Publications for 2014

2014

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FORGE : A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions.
Dunham I, Kulesha E, Iotchkova V, Morganella S, Birney E. Preprint DOI: 10.1101/013045
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VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D. Nucleic acids research Volume 43 (2015) p.D707-13 DOI: 10.1093/nar/gku1117
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. BMC bioinformatics Volume 15 (2014) p.369 DOI: 10.1186/s12859-014-0369-z
diXa: a data infrastructure for chemical safety assessment.
Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JC. Bioinformatics (Oxford, England) Volume 31 (2015) p.1505-1507 DOI: 10.1093/bioinformatics/btu827
Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.
Rawlings ND, Barrett AJ, Bateman A. Current protocols in bioinformatics Volume 48 (2014) p.1.25.1-33 DOI: 10.1002/0471250953.bi0125s48
Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.
Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W. Cell reports Volume 9 (2014) p.1990-2000 DOI: 10.1016/j.celrep.2014.11.034
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Lopez R, Cowley A, Li W, McWilliam H. Current protocols in bioinformatics Volume 48 (2014) p.3.12.1-50 DOI: 10.1002/0471250953.bi0312s48
TermGenie - a web-application for pattern-based ontology class generation.
Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ. Journal of biomedical semantics Volume 5 (2014) p.48 DOI: 10.1186/2041-1480-5-48
Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Molecular systems biology Volume 10 (2014) p.767 DOI: 10.15252/msb.20145112
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Meeting report: advancing practical applications of biodiversity ontologies.
Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N, Denslow MW, Gallery RE, Parnell JJ, Osumi-Sutherland D, Robbins RJ, Rocca-Serra P, Wieczorek J, Zheng J. Standards in Genomic Sciences Volume 9 (2014) p.17-17 DOI: 10.1186/1944-3277-9-17
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Structure, dynamics, assembly, and evolution of protein complexes.
Marsh JA, Teichmann SA. Annual review of biochemistry Volume 84 (2015) p.551-575 DOI: 10.1146/annurev-biochem-060614-034142
Ten recommendations for software engineering in research.
Hastings J, Haug K, Steinbeck C. GigaScience Volume 3 (2014) p.31 DOI: 10.1186/2047-217X-3-31
Analysis of the tryptic search space in UniProt databases.
Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Ríos D, O'Donovan C, Vizcaíno JA, Martin MJ. Proteomics Volume 15 (2015) p.48-57 DOI: 10.1002/pmic.201400227
Genetic resources for methane production from biomass described with the Gene Ontology.
Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Frontiers in Microbiology Volume 5 (2014) p.634 DOI: 10.3389/fmicb.2014.00634
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J. Bioinformatics (Oxford, England) Volume 31 (2015) p.1274-1278 DOI: 10.1093/bioinformatics/btu789
Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR, Zhang X, Steward A, Reuter N, Clarke J, Teichmann SA. Science (New York, N.Y.) Volume 346 (2014) p.1254346 DOI: 10.1126/science.1254346
Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery.
Schubert M, Iorio F. Pharmacogenomics Volume 15 (2014) p.1943-1946 DOI: 10.2217/pgs.14.157
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Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.
Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD. Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1170-1182 DOI: 10.1039/c4ib00086b
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Non-coding RNA gene families in the genomes of anopheline mosquitoes.
Dritsou V, Deligianni E, Dialynas E, Allen J, Poulakakis N, Louis C, Lawson D, Topalis P. BMC genomics Volume 15 (2014) p.1038 DOI: 10.1186/1471-2164-15-1038
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Science (New York, N.Y.) Volume 347 (2015) p.1258522 DOI: 10.1126/science.1258522
Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P. Plant & cell physiology Volume 56 (2015) p.e3 DOI: 10.1093/pcp/pcu183
Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O. The Plant cell Volume 26 (2014) p.4298-4310 DOI: 10.1105/tpc.114.130310
The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. Nucleic acids research Volume 43 (2015) p.D213-21 DOI: 10.1093/nar/gku1243
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Gene Ontology Consortium: going forward.
Gene Ontology Consortium. Nucleic acids research Volume 43 (2015) p.D1049-56 DOI: 10.1093/nar/gku1179
The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
Chipman AD, Ferrier DE, Brena C, Qu J, Hughes DS, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JC, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJ, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JH, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S. PLoS biology Volume 12 (2014) p.e1002005 DOI: 10.1371/journal.pbio.1002005
Small molecule annotation for the Protein Data Bank.
Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA. Database : the journal of biological databases and curation Volume 2014 (2014) p.bau116 DOI: 10.1093/database/bau116
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The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR.
Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang X. Molecular microbiology Volume 95 (2015) p.17-30 DOI: 10.1111/mmi.12844
Solid tumors of childhood display specific serum microRNA profiles.
Murray MJ, Raby KL, Saini HK, Bailey S, Wool SV, Tunnacliffe JM, Enright AJ, Nicholson JC, Coleman N. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology Volume 24 (2015) p.350-360 DOI: 10.1158/1055-9965.EPI-14-0669
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. PLoS genetics Volume 10 (2014) p.e1004798 DOI: 10.1371/journal.pgen.1004798
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INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.
INFRAFRONTIER Consortium. Nucleic acids research Volume 43 (2015) p.D1171-5 DOI: 10.1093/nar/gku1193
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Cell-Line Annotation on Europe PubMed Central
Kim J. Preprint DOI: 10.1101/011700
BioModels: ten-year anniversary.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C. Nucleic acids research Volume 43 (2015) p.D542-8 DOI: 10.1093/nar/gku1181
The IPD and IMGT/HLA database: allele variant databases.
Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG. Nucleic acids research Volume 43 (2015) p.D423-31 DOI: 10.1093/nar/gku1161
Anatomy of enzyme channels.
Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M. BMC bioinformatics Volume 15 (2014) p.379 DOI: 10.1186/s12859-014-0379-x
Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.
Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C. Cancer research Volume 75 (2015) p.194-202 DOI: 10.1158/0008-5472.CAN-13-3131
A community computational challenge to predict the activity of pairs of compounds.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community. Nature biotechnology Volume 32 (2014) p.1213-1222 DOI: 10.1038/nbt.3052
Content discovery and retrieval services at the European Nucleotide Archive.
Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 43 (2015) p.D23-9 DOI: 10.1093/nar/gku1129
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG. Nature biotechnology Volume 32 (2014) p.1250-1255 DOI: 10.1038/nbt.3079
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. Nucleic acids research Volume 43 (2015) p.D240-9 DOI: 10.1093/nar/gku1158
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium. Bioinformatics (Oxford, England) Volume 31 (2015) p.926-932 DOI: 10.1093/bioinformatics/btu739
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.
Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P. Genome research Volume 25 (2015) p.167-178 DOI: 10.1101/gr.177840.114
Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array.
Wong YC, Kwong QB, Lee HL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H. Microarrays (Basel, Switzerland) Volume 3 (2014) p.263-281 DOI: 10.3390/microarrays3040263
Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD. Nucleic acids research Volume 43 (2015) p.D130-7 DOI: 10.1093/nar/gku1063
Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol.
Bolli N, Manes N, McKerrell T, Chi J, Park N, Gundem G, Quail MA, Sathiaseelan V, Herman B, Crawley C, Craig JI, Conte N, Grove C, Papaemmanuil E, Campbell PJ, Varela I, Costeas P, Vassiliou GS. Haematologica Volume 100 (2015) p.214-222 DOI: 10.3324/haematol.2014.113381
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.
Louis A, Nguyen NT, Muffato M, Roest Crollius H. Nucleic acids research Volume 43 (2015) p.D682-9 DOI: 10.1093/nar/gku1112
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Europe PMC: a full-text literature database for the life sciences and platform for innovation.
Europe PMC Consortium. Nucleic acids research Volume 43 (2015) p.D1042-8 DOI: 10.1093/nar/gku1061
The GOA database: gene Ontology annotation updates for 2015.
Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C. Nucleic acids research Volume 43 (2015) p.D1057-63 DOI: 10.1093/nar/gku1113
The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.
Venkata C, Forster MJ, Howe PW, Steinbeck C. PloS one Volume 9 (2014) p.e111576 DOI: 10.1371/journal.pone.0111576
Origin of the response to adrenal and sex steroids: Roles of promiscuity and co-evolution of enzymes and steroid receptors.
Baker ME, Nelson DR, Studer RA. The Journal of steroid biochemistry and molecular biology Volume 151 (2015) p.12-24 DOI: 10.1016/j.jsbmb.2014.10.020
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Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features.
Ain QU, Méndez-Lucio O, Ciriano IC, Malliavin T, van Westen GJ, Bender A. Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1023-1033 DOI: 10.1039/c4ib00175c
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Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Nature Volume 515 (2014) p.371-375 DOI: 10.1038/nature13985
A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. Nature Volume 515 (2014) p.355-364 DOI: 10.1038/nature13992
Genenames.org: the HGNC resources in 2015.
Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. Nucleic acids research Volume 43 (2015) p.D1079-85 DOI: 10.1093/nar/gku1071
ArrayExpress update--simplifying data submissions.
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A. Nucleic acids research Volume 43 (2015) p.D1113-6 DOI: 10.1093/nar/gku1057
PomBase 2015: updates to the fission yeast database.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. Nucleic acids research Volume 43 (2015) p.D656-61 DOI: 10.1093/nar/gku1040
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Overview of gene structure in C. elegans.
Spieth J, Lawson D, Davis P, Williams G, Howe K. WormBook : the online review of C. elegans biology (2014) p.1-18 DOI: 10.1895/wormbook.1.65.2
Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM. Nature communications Volume 5 (2014) p.5135 DOI: 10.1038/ncomms6135
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Synaptic, transcriptional and chromatin genes disrupted in autism.
De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK, DDD Study, Homozygosity Mapping Collaborative for Autism, UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD. Nature Volume 515 (2014) p.209-215 DOI: 10.1038/nature13772
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RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium, Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry JM, Hatzigeorgiou A, Pruitt KD. Nucleic acids research Volume 43 (2015) p.D123-9 DOI: 10.1093/nar/gku991
Ensembl 2015.
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Holliday GL, Rahman SA, Furnham N, Thornton JM. Journal of molecular biology Volume 426 (2014) p.2098-2111 DOI: 10.1016/j.jmb.2014.03.008
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Wagih O, Parts L. G3 (Bethesda, Md.) Volume 4 (2014) p.547-552 DOI: 10.1534/g3.113.009431
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Huntley RP, Sawford T, Martin MJ, O'Donovan C. GigaScience Volume 3 (2014) p.4 DOI: 10.1186/2047-217X-3-4
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The ChEMBL database: a taster for medicinal chemists.
Papadatos G, Overington JP. Future medicinal chemistry Volume 6 (2014) p.361-364 DOI: 10.4155/fmc.14.8
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
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Ten simple rules for running interactive workshops.
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Eavesdropping cuckoos: further insights on great spotted cuckoo preference by magpie nests and egg colour.
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Information visualisation for science and policy: engaging users and avoiding bias.
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Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
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A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Tamuri AU, Goldman N, dos Reis M. Genetics Volume 197 (2014) p.257-271 DOI: 10.1534/genetics.114.162263
FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences.
Garcia L, Yachdav G, Martin MJ. F1000Research Volume 3 (2014) p.47 DOI: 10.12688/f1000research.3-47.v2
KEGGViewer, a BioJS component to visualize KEGG Pathways.
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FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences
Garcia L, Yachdav G, Martin M. Preprint DOI: 10.12688/f1000research.3-47.v1
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BioJS: an open source standard for biological visualisation - its status in 2014.
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PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers.
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Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.
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Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J. BMC systems biology Volume 8 (2014) p.13 DOI: 10.1186/1752-0509-8-13
Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.
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DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.
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Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.
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MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.
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Do climatic conditions affect host and parasite phenotypes differentially? A case study of magpies and great spotted cuckoos.
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Efficient ring perception for the Chemistry Development Kit.
May JW, Steinbeck C. Journal of cheminformatics Volume 6 (2014) p.3 DOI: 10.1186/1758-2946-6-3
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
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Genetic pleiotropy between multiple sclerosis and schizophrenia but not bipolar disorder: differential involvement of immune-related gene loci.
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InterProScan 5: genome-scale protein function classification.
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Reliable protocols for whole-mount fluorescent in situ hybridization (FISH) in the pea aphid Acyrthosiphon pisum: a comprehensive survey and analysis.
Chung CY, Cook CE, Lin GW, Huang TY, Chang CC. Insect science Volume 21 (2014) p.265-277 DOI: 10.1111/1744-7917.12086
PIP₃ induces the recycling of receptor tyrosine kinases.
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Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
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The EBI RDF platform: linked open data for the life sciences.
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Frequency and function of KIR+ CD8+ T cells in HTLV-1 infection.
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Delivering ICT Infrastructure for Biomedical Research
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A novel RCE1 isoform is required for H-Ras plasma membrane localization and is regulated by USP17.
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Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
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A survey of molecular descriptors used in mass spectrometry based proteomics.
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Editorial: Genomics and proteomics behind drug design.
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A predictive model for assistive technology adoption for people with dementia.
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diXa data warehouse: Exploring data from toxicogenomics studies
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The NAD Binding Domain and the Short Chain Dehydrogenase/Reductase (SDR) Superfamily
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Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.
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