Publications for 2012

2012

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Development and application of a DNA microarray-based yeast two-hybrid system.
Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE. Nucleic acids research Volume 41 (2013) p.1496-1507 DOI: 10.1093/nar/gks1329
Reuse of public genome-wide gene expression data.
Rung J, Brazma A. Nature reviews. Genetics Volume 14 (2013) p.89-99 DOI: 10.1038/nrg3394
Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC. PLoS computational biology Volume 8 (2012) p.e1002789 DOI: 10.1371/journal.pcbi.1002789
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Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.
Schulte I, Batty EM, Pole JC, Blood KA, Mo S, Cooke SL, Ng C, Howe KL, Chin SF, Brenton JD, Caldas C, Howarth KD, Edwards PA. BMC genomics Volume 13 (2012) p.719 DOI: 10.1186/1471-2164-13-719
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Enhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice.
Clare S, John V, Walker AW, Hill JL, Abreu-Goodger C, Hale C, Goulding D, Lawley TD, Mastroeni P, Frankel G, Enright AJ, Vigorito E, Dougan G. Infection and immunity Volume 81 (2013) p.723-732 DOI: 10.1128/iai.00969-12
HSM - a hybrid system based approach for modelling intracellular networks.
Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J. Gene Volume 518 (2013) p.70-77 DOI: 10.1016/j.gene.2012.11.084
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Cryo-electron microscopy--a primer for the non-microscopist.
Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S. The FEBS journal Volume 280 (2013) p.28-45 DOI: 10.1111/febs.12078
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Latent regulatory potential of human-specific repetitive elements.
Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT. Molecular cell Volume 49 (2013) p.262-272 DOI: 10.1016/j.molcel.2012.11.013
Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM. PloS one Volume 7 (2012) p.e50881 DOI: 10.1371/journal.pone.0050881
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UniProtKB amid the turmoil of plant proteomics research.
Schneider M, UniProt Consortium, Poux S. Frontiers in Plant Science Volume 3 (2012) p.270 DOI: 10.3389/fpls.2012.00270
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Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Nucleic acids research Volume 41 (2013) p.827-841 DOI: 10.1093/nar/gks1284
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Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J. BMC bioinformatics Volume 13 (2012) p.324 DOI: 10.1186/1471-2105-13-324
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Large-scale association analysis identifies new risk loci for coronary artery disease.
CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, DIAGRAM Consortium, CARDIOGENICS Consortium, Doney AS, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, MuTHER Consortium, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AF, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wellcome Trust Case Control Consortium, Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O'Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CN, Roberts R, Watkins H, Schunkert H, Samani NJ. Nature genetics Volume 45 (2013) p.25-33 DOI: 10.1038/ng.2480
Data management challenges in three-dimensional EM.
Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ. Nature structural & molecular biology Volume 19 (2012) p.1203-1207 DOI: 10.1038/nsmb.2426
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Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, 1000 Genomes Project Consortium. American journal of human genetics Volume 91 (2012) p.1022-1032 DOI: 10.1016/j.ajhg.2012.10.015
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Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C. Nucleic acids research Volume 41 (2013) p.D499-507 DOI: 10.1093/nar/gks1266
Ensembl 2013.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Yates A, Zadissa A, Searle SM. Nucleic acids research Volume 41 (2013) p.D48-55 DOI: 10.1093/nar/gks1236
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Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.
Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG. PloS one Volume 7 (2012) p.e50085 DOI: 10.1371/journal.pone.0050085
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ. Nucleic acids research Volume 41 (2013) p.D483-9 DOI: 10.1093/nar/gks1258
Facing growth in the European Nucleotide Archive.
Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V. Nucleic acids research Volume 41 (2013) p.D30-5 DOI: 10.1093/nar/gks1175
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New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA. Nucleic acids research Volume 41 (2013) p.D490-8 DOI: 10.1093/nar/gks1211
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Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Nucleic acids research Volume 41 (2013) p.D171-6 DOI: 10.1093/nar/gks1221
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. Nucleic acids research Volume 41 (2013) p.D1063-9 DOI: 10.1093/nar/gks1262
ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U. Nucleic acids research Volume 41 (2013) p.D987-90 DOI: 10.1093/nar/gks1174
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Skirting the pitfalls: a clear-cut nomenclature for H3K4 methyltransferases.
Bögershausen N, Bruford E, Wollnik B. Clinical genetics Volume 83 (2013) p.212-214 DOI: 10.1111/cge.12050
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Genomicus: five genome browsers for comparative genomics in eukaryota.
Louis A, Muffato M, Roest Crollius H. Nucleic acids research Volume 41 (2013) p.D700-5 DOI: 10.1093/nar/gks1156
DbVar and DGVa: public archives for genomic structural variation.
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM. Nucleic acids research Volume 41 (2013) p.D936-41 DOI: 10.1093/nar/gks1213
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HAMAP in 2013, new developments in the protein family classification and annotation system.
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium. Nucleic acids research Volume 41 (2013) p.D584-9 DOI: 10.1093/nar/gks1157
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IPD--the Immuno Polymorphism Database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG. Nucleic acids research Volume 41 (2013) p.D1234-40 DOI: 10.1093/nar/gks1140
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D456-63 DOI: 10.1093/nar/gks1146
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The International Nucleotide Sequence Database Collaboration.
Nakamura Y, Cochrane G, Karsch-Mizrachi I, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 41 (2013) p.D21-4 DOI: 10.1093/nar/gks1084
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A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K. Bioinformatics (Oxford, England) Volume 29 (2013) p.206-214 DOI: 10.1093/bioinformatics/bts669
The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D773-80 DOI: 10.1093/nar/gks1112
Genenames.org: the HGNC resources in 2013.
Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA. Nucleic acids research Volume 41 (2013) p.D545-52 DOI: 10.1093/nar/gks1066
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PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.
Sanseverino W, Hermoso A, D'Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR. Nucleic acids research Volume 41 (2013) p.D1167-71 DOI: 10.1093/nar/gks1183
Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium. Nucleic acids research Volume 41 (2013) p.D43-7 DOI: 10.1093/nar/gks1068
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Opportunities for text mining in the FlyBase genetic literature curation workflow.
