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
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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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
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ChEMBLSpace--a graphical explorer of the chemogenomic space covered by the ChEMBL database.
Fechner N, Papadatos G, Evans D, Morphy JR, Brewerton SC, Thorner D, Bodkin M. Bioinformatics (Oxford, England) Volume 29 (2013) p.523-524 DOI: 10.1093/bioinformatics/bts711
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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
Mapping small molecule binding data to structural domains.
Kruger FA, Rostom R, Overington JP. BMC bioinformatics Volume 13 Suppl 17 (2012) p.S11 DOI: 10.1186/1471-2105-13-S17-S11
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Evidence of long-term structured cuckoo parasitism on individual magpie hosts.
Molina-Morales M, Gabriel Martínez J, Martín-Gálvez D, A Dawson D, Rodríguez-Ruiz J, Burke T, Avilés JM. The Journal of animal ecology Volume 82 (2013) p.389-398 DOI: 10.1111/1365-2656.12022
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Do first-time breeding females imprint on their own eggs?
Soler M, Ruiz-Castellano C, Carra LG, Ontanilla J, Martín-Galvez D. Proceedings of the Royal Society B: Biological Sciences Volume 280 (2013) p.20122518 DOI: 10.1098/rspb.2012.2518
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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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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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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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
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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
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
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
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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
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
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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
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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ENCODE data in the UCSC Genome Browser: year 5 update.
Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. Nucleic acids research Volume 41 (2013) p.D56-63 DOI: 10.1093/nar/gks1172
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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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
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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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
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Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
Levy ED, De S, Teichmann SA. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.20461-20466 DOI: 10.1073/pnas.1209312109
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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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
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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
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Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.
Teichmann SA, Wigge PA, Charoensawan V. Cell cycle (Georgetown, Tex.) Volume 11 (2012) p.4487-4488 DOI: 10.4161/cc.22666
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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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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
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
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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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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A genome-wide study shows a limited contribution of rare copy number variants to Alzheimer's disease risk.
Chapman J, Rees E, Harold D, Ivanov D, Gerrish A, Sims R, Hollingworth P, Stretton A, GERAD1 Consortium, Holmans P, Owen MJ, O'Donovan MC, Williams J, Kirov G. Human molecular genetics Volume 22 (2013) p.816-824 DOI: 10.1093/hmg/dds476
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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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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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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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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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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, 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
Cheminformatics
Wegner JK, Sterling A, Guha R, Bender A, Faulon J-L, Hastings J, O'Boyle N, Overington J, Van Vlijmen H, Willighagen E. Communications of the ACM Volume 55 (2012) p.65-75 DOI: 10.1145/2366316.2366334
Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets.
Jupe S, Akkerman JW, Soranzo N, Ouwehand WH. Journal of thrombosis and haemostasis : JTH Volume 10 (2012) p.2399-2402 DOI: 10.1111/j.1538-7836.2012.04930.x
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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
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
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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
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
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Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome.
Gendrel AV, Apedaile A, Coker H, Termanis A, Zvetkova I, Godwin J, Tang YA, Huntley D, Montana G, Taylor S, Giannoulatou E, Heard E, Stancheva I, Brockdorff N. Developmental cell Volume 23 (2012) p.265-279 DOI: 10.1016/j.devcel.2012.06.011
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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
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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
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Towards the elucidation of the regulatory network guiding the insulin producing cells' differentiation.
Kapasa M, Vlachakis D, Kostadima M, Sotiropoulou G, Kossida S. Genomics Volume 100 (2012) p.212-221 DOI: 10.1016/j.ygeno.2012.07.002
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VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets.
Morganella S, Ceccarelli M. Bioinformatics (Oxford, England) Volume 28 (2012) p.2512-2514 DOI: 10.1093/bioinformatics/bts453
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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
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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
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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
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
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.
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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
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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
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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
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Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.
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DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA. Molecular cell Volume 47 (2012) p.183-192 DOI: 10.1016/j.molcel.2012.06.028
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Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium. Nature Volume 487 (2012) p.94-98 DOI: 10.1038/nature11041
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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
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Integrating literature-constrained and data-driven inference of signalling networks.
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First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans?
