Publications for 2011

2011

Effects of BMI and abdominal volume on the accuracy of step count obtained from a tri-axial accelerometer.
Cleland I, Nugent CD, Finlay DD, Burns W, Bougourd J, Stevens K, Armitage R.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2011 (2011) p.3656-3659

Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria.
Deng N, Zhang J, Zong C, Wang Y, Lu H, Yang P, Wang W, Young GW, Wang Y, Korge P, Lotz C, Doran P, Liem DA, Apweiler R, Weiss JN, Duan H, Ping P.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.M110.000117

Reactome: a database of reactions, pathways and biological processes.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.
Nucleic acids research Volume 39 (2011) p.D691-7

easyDAS: automatic creation of DAS servers.
Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H.
BMC bioinformatics Volume 12 (2011) p.23

Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C, BioDBCore Working Group.
Database : the journal of biological databases and curation Volume 2011 (2011) p.baq027

The genomic standards consortium: bringing standards to life for microbial ecology.
Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L, Karsch-Mizrachi I, Cochrane G, Nakamura Y, Sansone SA, Glöckner FO, Field D.
The ISME Journal Volume 5 (2011) p.1565-1567

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y.
PLoS Genetics Volume 7 (2011) p.e1001316

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
Nature methods Volume 8 (2011) p.528-529

Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.
PLoS Computational Biology Volume 7 (2011) p.e1001099

The representation of heart development in the gene ontology.
Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC.
Developmental biology Volume 354 (2011) p.9-17

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

Physiological and molecular evidence that environmental changes elicit morphological interconversion in the model diatom Phaeodactylum tricornutum.
De Martino A, Bartual A, Willis A, Meichenin A, Villazán B, Maheswari U, Bowler C.
Protist Volume 162 (2011) p.462-481

The Genomic Standards Consortium.
Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J.
PLoS Biology Volume 9 (2011) p.e1001088

Minimum information about a bioactive entity (MIABE).
Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.
Nature reviews. Drug discovery Volume 10 (2011) p.661-669

Gene expression differences among primates are associated with changes in a histone epigenetic modification.
Cain CE, Blekhman R, Marioni JC, Gilad Y.
Genetics Volume 187 (2011) p.1225-1234

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
Holliday GL, Fischer JD, Mitchell JB, Thornton JM.
The FEBS journal Volume 278 (2011) p.3835-3845

Collation and data-mining of literature bioactivity data for drug discovery.
Bellis LJ, Akhtar R, Al-Lazikani B, Atkinson F, Bento AP, Chambers J, Davies M, Gaulton A, Hersey A, Ikeda K, Krüger FA, Light Y, McGlinchey S, Santos R, Stauch B, Overington JP.
Biochemical Society transactions Volume 39 (2011) p.1365-1370

Conserved BK channel-protein interactions reveal signals relevant to cell death and survival.
Sokolowski B, Orchard S, Harvey M, Sridhar S, Sakai Y.
PloS one Volume 6 (2011) p.e28532

Comparative and demographic analysis of orang-utan genomes.
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.
Nature Volume 469 (2011) p.529-533

The sequence read archive.
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 39 (2011) p.D19-21

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts.
Caiazzo M, Dell'Anno MT, Dvoretskova E, Lazarevic D, Taverna S, Leo D, Sotnikova TD, Menegon A, Roncaglia P, Colciago G, Russo G, Carninci P, Pezzoli G, Gainetdinov RR, Gustincich S, Dityatev A, Broccoli V.
Nature Volume 476 (2011) p.224-227

Developmental influence of the cellular prion protein on the gene expression profile in mouse hippocampus.
Benvegnù S, Roncaglia P, Agostini F, Casalone C, Corona C, Gustincich S, Legname G.
Physiological genomics Volume 43 (2011) p.711-725

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

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.
Nature biotechnology Volume 29 (2011) p.415-420

Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C, BioDBCore Working Group.
Nucleic acids research Volume 39 (2011) p.D7-10

