1651

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

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

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

The Origin and Function of Anti-Fungal Peptides in C. elegans: Open Questions.
Pujol N, Davis PA, Ewbank JJ.
Front Immunol Volume 3 (2012) p.237

Automatic categorization of diverse experimental information in the bioscience literature.
Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold SJ, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW.
BMC Bioinformatics Volume 13 (2012) p.16

All Your Base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.
Genome Biol Volume 13 (2012) p.r13

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

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

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

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

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

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

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

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

MyDas, an extensible Java DAS server.
Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.
PLoS One Volume 7 (2012) p.e44180

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

GrameneMart: the BioMart data portal for the Gramene project.
Spooner W, Youens-Clark K, Staines D, Ware D.
Database (Oxford) Volume 2012 (2012) p.bar056

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

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

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

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

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.
Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA.
Integr Biol (Camb) Volume 4 (2012) p.1038-1048

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

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

Cheminformatics
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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

Mapping small molecule binding data to structural domains.
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BMC Bioinformatics Volume 13 Suppl 17 (2012) p.s11

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

Toxicogenomics Investigation Under the eTOX Project
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J Pharmacogenomics Pharmacoproteomics Volume S7 (2012) p.1-5

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

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

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

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

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

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

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

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

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.
BMC Syst Biol Volume 6 (2012) p.29

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

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

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

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

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

MetaBase--the wiki-database of biological databases.
Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, González V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J.
Nucleic Acids Res Volume 40 (2012) p.d1250-4

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM.
PLoS One Volume 7 (2012) p.e50881

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

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