Publications for 2011

2011

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Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Genome research Volume 22 (2012) p.602-610 DOI: 10.1101/gr.130468.111
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In vitro characterization of the activity of PF-05095808, a novel biological agent for hepatitis C virus therapy.
Lavender H, Brady K, Burden F, Delpuech-Adams O, Denise H, Palmer A, Perkins H, Savic B, Scott S, Smith-Burchnell C, Troke P, Wright JF, Suhy D, Corbau R. Antimicrobial agents and chemotherapy Volume 56 (2012) p.1364-1375 DOI: 10.1128/aac.05357-11
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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 DOI: 10.1002/pmic.201100562
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 DOI: 10.1186/1758-2946-3-54
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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 DOI: 10.1371/journal.pone.0028532
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European initiative towards quality standards in education and training for discovery, development and use of medicines.
Klech H, Brooksbank C, Price S, Verpillat P, Bühler FR, Dubois D, Haider N, Johnson C, Lindén HH, Payton T, Renn O, See W. European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences Volume 45 (2012) p.515-520 DOI: 10.1016/j.ejps.2011.12.005
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 DOI: 10.1371/journal.pone.0027541
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Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Journal of proteome research Volume 11 (2012) p.1412-1419 DOI: 10.1021/pr201071t
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The kinase Sgg modulates temporal development of macrochaetes in Drosophila by phosphorylation of Scute and Pannier.
Yang M, Hatton-Ellis E, Simpson P. Development (Cambridge, England) Volume 139 (2012) p.325-334 DOI: 10.1242/dev.074260
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Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L. Drug discovery today Volume 17 Suppl (2012) p.S3-15 DOI: 10.1016/j.drudis.2011.12.005
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Making your database available through Wikipedia: the pros and cons.
Finn RD, Gardner PP, Bateman A. Nucleic acids research Volume 40 (2012) p.D9-12 DOI: 10.1093/nar/gkr1195
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Celebrating structural biology.
Nature structural & molecular biology Volume 18 (2011) p.1304-1316 DOI: 10.1038/nsmb1211-1304
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D, VectorBase Consortium. Nucleic acids research Volume 40 (2012) p.D729-34 DOI: 10.1093/nar/gkr1089
Rhea--a manually curated resource of biochemical reactions.
Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C. Nucleic acids research Volume 40 (2012) p.D754-60 DOI: 10.1093/nar/gkr1126
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MetaBase--the wiki-database of biological databases.
Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, González V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J. Nucleic acids research Volume 40 (2012) p.D1250-4 DOI: 10.1093/nar/gkr1099
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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 DOI: 10.1002/prca.201100097
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FlyBase 101--the basics of navigating FlyBase.
McQuilton P, St Pierre SE, Thurmond J, FlyBase Consortium. Nucleic acids research Volume 40 (2012) p.D706-14 DOI: 10.1093/nar/gkr1030
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The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. Nucleic acids research Volume 40 (2012) p.D290-301 DOI: 10.1093/nar/gkr1065
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 DOI: 10.1093/bioinformatics/btr662
The UniProt-GO Annotation database in 2011.
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R. Nucleic acids research Volume 40 (2012) p.D565-70 DOI: 10.1093/nar/gkr1048
The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H. Nucleic acids research Volume 40 (2012) p.D841-6 DOI: 10.1093/nar/gkr1088
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C. Briefings in bioinformatics Volume 13 (2012) p.383-389 DOI: 10.1093/bib/bbr064
PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. Nucleic acids research Volume 40 (2012) p.D445-52 DOI: 10.1093/nar/gkr998
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Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S. Bioinformatics (Oxford, England) Volume 28 (2012) p.246-253 DOI: 10.1093/bioinformatics/btr634
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The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium. Nucleic acids research Volume 40 (2012) p.D559-64 DOI: 10.1093/nar/gkr1028
Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 40 (2012) p.D71-5 DOI: 10.1093/nar/gkr981
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SABIO-RK--database for biochemical reaction kinetics.
Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Müller W. Nucleic acids research Volume 40 (2012) p.D790-6 DOI: 10.1093/nar/gkr1046
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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 DOI: 10.1186/1471-2148-11-334
The BioSample Database (BioSD) at the European Bioinformatics Institute.