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Diverse epigenetic strategies interact to control epidermal differentiation.
Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, Sirokmány G, Donati G, Uribe-Lewis S, Pavlidis P, Murrell A, Markowetz F, Watt FM. Nature cell biology Volume 14 (2012) p.753-763 DOI: 10.1038/ncb2520
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
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A suggested new bacteriophage genus: "Viunalikevirus".
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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
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Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors.
Metzakopian E, Lin W, Salmon-Divon M, Dvinge H, Andersson E, Ericson J, Perlmann T, Whitsett JA, Bertone P, Ang SL. Development (Cambridge, England) Volume 139 (2012) p.2625-2634 DOI: 10.1242/dev.081034
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ISMB 2012 PROCEEDINGS PAPERS COMMITTEE.
Bioinformatics (Oxford, England) Volume 28 (2012) p.i2-i6 DOI: 10.1093/bioinformatics/bts287
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Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks.
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ISMB 2012 Proceedings Papers Committee. July 15 to July 19, 2012, Long Beach, CA, USA. Editorial.
Berger B. Bioinformatics (Oxford, England) Volume 28 (2012) p.i1 DOI: 10.1093/bioinformatics/bts281
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The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.
Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA. Biochemical Society transactions Volume 40 (2012) p.475-491 DOI: 10.1042/bst20120056
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L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language.
Boudon F, Pradal C, Cokelaer T, Prusinkiewicz P, Godin C. Frontiers in Plant Science Volume 3 (2012) p.76 DOI: 10.3389/fpls.2012.00076
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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.
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InterPro in 2011: new developments in the family and domain prediction database.
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In contrast to HIV, KIR3DS1 does not influence outcome in HTLV-1 retroviral infection.
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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
MELTING, a flexible platform to predict the melting temperatures of nucleic acids.
Dumousseau M, Rodriguez N, Juty N, Le Novère N. BMC bioinformatics Volume 13 (2012) p.101 DOI: 10.1186/1471-2105-13-101
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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
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Extent, causes, and consequences of small RNA expression variation in human adipose tissue.
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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
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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
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Evolution of oligomeric state through geometric coupling of protein interfaces.
Perica T, Chothia C, Teichmann SA. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.8127-8132 DOI: 10.1073/pnas.1120028109
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Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions.
Kaleta C, de Figueiredo LF, Schuster S. International journal of circumpolar health Volume 71 (2012) p.1-2 DOI: 10.3402/ijch.v71i0.18436
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
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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
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Structured chemical class definitions and automated matching for chemical ontology evolution.
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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
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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
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NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment.
Reynolds N, Latos P, Hynes-Allen A, Loos R, Leaford D, O'Shaughnessy A, Mosaku O, Signolet J, Brennecke P, Kalkan T, Costello I, Humphreys P, Mansfield W, Nakagawa K, Strouboulis J, Behrens A, Bertone P, Hendrich B. Cell stem cell Volume 10 (2012) p.583-594 DOI: 10.1016/j.stem.2012.02.020
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.
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Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.
Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV. Bioinformatics (Oxford, England) Volume 28 (2012) p.1783-1789 DOI: 10.1093/bioinformatics/bts250
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
Measuring the level of activity in community built bio-ontologies.
Malone J, Stevens R. Journal of biomedical informatics Volume 46 (2013) p.5-14 DOI: 10.1016/j.jbi.2012.04.002
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
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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
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The interface of protein structure, protein biophysics, and molecular evolution.
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. Protein science : a publication of the Protein Society Volume 21 (2012) p.769-785 DOI: 10.1002/pro.2071
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
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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
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The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012.
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Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells.
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Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level.
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Structure-based classification and ontology in chemistry.
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Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
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The genomic basis of adaptive evolution in threespine sticklebacks.
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NAD(+) biosynthesis and salvage--a phylogenetic perspective.
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Looking for Darwin in genomic sequences--validity and success of statistical methods.
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MageComet--web application for harmonizing existing large-scale experiment descriptions.
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The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions.
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Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
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Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.
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Systematic identification of genomic markers of drug sensitivity in cancer cells.
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Bioimage informatics: a new category in Bioinformatics.