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

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

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 11 (2011) p.4434-4438

Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding blaCTX-M-14.
Cottell JL, Webber MA, Coldham NG, Taylor DL, Cerdeño-Tárraga AM, Hauser H, Thomson NR, Woodward MJ, Piddock LJ.
Emerging infectious diseases Volume 17 (2011) p.645-652

Data standardization by the HUPO-PSI: how has the community benefitted?
Orchard S, Hermjakob H.
Methods in molecular biology (Clifton, N.J.) Volume 696 (2011) p.149-160

Preparing molecular interaction data for publication.
Orchard S, Hermjakob H.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.229-236

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. Clinical applications Volume 5 (2011) p.580-589

Autism candidate genes via mouse phenomics.
Meehan TF, Carr CJ, Jay JJ, Bult CJ, Chesler EJ, Blake JA.
Journal of biomedical informatics Volume 44 Suppl 1 (2011) p.S5-11

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel HR, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC.
Genome biology Volume 12 (2011) p.R81

Motor neuron impairment mediated by a sumoylated fragment of the glial glutamate transporter EAAT2.
Foran E, Bogush A, Goffredo M, Roncaglia P, Gustincich S, Pasinelli P, Trotti D.
Glia Volume 59 (2011) p.1719-1731

Mouse genomic variation and its effect on phenotypes and gene regulation.
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ.
Nature Volume 477 (2011) p.289-294

A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.
Nature Volume 478 (2011) p.476-482

The European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G.
Nucleic acids research Volume 39 (2011) p.D28-31

In-silico ADME models: a general assessment of their utility in drug discovery applications.
Gleeson MP, Hersey A, Hannongbua S.
Current topics in medicinal chemistry Volume 11 (2011) p.358-381

Logical development of the cell ontology.
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD.
BMC bioinformatics Volume 12 (2011) p.6

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.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.O111.015446

Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA.
Nucleic acids research Volume 39 (2011) p.D420-6

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic acids research Volume 39 (2011) p.D214-9

Rare and functional SIAE variants are not associated with autoimmune disease risk in up to 66,924 individuals of European ancestry.
Hunt KA, Smyth DJ, Balschun T, Ban M, Mistry V, Ahmad T, Anand V, Barrett JC, Bhaw-Rosun L, Bockett NA, Brand OJ, Brouwer E, Concannon P, Cooper JD, Dias KR, van Diemen CC, Dubois PC, Edkins S, Fölster-Holst R, Fransen K, Glass DN, Heap GA, Hofmann S, Huizinga TW, Hunt S, Langford C, Lee J, Mansfield J, Marrosu MG, Mathew CG, Mein CA, Müller-Quernheim J, Nutland S, Onengut-Gumuscu S, Ouwehand W, Pearce K, Prescott NJ, Posthumus MD, Potter S, Rosati G, Sambrook J, Satsangi J, Schreiber S, Shtir C, Simmonds MJ, Sudman M, Thompson SD, Toes R, Trynka G, Vyse TJ, Walker NM, Weidinger S, Zhernakova A, Zoledziewska M, Type 1 Diabetes Genetics Consortium, UK Inflammatory Bowel Disease (IBD) Genetics Consortium, Wellcome Trust Case Control Consortium, Weersma RK, Gough SC, Sawcer S, Wijmenga C, Parkes M, Cucca F, Franke A, Deloukas P, Rich SS, Todd JA, van Heel DA.
Nature genetics Volume 44 (2011) p.3-5

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.
Morris C, Pajon A, Griffiths SL, Daniel E, Savitsky M, Lin B, Diprose JM, da Silva AW, Pilicheva K, Troshin P, van Niekerk J, Isaacs N, Naismith J, Nave C, Blake R, Wilson KS, Stuart DI, Henrick K, Esnouf RM.
Acta crystallographica. Section D, Biological crystallography Volume 67 (2011) p.249-260

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".
Griffin JL, Atherton HJ, Steinbeck C, Salek RM.
BMC research notes Volume 4 (2011) p.272

The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P, Köhn M.
Biochemistry Volume 50 (2011) p.7579-7590

Celebrating structural biology.