McQuilton P, FlyBase Consortium. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas039 DOI: 10.1093/database/bas039
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Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M. Nucleic acids research Volume 41 (2013) p.D530-5 DOI: 10.1093/nar/gks1050
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High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.
Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K, Amos CI, Padyukov L, Toes RE, Huizinga TW, Wijmenga C, Trynka G, Franke L, Westra HJ, Alfredsson L, Hu X, Sandor C, de Bakker PI, Davila S, Khor CC, Heng KK, Andrews R, Edkins S, Hunt SE, Langford C, Symmons D, Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate, Wellcome Trust Case Control Consortium, Concannon P, Onengut-Gumuscu S, Rich SS, Deloukas P, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Ärlsetig L, Martin J, Rantapää-Dahlqvist S, Plenge RM, Raychaudhuri S, Klareskog L, Gregersen PK, Worthington J. Nature genetics Volume 44 (2012) p.1336-1340 DOI: 10.1038/ng.2462
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Annotating cancer variants and anti-cancer therapeutics in reactome.
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L. Cancers Volume 4 (2012) p.1180-1211 DOI: 10.3390/cancers4041180
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 29 (2013) p.132-134 DOI: 10.1093/bioinformatics/bts656
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FlyBase: improvements to the bibliography.
Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ, FlyBase consortium. Nucleic acids research Volume 41 (2013) p.D751-7 DOI: 10.1093/nar/gks1024
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Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Nucleic acids research Volume 41 (2013) p.D226-32 DOI: 10.1093/nar/gks1005
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Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case.
Kogej T, Blomberg N, Greasley PJ, Mundt S, Vainio MJ, Schamberger J, Schmidt G, Hüser J. Drug discovery today Volume 18 (2013) p.1014-1024 DOI: 10.1016/j.drudis.2012.10.011
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An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Nature Volume 491 (2012) p.56-65 DOI: 10.1038/nature11632
Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L. Cancers Volume 4 (2012) p.1180-1211 DOI: 10.3390/cancers4041180
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Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N. Nature Volume 491 (2012) p.705-710 DOI: 10.1038/nature11650
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Analyses of pig genomes provide insight into porcine demography and evolution.
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. Nature Volume 491 (2012) p.393-398 DOI: 10.1038/nature11622
A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs.
Manakov SA, Morton A, Enright AJ, Grant SG. Frontiers in neuroscience Volume 6 (2012) p.156 DOI: 10.3389/fnins.2012.00156
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D781-6 DOI: 10.1093/nar/gks1004
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Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.
Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas036 DOI: 10.1093/database/bas036
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Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.
Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F. Molecular bioSystems Volume 9 (2013) p.70-76 DOI: 10.1039/c2mb25325a
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J. BMC systems biology Volume 6 (2012) p.133 DOI: 10.1186/1752-0509-6-133
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The IMGT/HLA database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG. Nucleic acids research Volume 41 (2013) p.D1222-7 DOI: 10.1093/nar/gks949
Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC. Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177 DOI: 10.1093/bioinformatics/bts605
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Open data for drug discovery: learning from the biological community.
Hersey A, Senger S, Overington JP. Future medicinal chemistry Volume 4 (2012) p.1865-1867 DOI: 10.4155/fmc.12.159
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Journey to the genetic interior. Interview by Stephen S Hall.
Birney E. Scientific American Volume 307 (2012) p.80-2, 84
Abstracting knowledge from the Protein Data Bank.
Furnham N, Laskowski RA, Thornton JM. Biopolymers Volume 99 (2013) p.183-188 DOI: 10.1002/bip.22107
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The future of the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Biopolymers Volume 99 (2013) p.218-222 DOI: 10.1002/bip.22132
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Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ. The Plant cell Volume 24 (2012) p.3530-3557 DOI: 10.1105/tpc.112.102046
Analysis of variation at transcription factor binding sites in Drosophila and humans.
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Genome biology Volume 13 (2012) p.R49 DOI: 10.1186/gb-2012-13-9-r49
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InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G. Bioinformatics (Oxford, England) Volume 28 (2012) p.3163-3165 DOI: 10.1093/bioinformatics/bts577
*
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Genome biology Volume 13 (2012) p.R48 DOI: 10.1186/gb-2012-13-9-r48
*
An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
Nelson AC, Pillay N, Henderson S, Presneau N, Tirabosco R, Halai D, Berisha F, Flicek P, Stemple DL, Stern CD, Wardle FC, Flanagan AM. The Journal of pathology Volume 228 (2012) p.274-285 DOI: 10.1002/path.4082
MetaboLights: towards a new COSMOS of metabolomics data management.
Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL. Metabolomics : Official journal of the Metabolomic Society Volume 8 (2012) p.757-760 DOI: 10.1007/s11306-012-0462-0
*
RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011.
Robbins RJ, Cochrane G, Davies N, Dawyndt P, Kottmann R, Krishtalka LK, Morrison N, Tuama EÓ, San Gil I, Wooley J. Standards in genomic sciences Volume 7 (2012) p.153-158 DOI: 10.4056/sigs.3146509
*
Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.
Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC. Mammalian genome : official journal of the International Mammalian Genome Society Volume 23 (2012) p.641-652 DOI: 10.1007/s00335-012-9428-9
*
CING: an integrated residue-based structure validation program suite.
Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW. Journal of biomolecular NMR Volume 54 (2012) p.267-283 DOI: 10.1007/s10858-012-9669-7
*
MyDas, an extensible Java DAS server.
Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H. PloS one Volume 7 (2012) p.e44180 DOI: 10.1371/journal.pone.0044180
*
The mammalian gene function resource: the International Knockout Mouse Consortium.
Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W. Mammalian genome : official journal of the International Mammalian Genome Society Volume 23 (2012) p.580-586 DOI: 10.1007/s00335-012-9422-2
*
Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
Su Z, Gay LJ, Strange A, Palles C, Band G, Whiteman DC, Lescai F, Langford C, Nanji M, Edkins S, van der Winkel A, Levine D, Sasieni P, Bellenguez C, Howarth K, Freeman C, Trudgill N, Tucker AT, Pirinen M, Peppelenbosch MP, van der Laan LJ, Kuipers EJ, Drenth JP, Peters WH, Reynolds JV, Kelleher DP, McManus R, Grabsch H, Prenen H, Bisschops R, Krishnadath K, Siersema PD, van Baal JW, Middleton M, Petty R, Gillies R, Burch N, Bhandari P, Paterson S, Edwards C, Penman I, Vaidya K, Ang Y, Murray I, Patel P, Ye W, Mullins P, Wu AH, Bird NC, Dallal H, Shaheen NJ, Murray LJ, Koss K, Bernstein L, Romero Y, Hardie LJ, Zhang R, Winter H, Corley DA, Panter S, Risch HA, Reid BJ, Sargeant I, Gammon MD, Smart H, Dhar A, McMurtry H, Ali H, Liu G, Casson AG, Chow WH, Rutter M, Tawil A, Morris D, Nwokolo C, Isaacs P, Rodgers C, Ragunath K, MacDonald C, Haigh C, Monk D, Davies G, Wajed S, Johnston D, Gibbons M, Cullen S, Church N, Langley R, Griffin M, Alderson D, Deloukas P, Hunt SE, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Anderson M, Brooks C, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood N, Trynka G, Wijmenga C, Cazier JB, Atherfold P, Nicholson AM, Gellatly NL, Glancy D, Cooper SC, Cunningham D, Lind T, Hapeshi J, Ferry D, Rathbone B, Brown J, Love S, Attwood S, MacGregor S, Watson P, Sanders S, Ek W, Harrison RF, Moayyedi P, de Caestecker J, Barr H, Stupka E, Vaughan TL, Peltonen L, Spencer CC, Tomlinson I, Donnelly P, Jankowski JA, Esophageal Adenocarcinoma Genetics Consortium, Wellcome Trust Case Control Consortium 2. Nature genetics Volume 44 (2012) p.1131-1136 DOI: 10.1038/ng.2408
Metagenomic analysis: the challenge of the data bonanza.
Hunter CI, Mitchell A, Jones P, McAnulla C, Pesseat S, Scheremetjew M, Hunter S. Briefings in bioinformatics Volume 13 (2012) p.743-746 DOI: 10.1093/bib/bbs020
*
A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus.
Crossman LC, Chen H, Cerdeño-Tárraga AM, Brooks K, Quail MA, Pineiro SA, Hobley L, Sockett RE, Bentley SD, Parkhill J, Williams HN, Stine OC. The ISME journal Volume 7 (2013) p.148-160 DOI: 10.1038/ismej.2012.90
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA. Molecular & cellular proteomics : MCP Volume 11 (2012) p.1682-1689 DOI: 10.1074/mcp.o112.021543
The making of ENCODE: Lessons for big-data projects.
Birney E. Nature Volume 489 (2012) p.49-51 DOI: 10.1038/489049a
*
In support of the BMRB.
Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. Nature structural & molecular biology Volume 19 (2012) p.854-860 DOI: 10.1038/nsmb.2371
*
An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium. Nature Volume 489 (2012) p.57-74 DOI: 10.1038/nature11247
*
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Genome research Volume 22 (2012) p.1798-1812 DOI: 10.1101/gr.139105.112
*
Detection and imaging the expression of the trans-membrane protein CD44 in RT112 cells by use of enzyme-labeled antibodies and SECM.
Roberts WS, Davis F, Holmes JL, Collyer SD, Larcombe LD, Morgan SL, Higson SP. Biosensors & bioelectronics Volume 41 (2013) p.282-288 DOI: 10.1016/j.bios.2012.08.038
*
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. Genome Research Volume 22 (2012) p.1658-1667 DOI: 10.1101/gr.136838.111
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.
Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H. Proteomics Volume 12 (2012) p.2767-2772 DOI: 10.1002/pmic.201270126
*
The 2010 cryo-EM modeling challenge.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W. Biopolymers Volume 97 (2012) p.651-654 DOI: 10.1002/bip.22081
*
Seven newly identified loci for autoimmune thyroid disease.
Cooper JD, Simmonds MJ, Walker NM, Burren O, Brand OJ, Guo H, Wallace C, Stevens H, Coleman G, Wellcome Trust Case Control Consortium, Franklyn JA, Todd JA, Gough SC. Human molecular genetics Volume 21 (2012) p.5202-5208 DOI: 10.1093/hmg/dds357
Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC. Genome research Volume 22 (2012) p.2376-2384 DOI: 10.1101/gr.142281.112
*
MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.
Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P. PloS one Volume 7 (2012) p.e40938 DOI: 10.1371/journal.pone.0040938
An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.
Sipos B, Massingham T, Stütz AM, Goldman N. PloS one Volume 7 (2012) p.e43359 DOI: 10.1371/journal.pone.0043359
*
Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I. PloS one Volume 7 (2012) p.e41762 DOI: 10.1371/journal.pone.0041762
*
Metric distances derived from cosine similarity and Pearson and Spearman correlations
van Dongen S, Enright AJ.
*
Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.
Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJ, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WH, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JR, Platou CG, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney AS, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CN, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Wellcome Trust Case Control Consortium, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Investigators, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Asian Genetic Epidemiology Network–Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. Nature genetics Volume 44 (2012) p.981-990 DOI: 10.1038/ng.2383
*
BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S. Bioinformatics (Oxford, England) Volume 28 (2012) p.2693-2695 DOI: 10.1093/bioinformatics/bts494
Current challenges in genome annotation through structural biology and bioinformatics.
Furnham N, de Beer TA, Thornton JM. Current opinion in structural biology Volume 22 (2012) p.594-601 DOI: 10.1016/j.sbi.2012.07.005
*
Annotating Human P-Glycoprotein Bioassay Data.
Zdrazil B, Pinto M, Vasanthanathan P, Williams AJ, Balderud LZ, Engkvist O, Chichester C, Hersey A, Overington JP, Ecker GF. Molecular informatics Volume 31 (2012) p.599-609 DOI: 10.1002/minf.201200059
Transcriptional data: a new gateway to drug repositioning?
Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J. Drug discovery today Volume 18 (2013) p.350-357 DOI: 10.1016/j.drudis.2012.07.014
State-time spectrum of signal transduction logic models.
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J. Physical biology Volume 9 (2012) p.045003 DOI: 10.1088/1478-3975/9/4/045003
*
The Origin and Function of Anti-Fungal Peptides in C. elegans: Open Questions.
Pujol N, Davis PA, Ewbank JJ. Frontiers in immunology Volume 3 (2012) p.237 DOI: 10.3389/fimmu.2012.00237
*
Hepatitis E virus infection in Ghanaian blood donors - the importance of immunoassay selection and confirmation.
Meldal BH, Sarkodie F, Owusu-Ofori S, Allain JP. Vox sanguinis Volume 104 (2013) p.30-36 DOI: 10.1111/j.1423-0410.2012.01637.x
*
In the beginning there was babble...
Klionsky DJ, Bruford EA, Cherry JM, Hodgkin J, Laulederkind SJ, Singer AG. Autophagy Volume 8 (2012) p.1165-1167 DOI: 10.4161/auto.20665
*
A network-oriented perspective on cardiac calcium signaling.
George CH, Parthimos D, Silvester NC. American journal of physiology. Cell physiology Volume 303 (2012) p.C897-910 DOI: 10.1152/ajpcell.00388.2011
*
ADOPS--Automatic Detection Of Positively Selected Sites.
Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Fonseca NA, Vieira J. Journal of integrative bioinformatics Volume 9 (2012) p.200 DOI: 10.2390/biecoll-jib-2012-200
*
Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.
Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA. Integrative biology : quantitative biosciences from nano to macro Volume 4 (2012) p.1038-1048 DOI: 10.1039/c2ib20052j
*
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR. Omics : a journal of integrative biology Volume 16 (2012) p.431-442 DOI: 10.1089/omi.2012.0022
Low budget analysis of Direct-To-Consumer genomic testing familial data.
Glusman G, Cariaso M, Jimenez R, Swan D, Greshake B, Bhak J, Logan DW, Corpas M. F1000Research Volume 1 (2012) p.3 DOI: 10.12688/f1000research.1-3.v1
The future of DNA sequence archiving.
Cochrane G, Cook CE, Birney E. GigaScience Volume 1 (2012) p.2 DOI: 10.1186/2047-217x-1-2
Bioinformatics meets user-centred design: a perspective.
Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C. PLoS Computational Biology Volume 8 (2012) p.e1002554 DOI: 10.1371/journal.pcbi.1002554
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Genome research Volume 22 (2012) p.2163-2175 DOI: 10.1101/gr.136507.111
*
Gene family matters: expanding the HGNC resource.
Daugherty LC, Seal RL, Wright MW, Bruford EA. Human genomics Volume 6 (2012) p.4 DOI: 10.1186/1479-7364-6-4
*
Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.
arcOGEN Consortium, arcOGEN Collaborators, Zeggini E, Panoutsopoulou K, Southam L, Rayner NW, Day-Williams AG, Lopes MC, Boraska V, Esko T, Evangelou E, Hoffman A, Houwing-Duistermaat JJ, Ingvarsson T, Jonsdottir I, Jonnson H, Kerkhof HJ, Kloppenburg M, Bos SD, Mangino M, Metrustry S, Slagboom PE, Thorleifsson G, Raine EV, Ratnayake M, Ricketts M, Beazley C, Blackburn H, Bumpstead S, Elliott KS, Hunt SE, Potter SC, Shin SY, Yadav VK, Zhai G, Sherburn K, Dixon K, Arden E, Aslam N, Battley PK, Carluke I, Doherty S, Gordon A, Joseph J, Keen R, Koller NC, Mitchell S, O'Neill F, Paling E, Reed MR, Rivadeneira F, Swift D, Walker K, Watkins B, Wheeler M, Birrell F, Ioannidis JP, Meulenbelt I, Metspalu A, Rai A, Salter D, Stefansson K, Stykarsdottir U, Uitterlinden AG, van Meurs JB, Chapman K, Deloukas P, Ollier WE, Wallis GA, Arden N, Carr A, Doherty M, McCaskie A, Willkinson JM, Ralston SH, Valdes AM, Spector TD, Loughlin J. Lancet (London, England) Volume 380 (2012) p.815-823 DOI: 10.1016/s0140-6736(12)60681-3
*
MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.
Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C. The Journal of biological chemistry Volume 287 (2012) p.29516-29528 DOI: 10.1074/jbc.m111.335943
*
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium. Nature Volume 487 (2012) p.94-98 DOI: 10.1038/nature11041
*
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo JB, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara SM, Marsh K, Jiang H, Su XZ, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White NJ, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail MA, Turner DJ, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan JC, Ferdig MT, Amambua-Ngwa A, Conway DJ, Takala-Harrison S, Plowe CV, Rayner JC, Rockett KA, Clark TG, Newbold CI, Berriman M, MacInnis B, Kwiatkowski DP. Nature Volume 487 (2012) p.375-379 DOI: 10.1038/nature11174
*
Safe, long-term hepatic expression of anti-HCV shRNA in a nonhuman primate model.
Suhy DA, Kao SC, Mao T, Whiteley L, Denise H, Souberbielle B, Burdick AD, Hayes K, Wright JF, Lavender H, Roelvink P, Kolykhalov A, Brady K, Moschos SA, Hauck B, Zelenaia O, Zhou S, Scribner C, High KA, Renison SH, Corbau R. Molecular therapy : the journal of the American Society of Gene Therapy Volume 20 (2012) p.1737-1749 DOI: 10.1038/mt.2012.119
*
First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans?
Matos KS, da Cunha EF, da Silva Gonçalves A, Wilter A, Kuča K, França TC, Ramalho TC. Journal of biomolecular structure & dynamics Volume 30 (2012) p.546-558 DOI: 10.1080/07391102.2012.687521
*
Integrating literature-constrained and data-driven inference of signalling networks.
Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J. Bioinformatics Volume 28 (2012) p.2311-2317 DOI: 10.1093/bioinformatics/bts363
Error-correcting properties of the SOLiD Exact Call Chemistry.
Massingham T, Goldman N. BMC bioinformatics Volume 13 (2012) p.145 DOI: 10.1186/1471-2105-13-145
*
Modeling gene expression using chromatin features in various cellular contexts.
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Genome biology Volume 13 (2012) p.R53 DOI: 10.1186/gb-2012-13-9-r53
*
ISMB 2012 PROCEEDINGS PAPERS COMMITTEE.
Bioinformatics Volume 28 (2012) p.i2-i6
Paralogous annotation of disease-causing variants in long QT syndrome genes.
Ware JS, Walsh R, Cunningham F, Birney E, Cook SA. Human mutation Volume 33 (2012) p.1188-1191 DOI: 10.1002/humu.22114
Large-scale analysis of microRNA evolution.
Guerra-Assunção JA, Enright AJ. BMC genomics Volume 13 (2012) p.218 DOI: 10.1186/1471-2164-13-218
*
ISMB 2012 Proceedings Papers Committee. July 15 to July 19, 2012, Long Beach, CA, USA. Editorial.
Berger B. Bioinformatics Volume 28 (2012) p.i1 DOI: 10.1093/bioinformatics/bts281
*
Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks.
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM. Molecular cell Volume 46 (2012) p.871-883 DOI: 10.1016/j.molcel.2012.05.039
*
The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium. Nature Volume 485 (2012) p.635-641 DOI: 10.1038/nature11119
Natural product-likeness score revisited: an open-source, open-data implementation.
Jayaseelan KV, Moreno P, Truszkowski A, Ertl P, Steinbeck C. BMC bioinformatics Volume 13 (2012) p.106 DOI: 10.1186/1471-2105-13-106
*
InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong S. Nucleic acids research Volume 40 (2012) p.4725-4725 DOI: 10.1093/nar/gks456
*
The YARHG domain: an extracellular domain in search of a function.
Coggill P, Bateman A. PloS one Volume 7 (2012) p.e35575 DOI: 10.1371/journal.pone.0035575
*
Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.
Shen PS, Domek MJ, Sanz-García E, Makaju A, Taylor RM, Hoggan R, Culumber MD, Oberg CJ, Breakwell DP, Prince JT, Belnap DM. Journal of virology Volume 86 (2012) p.7907-7917 DOI: 10.1128/jvi.00407-12
*
Extent, causes, and consequences of small RNA expression variation in human adipose tissue.
Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J, MuTHER Consortium, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM. PLoS genetics Volume 8 (2012) p.e1002704 DOI: 10.1371/journal.pgen.1002704
*
Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A. Circulation Volume 125 (2012) p.2751-2761 DOI: 10.1161/circulationaha.111.044354
*
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.
Britto R, Sallou O, Collin O, Michaux G, Primig M, Chalmel F. Nucleic acids research Volume 40 (2012) p.W458-65 DOI: 10.1093/nar/gks380
graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P. Bioinformatics (Oxford, England) Volume 28 (2012) p.1665-1667 DOI: 10.1093/bioinformatics/bts258
*
Directly e-mailing authors of newly published papers encourages community curation.
Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH, FlyBase Consortium. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas024 DOI: 10.1093/database/bas024
*
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK. BMC systems biology Volume 6 (2012) p.29 DOI: 10.1186/1752-0509-6-29
*
Extracellular membrane vesicles and immune regulation in the brain.
Cossetti C, Smith JA, Iraci N, Leonardi T, Alfaro-Cervello C, Pluchino S. Frontiers in physiology Volume 3 (2012) p.117 DOI: 10.3389/fphys.2012.00117
Structured chemical class definitions and automated matching for chemical ontology evolution.
Duan L, Hastings J, de Matos P, Ennis M, Steinbeck C. Journal of cheminformatics Volume 4 (2012) p.P5-P5
Molecular interaction databases.
Orchard S. Proteomics Volume 12 (2012) p.1656-1662 DOI: 10.1002/pmic.201100484
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium. Nature methods Volume 9 (2012) p.459-462 DOI: 10.1038/nmeth.1974
Improvements in the Protein Identifier Cross-Reference service.
Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA. Nucleic acids research Volume 40 (2012) p.W276-80 DOI: 10.1093/nar/gks338
PSI-Search: iterative HOE-reduced profile SSEARCH searching.
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. Bioinformatics (Oxford, England) Volume 28 (2012) p.1650-1651 DOI: 10.1093/bioinformatics/bts240
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.
Jupp S, Stevens R, Hoehndorf R. Journal of biomedical semantics Volume 3 Suppl 1 (2012) p.S3 DOI: 10.1186/2041-1480-3-s1-s3
*
Transcription factors of Lotus: regulation of isoflavonoid biosynthesis requires coordinated changes in transcription factor activity.
Shelton D, Stranne M, Mikkelsen L, Pakseresht N, Welham T, Hiraka H, Tabata S, Sato S, Paquette S, Wang TL, Martin C, Bailey P. Plant physiology Volume 159 (2012) p.531-547 DOI: 10.1104/pp.112.194753
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A, Vilella AJ, Goldman N. Bioinformatics (Oxford, England) Volume 28 (2012) p.1684-1691 DOI: 10.1093/bioinformatics/bts198
*
Patterns of cis regulatory variation in diverse human populations.
Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET. PLoS genetics Volume 8 (2012) p.e1002639 DOI: 10.1371/journal.pgen.1002639
Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting.
Zheng-Bradley X, Flicek P. Human mutation Volume 33 (2012) p.1016-1019 DOI: 10.1002/humu.22024
*
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012.
Attwood TK, Coletta A, Muirhead G, Pavlopoulou A, Philippou PB, Popov I, Romá-Mateo C, Theodosiou A, Mitchell AL. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas019 DOI: 10.1093/database/bas019
*
Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level.
Fanucchi F, Alpi E, Olivieri S, Cannistraci CV, Bachi A, Alpi A, Alessio M. Biochimica et biophysica acta Volume 1824 (2012) p.813-825 DOI: 10.1016/j.bbapap.2012.03.015
Structure-based classification and ontology in chemistry.