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The Protein Data Bank at 40: reflecting on the past to prepare for the future.
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HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.
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Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
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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
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GrameneMart: the BioMart data portal for the Gramene project.
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Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis.
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Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome.
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Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
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The KUPKB: a novel Web application to access multiomics data on kidney disease.
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Identification and localisation of the NB-LRR gene family within the potato genome.
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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
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HIPPIE: Integrating protein interaction networks with experiment based quality scores.
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ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
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Toward community standards in the quest for orthologs.
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The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer.
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PRIDE Inspector: a tool to visualize and validate MS proteomics data.
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Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke.
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Isoelectric point optimization using peptide descriptors and support vector machines.
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Hepatitis B virus in transfusion medicine: still a problem?
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Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression.
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WormBase: Annotating many nematode genomes
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Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.
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From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.
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The bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling.
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Blind testing of routine, fully automated determination of protein structures from NMR data.
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Three hybrid classifiers for the detection of emotions in suicide notes.
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Automatic categorization of diverse experimental information in the bioscience literature.
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Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles.
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Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.
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Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
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An updated nomenclature for keratin-associated proteins (KAPs).
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Global analysis of small molecule binding to related protein targets.
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Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
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De novo assembly and genotyping of variants using colored de Bruijn graphs.
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Self-organizing ontology of biochemically relevant small molecules.
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Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
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Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.
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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.
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Mapping the human phosphatome on growth pathways.
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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.
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
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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Requirements for semantic biobanks.
Andrade AQ, Kreuzthaler M, Hastings J, Krestyaninova M, Schulz S. Studies in health technology and informatics Volume 180 (2012) p.569-573
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Detecting structural invariants in biological reaction networks.
Behre J, de Figueiredo LF, Schuster S, Kaleta C. Methods in molecular biology (Clifton, N.J.) Volume 804 (2012) p.377-407 DOI: 10.1007/978-1-61779-361-5_20
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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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
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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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Ontologies for human behavior analysis and their application to clinical data.
Hastings J, Schulz S. International review of neurobiology Volume 103 (2012) p.89-107 DOI: 10.1016/b978-0-12-388408-4.00005-8
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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
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
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How to use the IUPHAR receptor database to navigate pharmacological data.
Mpamhanga CP, Sharman JL, Harmar AJ, NC-IUPHAR. Methods in molecular biology (Clifton, N.J.) Volume 897 (2012) p.15-29 DOI: 10.1007/978-1-61779-909-9_2
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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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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
How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.
Vaquerizas JM, Teichmann SA, Luscombe NM. Methods in molecular biology (Clifton, N.J.) Volume 786 (2012) p.3-19 DOI: 10.1007/978-1-61779-292-2_1
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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/gb-2012-13-3-148
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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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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
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The role of variation at AβPP, PSEN1, PSEN2, and MAPT in late onset Alzheimer's disease.
Gerrish A, Russo G, Richards A, Moskvina V, Ivanov D, Harold D, Sims R, Abraham R, Hollingworth P, Chapman J, Hamshere M, Pahwa JS, Dowzell K, Williams A, Jones N, Thomas C, Stretton A, Morgan AR, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Morgan K, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Johnston JA, Holmes C, Mann D, Smith AD, Love S, Kehoe PG, Hardy J, Mead S, Fox N, Rossor M, Collinge J, Maier W, Jessen F, Kölsch H, Heun R, Schürmann B, van den Bussche H, Heuser I, Kornhuber J, Wiltfang J, Dichgans M, Frölich L, Hampel H, Hüll M, Rujescu D, Goate AM, Kauwe JS, Cruchaga C, Nowotny P, Morris JC, Mayo K, Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Davies G, Harris SE, Starr JM, Deary IJ, Al-Chalabi A, Shaw CE, Tsolaki M, Singleton AB, Guerreiro R, Mühleisen TW, Nöthen MM, Moebus S, Jöckel KH, Klopp N, Wichmann HE, Carrasquillo MM, Pankratz VS, Younkin SG, Jones L, Holmans PA, O'Donovan MC, Owen MJ, Williams J. Journal of Alzheimer's disease : JAD Volume 28 (2012) p.377-387 DOI: 10.3233/JAD-2011-110824
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