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H. Nucleic acids research Volume 40 (2012) p.D64-70 DOI: 10.1093/nar/gkr937
InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY. Nucleic acids research Volume 40 (2012) p.D306-12 DOI: 10.1093/nar/gkr948
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Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Genome research Volume 22 (2012) p.9-24 DOI: 10.1101/gr.127597.111
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The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.
Li JW, Robison K, Martin M, Sjödin A, Usadel B, Young M, Olivares EC, Bolser DM. Nucleic acids research Volume 40 (2012) p.D1313-7 DOI: 10.1093/nar/gkr1058
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, Yates A, Zadissa A, Searle SM. Nucleic acids research Volume 40 (2012) p.D84-90 DOI: 10.1093/nar/gkr991
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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Bateman A. Nucleic acids research Volume 40 (2012) p.D343-50 DOI: 10.1093/nar/gkr987
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The International Nucleotide Sequence Database Collaboration.
Karsch-Mizrachi I, Nakamura Y, Cochrane G, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 40 (2012) p.D33-7 DOI: 10.1093/nar/gkr1006
Major submissions tool developments at the European Nucleotide Archive.
Amid C, Birney E, Bower L, Cerdeño-Tárraga A, Cheng Y, Cleland I, Faruque N, Gibson R, Goodgame N, Hunter C, Jang M, Leinonen R, Liu X, Oisel A, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Rivière S, Rossello M, Senf A, Smirnov D, Ten Hoopen P, Vaughan D, Vaughan R, Zalunin V, Cochrane G. Nucleic acids research Volume 40 (2012) p.D43-7 DOI: 10.1093/nar/gkr946
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Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E. Nucleic acids research Volume 40 (2012) p.D91-7 DOI: 10.1093/nar/gkr895
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WormBase 2012: more genomes, more data, new website.
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW. Nucleic acids research Volume 40 (2012) p.D735-41 DOI: 10.1093/nar/gkr954
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A. Nucleic acids research Volume 40 (2012) p.D1077-81 DOI: 10.1093/nar/gkr913
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Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X, Coffey AJ, Turner DJ, Swerdlow H, Burton J, Quail MA, Conrad DF, Enright AJ, Tyler-Smith C, Xue Y. Human genetics Volume 131 (2012) p.665-674 DOI: 10.1007/s00439-011-1111-9
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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 DOI: 10.1074/mcp.o111.015446
The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N. Molecular Biology and Evolution Volume 29 (2012) p.1125-1139 DOI: 10.1093/molbev/msr272
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 DOI: 10.1002/pmic.201190117
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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 DOI: 10.1371/journal.pone.0027044
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PomBase: a comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG. Nucleic acids research Volume 40 (2012) p.D695-9 DOI: 10.1093/nar/gkr853
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 DOI: 10.1371/journal.pone.0026345
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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 DOI: 10.1038/msb.2011.77
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 DOI: 10.1093/database/bar047
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 DOI: 10.1038/nature10547
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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 DOI: 10.1093/database/bar031
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The Sequence Read Archive: explosive growth of sequencing data.
Kodama Y, Shumway M, Leinonen R, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 40 (2012) p.D54-6 DOI: 10.1093/nar/gkr854
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM. Nucleic acids research Volume 40 (2012) p.D776-82 DOI: 10.1093/nar/gkr852
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 DOI: 10.1002/pmic.201100363
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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 DOI: 10.1186/1758-2946-3-37
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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 DOI: 10.1038/nature10530
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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 DOI: 10.1371/journal.pone.0026133
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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 DOI: 10.1038/msb.2011.75
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 DOI: 10.1021/ci200227u
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 DOI: 10.1371/journal.pone.0025513
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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 DOI: 10.1016/j.str.2011.08.006
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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 DOI: 10.4056/sigs.2084864
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 DOI: 10.1042/bst0391365
ChEMBL: a large-scale bioactivity database for drug discovery.
Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP. Nucleic acids research Volume 40 (2012) p.D1100-7 DOI: 10.1093/nar/gkr777
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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 DOI: 10.1261/rna.2750811
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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 DOI: 10.1186/gb-2011-12-9-r90
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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 DOI: 10.2390/biecoll-jib-2011-182
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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 DOI: 10.1101/gr.126599.111
*
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 DOI: 10.1186/gb-2011-12-9-r84
*
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 DOI: 10.1038/nature10413
*
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 DOI: 10.1371/journal.pgen.1002270
*
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 DOI: 10.1002/pmic.201100066
*
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 DOI: 10.1016/j.str.2011.05.015
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 DOI: 10.1038/nrd3503
*
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 DOI: 10.1126/scisignal.2002212
*
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 DOI: 10.1038/msb.2011.57
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 DOI: 10.1186/1756-0500-4-313
*
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 DOI: 10.1186/gb-2011-12-8-r81
*
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 DOI: 10.1038/ng.906
*
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 DOI: 10.1038/nature10414
*
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 DOI: 10.1186/1752-0509-5-124
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 DOI: 10.1021/bi201095z
*
Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.
Hödar C, Moreno P, di Genova A, Latorre M, Reyes-Jara A, Maass A, González M, Cambiazo V. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine Volume 25 (2012) p.75-93 DOI: 10.1007/s10534-011-9484-8
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 DOI: 10.1186/2041-1480-2-s5-s3
*
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited.
Hess J, Goldman N. PloS one Volume 6 (2011) p.e22783 DOI: 10.1371/journal.pone.0022783
*
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 DOI: 10.1042/bst0390977
*
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 DOI: 10.1186/1756-0500-4-272
Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H. Bioinformatics Volume 27 (2011) p.2616-2617 DOI: 10.1093/bioinformatics/btr433
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 DOI: 10.1093/database/bar030
*
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 DOI: 10.1002/glia.21218
*
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 DOI: 10.1101/gr.121541.111
*
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 DOI: 10.1038/nature10158
*
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 DOI: 10.1073/pnas.1019276108
*
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 DOI: 10.1371/journal.pbio.1001091
*
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 DOI: 10.1038/nature10284
*
The EBI Metagenomics Archive, Integration and Analysis resource
Hunter C, Cochrane G, Apweiler R, Hunter S. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches Wiley-Blackwell DOI: 10.1002/9781118010518.ch38
*
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 DOI: 10.1242/dev.063594
*
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 DOI: 10.1038/nmeth.1637
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 DOI: 10.1074/mcp.m111.008490
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 DOI: 10.1093/bioinformatics/btr375
*
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 DOI: 10.1038/msb.2011.36
*
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 DOI: 10.1016/j.jmb.2011.06.005
*
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 DOI: 10.1371/journal.pbio.1001088
*
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 DOI: 10.1186/1471-2229-11-104
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 DOI: 10.1111/j.1742-4658.2011.08190.x
*
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 DOI: 10.1038/ng.862
*
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 DOI: 10.1093/bioinformatics/btr330
*
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 DOI: 10.1093/nar/gkr411
Protein structure databases.
Laskowski RA. Molecular biotechnology Volume 48 (2011) p.183-198 DOI: 10.1007/s12033-010-9372-4
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 DOI: 10.1186/1471-2105-12-218
*
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 DOI: 10.1016/j.protis.2011.02.002
*
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 DOI: 10.1186/1471-2105-12-143
*
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 DOI: 10.1016/j.jprot.2011.04.029
A revised nomenclature for transcribed human endogenous retroviral loci.
Mayer J, Blomberg J, Seal RL. Mobile DNA Volume 2 (2011) p.7 DOI: 10.1186/1759-8753-2-7
*
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 DOI: 10.1093/database/baq039
*
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 DOI: 10.1002/elps.201000677
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 DOI: 10.1002/pmic.201000602
*
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 DOI: 10.1038/nbt.1823
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 DOI: 10.1186/1758-2946-3-s1-o6
*
A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium. PLoS biology Volume 9 (2011) p.e1001046 DOI: 10.1371/journal.pbio.1001046
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 DOI: 10.1186/1758-2946-3-s1-p19
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 DOI: 10.1186/1471-2105-12-104
*
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 DOI: 10.1016/j.yexcr.2011.03.023
*
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 DOI: 10.1136/gut.2010.234179
*
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 DOI: 10.1038/ismej.2011.39
*
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 DOI: 10.1128/jb.00321-11
*
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 DOI: 10.1016/j.gep.2011.03.004
*
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 DOI: 10.3201/eid1704.101009
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 DOI: 10.1093/database/bar009
*
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 DOI: 10.1186/gb-2011-12-3-402
*
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 DOI: 10.1107/s0907444911007943
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 DOI: 10.1107/s090744491004117x
*
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 DOI: 10.1016/j.ydbio.2011.03.011
Chromatin and heritability: how epigenetic studies can complement genetic approaches.
