Publications for 2014

2014

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.
Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC.
Nature communications Volume 5 (2014) p.2997

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.
Cossetti C, Iraci N, Mercer TR, Leonardi T, Alpi E, Drago D, Alfaro-Cervello C, Saini HK, Davis MP, Schaeffer J, Vega B, Stefanini M, Zhao C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS, Pluchino S.
Molecular cell Volume 56 (2014) p.193-204

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.
Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F.
Nature genetics Volume 46 (2014) p.753-758

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.
Pinnick KE, Nicholson G, Manolopoulos KN, McQuaid SE, Valet P, Frayn KN, Denton N, Min JL, Zondervan KT, Fleckner J, MolPAGE Consortium, McCarthy MI, Holmes CC, Karpe F.
Diabetes Volume 63 (2014) p.3785-3797

Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J.
G3 (Bethesda, Md.) Volume 4 (2014) p.433-445

RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A.
PloS one Volume 9 (2014) p.e107026

Fast randomization of large genomic datasets while preserving alteration counts.
Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 30 (2014) p.i617-23

Single Cell Genomics meeting in Stockholm: from single cells to cell types.
Scialdone A, Achim K, Marioni JC.
Genome biology Volume 15 (2014) p.496

WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic acids research Volume 42 (2014) p.D789-93

The ChEMBL bioactivity database: an update.
Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP.
Nucleic acids research Volume 42 (2014) p.D1083-90

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM.
Biopolymers Volume 101 (2014) p.659-668

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

The Protein Data Bank archive as an open data resource.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Journal of computer-aided molecular design Volume 28 (2014) p.1009-1014

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.E3366

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

Response to On prompt update of literature references in the Protein Data Bank.
Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 70 (2014) p.2780

Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.
Nature Volume 512 (2014) p.445-448

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 Volume (2014) p.1-18

Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.
Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q, Kamatani Y, Bennet AM, Tamm R, Trompet S, Guðbjartsson DF, Flachsbart F, Rose G, Viktorin A, Fischer K, Nygaard M, Cordell HJ, Crocco P, van den Akker EB, Böhringer S, Helmer Q, Nelson CP, Saunders GI, Alver M, Andersen-Ranberg K, Breen ME, van der Breggen R, Caliebe A, Capri M, Cevenini E, Collerton JC, Dato S, Davies K, Ford I, Gampe J, Garagnani P, de Geus EJ, Harrow J, van Heemst D, Heijmans BT, Heinsen FA, Hottenga JJ, Hofman A, Jeune B, Jonsson PV, Lathrop M, Lechner D, Martin-Ruiz C, Mcnerlan SE, Mihailov E, Montesanto A, Mooijaart SP, Murphy A, Nohr EA, Paternoster L, Postmus I, Rivadeneira F, Ross OA, Salvioli S, Sattar N, Schreiber S, Stefánsson H, Stott DJ, Tiemeier H, Uitterlinden AG, Westendorp RG, Willemsen G, Samani NJ, Galan P, Sørensen TI, Boomsma DI, Jukema JW, Rea IM, Passarino G, de Craen AJ, Christensen K, Nebel A, Stefánsson K, Metspalu A, Magnusson P, Blanché H, Christiansen L, Kirkwood TB, van Duijn CM, Franceschi C, Houwing-Duistermaat JJ, Slagboom PE.
Human molecular genetics Volume 23 (2014) p.4420-4432

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z.
Genome biology Volume 15 (2014) p.459

Identifying cell types from spatially referenced single-cell expression datasets.
Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J.
PLoS computational biology Volume 10 (2014) p.e1003824

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.
eLife Volume 3 (2014) p.e02626

Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.
Clarkson CS, Weetman D, Essandoh J, Yawson AE, Maslen G, Manske M, Field SG, Webster M, Antão T, MacInnis B, Kwiatkowski D, Donnelly MJ.
Nature communications Volume 5 (2014) p.4248

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

Archaic humans: Four makes a party.
Birney E, Pritchard JK.
Nature Volume 505 (2014) p.32-34

Integrative knowledge management to enhance pharmaceutical R&D.
Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F.
Nature reviews. Drug discovery Volume 13 (2014) p.239-240