Hastings J, Magka D, Batchelor C, Duan L, Stevens R, Ennis M, Steinbeck C. Journal of Cheminformatics Volume 4 (2012) p.8 DOI: 10.1186/1758-2946-4-8
*
The genomic basis of adaptive evolution in threespine sticklebacks.
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C, Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM. Nature Volume 484 (2012) p.55-61 DOI: 10.1038/nature10944
Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ, Swertz MA. Human mutation Volume 33 (2012) p.867-873 DOI: 10.1002/humu.22070
*
Looking for Darwin in genomic sequences--validity and success of statistical methods.
Zhai W, Nielsen R, Goldman N, Yang Z. Molecular biology and evolution Volume 29 (2012) p.2889-2893 DOI: 10.1093/molbev/mss104
*
MageComet--web application for harmonizing existing large-scale experiment descriptions.
Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H. Bioinformatics (Oxford, England) Volume 28 (2012) p.1402-1403 DOI: 10.1093/bioinformatics/bts148
*
The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions.
Fonseca NA, Vieira CP, Schlötterer C, Vieira J. Fly Volume 6 (2012) p.71-74 DOI: 10.4161/fly.19423
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H. Nature methods Volume 9 (2012) p.345-350 DOI: 10.1038/nmeth.1931
*
Systematic identification of genomic markers of drug sensitivity in cancer cells.
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O'Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH. Nature Volume 483 (2012) p.570-575 DOI: 10.1038/nature11005
*
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.E944-53 DOI: 10.1073/pnas.1110156109
*
Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.
Melas IN, Mitsos A, Messinis DE, Weiss TS, Rodriguez JS, Alexopoulos LG. Molecular bioSystems Volume 8 (2012) p.1571-1584 DOI: 10.1039/c2mb05482e
PRIDE: quality control in a proteomics data repository.
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas004 DOI: 10.1093/database/bas004
*
AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas003 DOI: 10.1093/database/bas003
Biocurators and biocuration: surveying the 21st century challenges.
Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios L, Gaudet P. Database : the journal of biological databases and curation Volume 2012 (2012) p.bar059 DOI: 10.1093/database/bar059
Implementing an X-ray validation pipeline for the Protein Data Bank.
Gore S, Velankar S, Kleywegt GJ. Acta crystallographica. Section D, Biological crystallography Volume 68 (2012) p.478-483 DOI: 10.1107/s0907444911050359
ELIXIR: a distributed infrastructure for European biological data.
Crosswell LC, Thornton JM. Trends in biotechnology Volume 30 (2012) p.241-242 DOI: 10.1016/j.tibtech.2012.02.002
*
Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Schwarz MA, Thornton J, Xu H, Awasthi N, Schwarz RE. PloS one Volume 7 (2012) p.e33101 DOI: 10.1371/journal.pone.0033101
*
BLUEPRINT to decode the epigenetic signature written in blood.
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S. Nature biotechnology Volume 30 (2012) p.224-226 DOI: 10.1038/nbt.2153
*
Insights into hominid evolution from the gorilla genome sequence.
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Nature Volume 483 (2012) p.169-175 DOI: 10.1038/nature10842
*
Bioimage informatics: a new category in Bioinformatics.
Peng H, Bateman A, Valencia A, Wren JD. Bioinformatics Volume 28 (2012) p.1057 DOI: 10.1093/bioinformatics/bts111
Analyzing protein-protein interaction networks.
Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Journal of proteome research Volume 11 (2012) p.2014-2031 DOI: 10.1021/pr201211w
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM. PLoS computational biology Volume 8 (2012) p.e1002403 DOI: 10.1371/journal.pcbi.1002403
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
Reisinger F, Krishna R, Ghali F, Ríos D, Hermjakob H, Vizcaíno JA, Jones AR. Proteomics Volume 12 (2012) p.790-794 DOI: 10.1002/pmic.201100577
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Griss J, Reisinger F, Hermjakob H, Vizcaíno JA. Proteomics Volume 12 (2012) p.795-798 DOI: 10.1002/pmic.201100578
*
The Protein Data Bank at 40: reflecting on the past to prepare for the future.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Structure (London, England : 1993) Volume 20 (2012) p.391-396 DOI: 10.1016/j.str.2012.01.010
*
HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.
Lam MP, Vivanco F, Scholten A, Hermjakob H, Van Eyk J, Ping P. Proteomics Volume 12 (2012) p.749-751 DOI: 10.1002/pmic.201270015
*
Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
Auburn S, Campino S, Miotto O, Djimde AA, Zongo I, Manske M, Maslen G, Mangano V, Alcock D, MacInnis B, Rockett KA, Clark TG, Doumbo OK, Ouédraogo JB, Kwiatkowski DP. PloS one Volume 7 (2012) p.e32891 DOI: 10.1371/journal.pone.0032891
All Your Base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N. Genome biology Volume 13 (2012) p.R13 DOI: 10.1186/gb-2012-13-2-r13
*
OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. Nature methods Volume 9 (2012) p.245-253 DOI: 10.1038/nmeth.1896
*
Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis.
Masforrol Y, Gil J, González LJ, Pérez-Riverol Y, Fernández-de-Cossío J, Sánchez A, Betancourt LH, Garay HE, Cabrales A, Albericio F, Yang H, Zubarev RA, Besada V, Acosta OR. ACS combinatorial science Volume 14 (2012) p.145-149 DOI: 10.1021/co200159r
*
GrameneMart: the BioMart data portal for the Gramene project.
Spooner W, Youens-Clark K, Staines D, Ware D. Database : the journal of biological databases and curation Volume 2012 (2012) p.bar056 DOI: 10.1093/database/bar056
*
The mzIdentML data standard for mass spectrometry-based proteomics results.