Birney E. Trends in genetics : TIG Volume 27 (2011) p.172-176 DOI: 10.1016/j.tig.2011.02.005
*
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 DOI: 10.1152/physiolgenomics.00205.2010
*
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 DOI: 10.1371/journal.pcbi.1001099
*
Quality control in proteomics.
Martens L, Vizcaíno JA, Banks R. Proteomics Volume 11 (2011) p.1015-1016 DOI: 10.1002/pmic.201190020
*
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 DOI: 10.1038/nrd3367
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 DOI: 10.1261/rna.2536111
*
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 DOI: 10.1371/journal.pgen.1001316
*
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 DOI: 10.1186/gb-2011-12-2-401
*
A common layer of interoperability for biomedical ontologies based on OWL EL.
Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV. Bioinformatics Volume 27 (2011) p.1001-1008 DOI: 10.1093/bioinformatics/btr058
Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G. Science signaling Volume 4 (2011) p.pe10 DOI: 10.1126/scisignal.2001844
*
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 DOI: 10.1534/genetics.110.126177
*
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 DOI: 10.1093/bioinformatics/btr048
*
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 DOI: 10.1038/nature09708
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 DOI: 10.1101/gr.114819.110
*
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 DOI: 10.1186/1471-2105-12-23
*
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 DOI: 10.1186/1471-2105-12-22
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 DOI: 10.1093/bioinformatics/btr012
*
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 DOI: 10.1093/sysbio/syq088
*
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 DOI: 10.1186/1472-6807-11-2
*
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 DOI: 10.1093/database/baq027
Assemblies: the good, the bad, the ugly.
Birney E. Nature methods Volume 8 (2011) p.59-60 DOI: 10.1038/nmeth0111-59
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 DOI: 10.1007/978-1-60761-987-1_6
*
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 DOI: 10.1007/978-1-61779-027-0_2
*
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 DOI: 10.1007/978-1-60761-977-2_16
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 DOI: 10.1007/978-1-61779-040-9_7
*
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 DOI: 10.2144/000113591
Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature.
Wright MW, Bruford EA. Human genomics Volume 5 (2011) p.90-98 DOI: 10.1186/1479-7364-5-2-90
*
Reporting Adverse Events: Basis for a Common Representation.
Courtot M, Brinkman RR, Ruttenberg A. CEURS proceedings: International Conference on Biomedical Ontologies Volume 833 (2011)
*
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 (2011) p.369-373
Omics technologies, data and bioinformatics principles.
Schneider MV, Orchard S. Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.3-30 DOI: 10.1007/978-1-61779-027-0_1
*
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 DOI: 10.3233/ao-2011-0086
*
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 DOI: 10.1038/nature09687
*
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 DOI: 10.3233/ao-2011-0087
*
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 DOI: 10.2174/156802611794480927
*
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 DOI: 10.3233/978-1-60750-799-4-63
Retroactivity as a Criterion to Define Modules in Signaling Networks
Saez-Rodriguez J, Conzelmann H, Ederer M, Gilles ED. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology Springer New York DOI: 10.1007/978-1-4419-6766-4_7
*
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 DOI: 10.1109/iembs.2011.6090629
*
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
*
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 DOI: 10.1093/nar/gkq1243
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 DOI: 10.1007/978-1-60761-977-2_2
*
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)
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 DOI: 10.1098/rstb.2010.0286
Preparing molecular interaction data for publication.
Orchard S, Hermjakob H. Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.229-236 DOI: 10.1007/978-1-60761-977-2_15
*
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 DOI: 10.1098/rstb.2010.0298
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 DOI: 10.1007/978-1-60761-987-1_9