Nature structural & molecular biology Volume 18 (2011) p.1304-1316

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.
Camacho R, Pereira M, Costa VS, Fonseca NA, Adriano C, Simões CJ, Brito RM.
Journal of integrative bioinformatics Volume 8 (2011) p.182

A posteriori quality control for the curation and reuse of public proteomics data.
Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, Apweiler R, Martens L.
Proteomics Volume 11 (2011) p.2182-2194

Predicting Malignancy from Mammography Findings and Surgical Biopsies.
Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Volume 2011 (2011) p.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA (New York, N.Y.) Volume 17 (2011) p.578-594

PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.
Nucleic Acids Research Volume 39 (2011) p.D402-10

Computational metabolomics – a field at the boundaries of cheminformatics and bioinformatics.
Steinbeck C, Kuhn S, Jayaseelan KV, Moreno P.
Journal of cheminformatics Volume 3 (2011) p.O6-O6

Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues.
Moreno P, Jayaseelan K, Steinbeck C.
Journal of cheminformatics Volume 3 (2011) p.P19-P19

Omics technologies, data and bioinformatics principles.
Schneider MV, Orchard S.
Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.3-30

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.
BMC bioinformatics Volume 12 (2011) p.218

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements.
De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D.
Nature Volume 480 (2011) p.259-263

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.
Lakner C, Holder MT, Goldman N, Naylor GJ.
Systematic biology Volume 60 (2011) p.161-174

Atomic resolution insights into curli fiber biogenesis.
Taylor JD, Zhou Y, Salgado PS, Patwardhan A, McGuffie M, Pape T, Grabe G, Ashman E, Constable SC, Simpson PJ, Lee WC, Cota E, Chapman MR, Matthews SJ.
Structure (London, England : 1993) Volume 19 (2011) p.1307-1316

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.
BMC bioinformatics Volume 12 (2011) p.104

Human metabolic profiles are stably controlled by genetic and environmental variation.
Nicholson G, Rantalainen M, Maher AD, Li JV, Malmodin D, Ahmadi KR, Faber JH, Hallgrímsdóttir IB, Barrett A, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, The Molpage Consortium, Silverman BW, Donnelly P, Nicholson JK, Allen M, Zondervan KT, Lindon JC, Spector TD, McCarthy MI, Holmes E, Baunsgaard D, Holmes CC.
Molecular Systems Biology Volume 7 (2011) p.525

Data standards for Omics data: the basis of data sharing and reuse.
Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA.
Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.31-69

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.
Puri V, Goyal A, Sankaranarayanan R, Enright AJ, Vaidya T.
BMC evolutionary biology Volume 11 (2011) p.334

Anatomy ontologies and potential users: bridging the gap.
Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H.
Journal of biomedical semantics Volume 2 Suppl 4 (2011) p.S3

Messenger RNA and microRNA profiling during early mouse EB formation.
Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S, Enright AJ.
Gene expression patterns : GEP Volume 11 (2011) p.334-344

UniProt Knowledgebase: a hub of integrated protein data.
Magrane M, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar009

RNAcentral: A vision for an international database of RNA sequences.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNA (New York, N.Y.) Volume 17 (2011) p.1941-1946

Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC.
Gut Volume 60 (2011) p.1317-1326

A revised nomenclature for transcribed human endogenous retroviral loci.
Mayer J, Blomberg J, Seal RL.
Mobile DNA Volume 2 (2011) p.7

The International Nucleotide Sequence Database Collaboration.
Cochrane G, Karsch-Mizrachi I, Nakamura Y, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 39 (2011) p.D15-8

MiR-221 influences effector functions and actin cytoskeleton in mast cells.
Mayoral RJ, Deho L, Rusca N, Bartonicek N, Saini HK, Enright AJ, Monticelli S.
PloS one Volume 6 (2011) p.e26133

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.6-8

Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily.
Bingle CD, Seal RL, Craven CJ.
Biochemical Society transactions Volume 39 (2011) p.977-983

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.
Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D.
BMC plant biology Volume 11 (2011) p.104

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

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.
Galperin MY, Cochrane GR.
Nucleic acids research Volume 39 (2011) p.D1-6

Computational biology for ageing.
Wieser D, Papatheodorou I, Ziehm M, Thornton JM.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.51-63