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D. Molecular & cellular proteomics : MCP Volume 11 (2012) p.M111.014381 DOI: 10.1074/mcp.m111.014381
*
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E. Bioinformatics (Oxford, England) Volume 28 (2012) p.1086-1092 DOI: 10.1093/bioinformatics/bts094
*
Foreword
Goldman N, Yang Z. Codon Evolution: Mechanisms and Models Oxford University Press
*
The KUPKB: a novel Web application to access multiomics data on kidney disease.
Klein J, Jupp S, Moulos P, Fernandez M, Buffin-Meyer B, Casemayou A, Chaaya R, Charonis A, Bascands JL, Stevens R, Schanstra JP. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 26 (2012) p.2145-2153 DOI: 10.1096/fj.11-194381
*
On the need for an international effort to capture, share and use crystallization screening data.
Newman J, Bolton EE, Müller-Dieckmann J, Fazio VJ, Gallagher DT, Lovell D, Luft JR, Peat TS, Ratcliffe D, Sayle RA, Snell EH, Taylor K, Vallotton P, Velanker S, von Delft F. Acta crystallographica. Section F, Structural biology and crystallization communications Volume 68 (2012) p.253-258 DOI: 10.1107/s1744309112002618
*
Identification and localisation of the NB-LRR gene family within the potato genome.
Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I. BMC genomics Volume 13 (2012) p.75 DOI: 10.1186/1471-2164-13-75
*
HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA. PloS one Volume 7 (2012) p.e31826 DOI: 10.1371/journal.pone.0031826
*
ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM. Bioinformatics Volume 28 (2012) p.1001-1008 DOI: 10.1093/bioinformatics/bts081
*
Toward community standards in the quest for orthologs.
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J, Quest for Orthologs Consortium. Bioinformatics (Oxford, England) Volume 28 (2012) p.900-904 DOI: 10.1093/bioinformatics/bts050
*
The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer.
Ng CK, Cooke SL, Howe K, Newman S, Xian J, Temple J, Batty EM, Pole JC, Langdon SP, Edwards PA, Brenton JD. The Journal of pathology Volume 226 (2012) p.703-712 DOI: 10.1002/path.3980
*
PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA. Nature biotechnology Volume 30 (2012) p.135-137 DOI: 10.1038/nbt.2112
*
Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke.
International Stroke Genetics Consortium (ISGC), Wellcome Trust Case Control Consortium 2 (WTCCC2), Bellenguez C, Bevan S, Gschwendtner A, Spencer CC, Burgess AI, Pirinen M, Jackson CA, Traylor M, Strange A, Su Z, Band G, Syme PD, Malik R, Pera J, Norrving B, Lemmens R, Freeman C, Schanz R, James T, Poole D, Murphy L, Segal H, Cortellini L, Cheng YC, Woo D, Nalls MA, Müller-Myhsok B, Meisinger C, Seedorf U, Ross-Adams H, Boonen S, Wloch-Kopec D, Valant V, Slark J, Furie K, Delavaran H, Langford C, Deloukas P, Edkins S, Hunt S, Gray E, Dronov S, Peltonen L, Gretarsdottir S, Thorleifsson G, Thorsteinsdottir U, Stefansson K, Boncoraglio GB, Parati EA, Attia J, Holliday E, Levi C, Franzosi MG, Goel A, Helgadottir A, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Worrall BB, Kittner SJ, Mitchell BD, Kissela B, Meschia JF, Thijs V, Lindgren A, Macleod MJ, Slowik A, Walters M, Rosand J, Sharma P, Farrall M, Sudlow CL, Rothwell PM, Dichgans M, Donnelly P, Markus HS. Nature genetics Volume 44 (2012) p.328-333 DOI: 10.1038/ng.1081
*
Isoelectric point optimization using peptide descriptors and support vector machines.
Perez-Riverol Y, Audain E, Millan A, Ramos Y, Sanchez A, Vizcaíno JA, Wang R, Müller M, Machado YJ, Betancourt LH, González LJ, Padrón G, Besada V. Journal of proteomics Volume 75 (2012) p.2269-2274 DOI: 10.1016/j.jprot.2012.01.029
*
Hepatitis B virus in transfusion medicine: still a problem?
Allain JP, Candotti D, ISBT HBV Safety Collaborative Group. Biologicals : journal of the International Association of Biological Standardization Volume 40 (2012) p.180-186 DOI: 10.1016/j.biologicals.2011.09.014
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation.
Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N, Hunter S. Database : the journal of biological databases and curation Volume 2012 (2012) p.bar068 DOI: 10.1093/database/bar068
*
Outcome of the first electron microscopy validation task force meeting.
Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Structure (London, England : 1993) Volume 20 (2012) p.205-214 DOI: 10.1016/j.str.2011.12.014
A transcription factor collective defines cardiac cell fate and reflects lineage history.
Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. Cell Volume 148 (2012) p.473-486 DOI: 10.1016/j.cell.2012.01.030
*
Blind testing of routine, fully automated determination of protein structures from NMR data.
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM. Structure (London, England : 1993) Volume 20 (2012) p.227-236 DOI: 10.1016/j.str.2012.01.002
*
Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.
Schmidt D, Schwalie P, Wilson M, Ballester B, Gonçalves Â, Kutter C, Brown G, Marshall A, Flicek P, Odom D. Cell Volume 148 (2012) p.832-832 DOI: 10.1016/j.cell.2012.02.001
WormBase: Annotating many nematode genomes
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg P. Worm Volume 1 (2012) p.15-21
*
The bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling.
Quin MB, Berrisford JM, Newman JA, Baslé A, Lewis RJ, Marles-Wright J. Structure (London, England : 1993) Volume 20 (2012) p.350-363 DOI: 10.1016/j.str.2012.01.003
*
A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. Science (New York, N.Y.) Volume 335 (2012) p.823-828 DOI: 10.1126/science.1215040
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The HUPO initiative on Model Organism Proteomes, iMOP.
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X. Proteomics Volume 12 (2012) p.340-345 DOI: 10.1002/pmic.201290014
From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H. Proteomics Volume 12 (2012) p.351-355 DOI: 10.1002/pmic.201290016
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Correction: Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival.
Sokolowski B, Orchard S, Harvey M, Sridhar S, Sakai Y. PloS one Volume 7 (2012)
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Toward interoperable bioscience data.
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Nature genetics Volume 44 (2012) p.121-126 DOI: 10.1038/ng.1054
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Automatic categorization of diverse experimental information in the bioscience literature.
Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold SJ, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW. BMC bioinformatics Volume 13 (2012) p.16 DOI: 10.1186/1471-2105-13-16
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Populous: a tool for building OWL ontologies from templates.
Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R. BMC bioinformatics Volume 13 Suppl 1 (2012) p.S5 DOI: 10.1186/1471-2105-13-s1-s5
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A combined functional annotation score for non-synonymous variants.
Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E. Human heredity Volume 73 (2012) p.47-51 DOI: 10.1159/000334984
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Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.
Emery L, Whelan S, Hirschi KD, Pittman JK. Frontiers in Plant Science Volume 3 (2012) p.1 DOI: 10.3389/fpls.2012.00001
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Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Cell Volume 148 (2012) p.335-348 DOI: 10.1016/j.cell.2011.11.058
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Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.1204-1209 DOI: 10.1073/pnas.1115761109
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De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G. Nature genetics Volume 44 (2012) p.226-232 DOI: 10.1038/ng.1028
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Self-organizing ontology of biochemically relevant small molecules.
Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M. BMC bioinformatics Volume 13 (2012) p.3 DOI: 10.1186/1471-2105-13-3
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Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND. PLoS computational biology Volume 8 (2012) p.e1002330 DOI: 10.1371/journal.pcbi.1002330
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Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.
Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA. BMC genomics Volume 13 (2012) p.1 DOI: 10.1186/1471-2164-13-1
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Delivering ICT Infrastructure for Biomedical Research
Nyronen TH, Laitinen J, Tourunen O, Sternkopf D, Laurikainen R, Oster P, Lehtovuori PT, Miettinen TA, Simonen T, Perheentupa T, Vastrik I, Kallioniemi O, Lyall A, Thornton JM.
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Women in science.
Dean C, Osborn M, Oshlack A, Thornton J. Genome biology Volume 13 (2012) p.148 DOI: 10.1186/gb4005
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Shouldn't enantiomeric purity be included in the minimum information about a bioactive entity? Response from the MIABE group
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, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Nature reviews. Drug discovery Volume 11 (2012) p.730 DOI: 10.1038/nrd3503-c2
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Toxicology ontology perspectives.
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C. ALTEX Volume 29 (2012) p.139-156 DOI: 10.14573/altex.2012.2.139
Modeling signaling networks using high-throughput phospho-proteomics.
Terfve C, Saez-Rodriguez J. Advances in experimental medicine and biology Volume 736 (2012) p.19-57 DOI: 10.1007/978-1-4419-7210-1_2
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Mapping the human phosphatome on growth pathways.
Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. Molecular systems biology Volume 8 (2012) p.603 DOI: 10.1038/msb.2012.36
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Access and use of the GUDMAP database of genitourinary development.
Davies JA, Little MH, Aronow B, Armstrong J, Brennan J, Lloyd-MacGilp S, Armit C, Harding S, Piu X, Roochun Y, Haggarty B, Houghton D, Davidson D, Baldock R. Methods in molecular biology (Clifton, N.J.) Volume 886 (2012) p.185-201 DOI: 10.1007/978-1-61779-851-1_17
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Revisiting the training of logic models of protein signaling networks with ASP
Videla S, Guziolowski C, Eduati F, Thiele S, Grabe N, Saez-Rodriguez J, Siegel A. Computational Methods in Systems Biology Springer Berlin Heidelberg DOI: 10.1007/978-3-642-33636-2_20
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Predicting the secondary structure of proteins using machine learning algorithms.
Camacho R, Ferreira R, Rosa N, Guimarães V, Fonseca NA, Costa VS, de Sousa M, Magalhães A. International journal of data mining and bioinformatics Volume 6 (2012) p.571-584 DOI: 10.1504/ijdmb.2012.050265
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An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS.
Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G, Manske M, Imwong M, Dondorp AM, Kwiatkowski DP, Quail MA, Swerdlow H. The open genomics journal Volume 5 (2012) DOI: 10.2174/1875693x01205010018
WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW. Worm Volume 1 (2012) p.15-21 DOI: 10.4161/worm.19574
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Food for thought ... A toxicology ontology roadmap.
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C. ALTEX Volume 29 (2012) p.129-137 DOI: 10.14573/altex.2012.2.129
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Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer.
Sanchez A, Sun W, Ma J, Betancourt L, Perez-Riverol Y, de-Cossio JF, Padron G, Jiang Y, He F, Gonzalez LJ, Besada V. European journal of mass spectrometry (Chichester, England) Volume 18 (2012) p.505-508 DOI: 10.1255/ejms.1204
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Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.
Prins P, Goto N, Yates A, Gautier L, Willis S, Fields C, Katayama T. Methods in molecular biology (Clifton, N.J.) Volume 856 (2012) p.513-527 DOI: 10.1007/978-1-61779-585-5_21
A database for chemical proteomics: ChEBI.
de Matos P, Adams N, Hastings J, Moreno P, Steinbeck C. Methods in molecular biology (Clifton, N.J.) Volume 803 (2012) p.273-296 DOI: 10.1007/978-1-61779-364-6_19
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Evaluation of a technology enabled garment for older walkers.
Burns WP, Nugent CD, McCullagh PJ, Finlay DD, Cleland I, Scotney BW, McClean SI, McCann J, Gueldenring D. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2012 (2012) p.2100-2103 DOI: 10.1109/embc.2012.6346374
Accessing and using chemical property databases.
Hastings J, Josephs Z, Steinbeck C. Methods in molecular biology (Clifton, N.J.) Volume 929 (2012) p.193-219 DOI: 10.1007/978-1-62703-050-2_9
Toxicogenomics Investigation Under the eTOX Project
Taboureau O, Hersey A, Audouze K, Gautier L, Jacobsen UP, Akhtar R, Atkinson F, Overington JP, Brunak S. Journal of pharmacogenomics & pharmacoproteomics Volume S7 (2012) p.1-5