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2156-2158

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.
de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL.
Journal of theoretical biology Volume 271 (2011) p.136-144

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.
Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, Fonseca NA.
International journal of legal medicine Volume 125 (2011) p.629-636

Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project.
Nature genetics Volume 43 (2011) p.712-714

Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project.
Nature Volume 470 (2011) p.59-65

The functional spectrum of low-frequency coding variation.
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project.
Genome biology Volume 12 (2011) p.R84

Demographic history and rare allele sharing among human populations.
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, 1000 Genomes Project, Bustamante CD.
Proceedings of the National Academy of Sciences of the United States of America Volume 108 (2011) p.11983-11988

A novel strategy for NMR resonance assignment and protein structure determination.
Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH.
Journal of biomolecular NMR Volume 49 (2011) p.27-38

UKPMC: a full text article resource for the life sciences.
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, Lewin I, Lyte V, MacIntyre R, Mansoor S, Mason L, McNaught J, Newbold E, Nobata C, Ong E, Pillai S, Rebholz-Schuhmann D, Rosie H, Rowbotham R, Rupp CJ, Stoehr P, Vaughan P.
Nucleic acids research Volume 39 (2011) p.D58-65

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.
Genome research Volume 21 (2011) p.1757-1767

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.
Genome research Volume 21 (2011) p.2224-2241

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
Molecular Systems Biology Volume 7 (2011) p.539

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.
Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.M111.008490

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

Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2616-2617

Ensembl 2011.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM.
Nucleic acids research Volume 39 (2011) p.D800-6

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.
Nucleic acids research Volume 39 (2011) p.D1002-4

Modernizing reference genome assemblies.
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T.
PLoS biology Volume 9 (2011) p.e1001091

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

Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D.
Nucleic acids research Volume 39 (2011) p.D1085-94

Minimum Information About a Simulation Experiment (MIASE).
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N.
PLoS computational biology Volume 7 (2011) p.e1001122

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H.
Proteomics Volume 11 (2011) p.4284-4290

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

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

genenames.org: the HGNC resources in 2011.
Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA.
Nucleic acids research Volume 39 (2011) p.D514-9

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

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

POPISK: T-cell reactivity prediction using support vector machines and string kernels.
Tung CW, Ziehm M, Kämper A, Kohlbacher O, Ho SY.
BMC bioinformatics Volume 12 (2011) p.446

The impact of focused Gene Ontology curation of specific mammalian systems.
Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC.
PloS one Volume 6 (2011) p.e27541

Ten simple rules for getting help from online scientific communities.
Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H.
PLoS computational biology Volume 7 (2011) p.e1002202

Structural annotation of Mycobacterium tuberculosis proteome.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R, OSDD Consortium, Brahmachari SK, Chandra N.
PloS one Volume 6 (2011) p.e27044

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, Murray-Rust P.
Journal of Cheminformatics Volume 3 (2011) p.37

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.
Alic N, Andrews TD, Giannakou ME, Papatheodorou I, Slack C, Hoddinott MP, Cochemé HM, Schuster EF, Thornton JM, Partridge L.
Molecular Systems Biology Volume 7 (2011) p.502

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

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

Genome sequence and analysis of the tuber crop potato.
Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sønderkær M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert Bt, Goverse A, van Ham RC, Visser RG.
Nature Volume 475 (2011) p.189-195

Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar030

In silico analysis of accurate proteomics, complemented by selective isolation of peptides.
Perez-Riverol Y, Sánchez A, Ramos Y, Schmidt A, Müller M, Betancourt L, González LJ, Vera R, Padron G, Besada V.
Journal of proteomics Volume 74 (2011) p.2071-2082

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.
Nature Volume 477 (2011) p.419-423

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

Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: evaluation in proteomic studies using peptide-centric database searches.
Betancourt LH, Sánchez A, Pérez Y, Fernandez de Cossio J, Gil J, Toledo P, Iguchi S, Aimoto S, González LJ, Padrón G, Takao T, Besada V.
Journal of proteomics Volume 74 (2011) p.2210-2213

myKaryoView: a light-weight client for visualization of genomic data.
Jimenez RC, Salazar GA, Gel B, Dopazo J, Mulder N, Corpas M.
PloS one Volume 6 (2011) p.e26345

Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature.
Wright MW, Bruford EA.
Human genomics Volume 5 (2011) p.90-98

Genome of Streptococcus oralis strain Uo5.
Reichmann P, Nuhn M, Denapaite D, Brückner R, Henrich B, Maurer P, Rieger M, Klages S, Reinhard R, Hakenbeck R.
Journal of bacteriology Volume 193 (2011) p.2888-2889

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P.
BMC research notes Volume 4 (2011) p.313

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs.
Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC.
Nucleic acids research Volume 39 (2011) p.W190-6

MIREOT: The minimum information to reference an external ontology term
Courtot M, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A.
Applied ontology Volume 6 (2011) p.23-33

mzML--a community standard for mass spectrometry data.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.R110.000133

Controlled vocabularies and semantics in systems biology.
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.
Molecular Systems Biology Volume 7 (2011) p.543

A common layer of interoperability for biomedical ontologies based on OWL EL.
Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV.
Bioinformatics (Oxford, England) Volume 27 (2011) p.1001-1008

Revision history aware repositories of computational models of biological systems.
Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PM.
BMC bioinformatics Volume 12 (2011) p.22

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

Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A.
Bioinformatics (Oxford, England) Volume 27 (2011) p.973-979

The GUDMAP database--an online resource for genitourinary research.
Harding SD, Armit C, Armstrong J, Brennan J, Cheng Y, Haggarty B, Houghton D, Lloyd-MacGilp S, Pi X, Roochun Y, Sharghi M, Tindal C, McMahon AP, Gottesman B, Little MH, Georgas K, Aronow BJ, Potter SS, Brunskill EW, Southard-Smith EM, Mendelsohn C, Baldock RA, Davies JA, Davidson D.
Development (Cambridge, England) Volume 138 (2011) p.2845-2853

Modularization requirements in bio-ontologies: A case study of ChEbi
Hastings J, Batchelor C, Steinbeck C, Schulz S.
Advances in molecular bioinformatics Volume 230 (2011) p.63-70

Developing a kidney and urinary pathway knowledge base.
Jupp S, Klein J, Schanstra J, Stevens R.
Journal of biomedical semantics Volume 2 Suppl 2 (2011) p.S7

Hematopoietic cell types: prototype for a revised cell ontology.
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ.
Journal of biomedical informatics Volume 44 (2011) p.75-79

Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors.
Pelé J, Abdi H, Moreau M, Thybert D, Chabbert M.
PloS one Volume 6 (2011) p.e19094

Reporting Adverse Events: Basis for a Common Representation.
Courtot M, Brinkman RR, Ruttenberg A.
CEURS proceedings: International Conference on Biomedical Ontologies Volume 833 (2011) p.

DAS writeback: a collaborative annotation system.
Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.
BMC bioinformatics Volume 12 (2011) p.143

Reactome pathway analysis to enrich biological discovery in proteomics data sets.
Haw R, Hermjakob H, D'Eustachio P, Stein L.
Proteomics Volume 11 (2011) p.3598-3613

New gene functions in megakaryopoiesis and platelet formation.
Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Mägi R, Meacham S, Okada Y, Pirastu N, Sorice R, Teumer A, Voss K, Zhang W, Ramirez-Solis R, Bis JC, Ellinghaus D, Gögele M, Hottenga JJ, Langenberg C, Kovacs P, O'Reilly PF, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, Ellen van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, D'Adamo P, Davies G, de Boer RA, de Geus EJ, Döring A, Elliott P, Erdmann J, Evans DM, Falchi M, Feng W, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kühnel B, Kyrtsonis MC, Lagou V, Lloyd-Jones H, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nakamura Y, Nauck M, Navis G, Nöthlings U, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Tang WH, Taylor K, Tenesa A, Lay Thein S, Tönjes A, Uda M, Ulivi S, van Veldhuisen DJ, Visscher PM, Völker U, Wichmann HE, Wiggins KL, Willemsen G, Yang TP, Hua Zhao J, Zitting P, Bradley JR, Dedoussis GV, Gasparini P, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, Joost van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Rendon A, Ferreira MA, Ouwehand WH, Soranzo N.
Nature Volume 480 (2011) p.201-208

Building the OBO Foundry-One Policy at a Time
Courtot M, Mungall C, Brinkman RR, Ruttenberg A.
CEURS proceedings: International Conference on Biomedical Ontologies Volume 833 (2011) p.

Overcoming the ontology enrichment bottleneck with Quick Term Templates
Rocca-Serra P, Ruttenberg A, O'Connor MJ, Whetzel PL, Schober D, Greenbaum J, Courtot M, Brinkman RR, Sansone SA, Scheuermann R, Peters B.
Applied ontology Volume 6 (2011) p.13-22

Using semantic web technologies to manage complexity and change in biomedical data.
Stevens R, Jupp S, Klein J, Schanstra J.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2011 (2011) p.3708-3711

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS.
Genome research Volume 21 (2011) p.456-464

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar047

The Reactome BioMart.
Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar031

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

Peptide fractionation by acid pH SDS-free electrophoresis.
Ramos Y, Garcia Y, Pérez-Riverol Y, Leyva A, Padrón G, Sánchez A, Castellanos-Serra L, González LJ, Besada V.
Electrophoresis Volume 32 (2011) p.1323-1326

The IMGT/HLA database.
Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic acids research Volume 39 (2011) p.D1171-6

EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W.
Nucleic acids research Volume 39 (2011) p.D456-64

"4D Biology for health and disease" workshop report.
Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ.
New biotechnology Volume 28 (2011) p.291-293

EST analysis pipeline: use of distributed computing resources.
González FJ, Vizcaíno JA.
Methods in molecular biology (Clifton, N.J.) Volume 722 (2011) p.103-120

A guide to UniProt for protein scientists.
O'Donovan C, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.25-35

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

Quality control in proteomics.
Martens L, Vizcaíno JA, Banks R.
Proteomics Volume 11 (2011) p.1015-1016

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.
Kosiol C, Goldman N.
Journal of molecular biology Volume 411 (2011) p.910-923

Protein structure databases.
Laskowski RA.
Molecular biotechnology Volume 48 (2011) p.183-198

Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R.
Genome biology Volume 12 (2011) p.402

Contributions of the EMERALD project to assessing and improving microarray data quality.
Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.
BioTechniques Volume 50 (2011) p.27-31

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.
Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT.
Nature genetics Volume 43 (2011) p.948-955

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

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M.
Bioinformatics (Oxford, England) Volume 27 (2011) p.589-591

A new generation of crystallographic validation tools for the protein data bank.
Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.
Structure (London, England : 1993) Volume 19 (2011) p.1395-1412

Solving the Problem: Genome Annotation Standards before the Data Deluge.
Klimke W, O'Donovan C, White O, Brister JR, Clark K, Fedorov B, Mizrachi I, Pruitt KD, Tatusova T.
Standards in genomic sciences Volume 5 (2011) p.168-193

Comparing signaling networks between normal and transformed hepatocytes using discrete logical models.
Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK.
Cancer research Volume 71 (2011) p.5400-5411

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

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.
Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M.
PloS one Volume 6 (2011) p.e25513

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.
Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP.
Genome biology Volume 12 (2011) p.R90

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, MolPAGE Consortium, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan KT, Spector TD, Nicholson JK, Lindon JC, Baunsgaard D, Holmes E, McCarthy MI, Holmes CC.
PLoS genetics Volume 7 (2011) p.e1002270

Submitting proteomics data to PRIDE using PRIDE Converter.
Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.237-253

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lef?vre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng Z, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song X, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC.
Genome biology Volume 12 (2011) p.414-414

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
Journal of chemical information and modeling Volume 51 (2011) p.2778-2786

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

Proteomic temporal profile of human brain endothelium after oxidative stress.
Ning M, Sarracino DA, Kho AT, Guo S, Lee SR, Krastins B, Buonanno FS, Vizcaíno JA, Orchard S, McMullin D, Wang X, Lo EH.
Stroke Volume 42 (2011) p.37-43