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.
Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D.
PLoS genetics Volume 10 (2014) p.e1004109

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Delaneau O, Marchini J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium.
Nature communications Volume 5 (2014) p.3934

TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Nucleic acids research Volume 42 (2014) p.D922-5

Assessing the state of substitution models describing noncoding RNA evolution.
Allen JE, Whelan S.
Genome biology and evolution Volume 6 (2014) p.65-75

OAE: The Ontology of Adverse Events.
He Y, Sarntivijai S, Lin Y, Xiang Z, Guo A, Zhang S, Jagannathan D, Toldo L, Tao C, Smith B.
Journal of biomedical semantics Volume 5 (2014) p.29

Functional annotation of noncoding sequence variants.
Ritchie GR, Dunham I, Zeggini E, Flicek P.
Nature methods Volume 11 (2014) p.294-296

Assembly information services in the European Nucleotide Archive.
Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 42 (2014) p.D38-43

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.
Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L.
BMC bioinformatics Volume 15 (2014) p.75

A controlled vocabulary for pathway entities and events.
Jupe S, Jassal B, Williams M, Wu G.
Database : the journal of biological databases and curation Volume 2014 (2014) p.

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.
Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S, FANTOM Consortium.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.5289-5294

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Genome biology Volume 15 (2014) p.R88

An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A.
Nature Volume 507 (2014) p.455-461

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

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A.
Nucleic acids research Volume 42 (2014) p.D364-73

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Waller M, Barrett AJ, Bateman A.
Nucleic acids research Volume 42 (2014) p.D503-9

Use of internet search logs to evaluate potential drug adverse events.
Sarntivijai S, Abernethy DR.
Clinical pharmacology and therapeutics Volume 96 (2014) p.149-150

jmzTab: a java interface to the mzTab data standard.
Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.
Proteomics Volume 14 (2014) p.1328-1332

Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.
Maina AN, Mwaura FB, Oyugi J, Goulding D, Toribio AL, Kariuki S.
Current microbiology Volume 68 (2014) p.64-70

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.
Biochimica et biophysica acta Volume 1844 (2014) p.63-76

BioModels linked dataset.
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C.
BMC systems biology Volume 8 (2014) p.91

Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress.
Foijer F, Xie SZ, Simon JE, Bakker PL, Conte N, Davis SH, Kregel E, Jonkers J, Bradley A, Sorger PK.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.13427-13432

Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.
Denise H, Moschos SA, Sidders B, Burden F, Perkins H, Carter N, Stroud T, Kennedy M, Fancy SA, Lapthorn C, Lavender H, Kinloch R, Suhy D, Corbau R.
Molecular therapy. Nucleic acids Volume 3 (2014) p.e145

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

Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG.
Trends in biotechnology Volume 32 (2014) p.396-399

A predictive model for assistive technology adoption for people with dementia.
Zhang S, McClean SI, Nugent CD, Donnelly MP, Galway L, Scotney BW, Cleland I.
IEEE journal of biomedical and health informatics Volume 18 (2014) p.375-383

Evaluation of prompted annotation of activity data recorded from a smart phone.
Cleland I, Han M, Nugent C, Lee H, McClean S, Zhang S, Lee S.
Sensors (Basel, Switzerland) Volume 14 (2014) p.15861-15879

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

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.
Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Rydén M, Arner P, FANTOM Consortium.
PloS one Volume 9 (2014) p.e80274

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA.
Nucleic acids research Volume 42 (2014) p.D600-6

The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
Davis OS, Band G, Pirinen M, Haworth CM, Meaburn EL, Kovas Y, Harlaar N, Docherty SJ, Hanscombe KB, Trzaskowski M, Curtis CJ, Strange A, Freeman C, Bellenguez C, Su Z, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Barroso I, Peltonen L, Dale PS, Petrill SA, Schalkwyk LS, Craig IW, Lewis CM, Price TS, Wellcome Trust Case Control Consortium 2, Donnelly P, Plomin R, Spencer CC.
Nature communications Volume 5 (2014) p.4204

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.
Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.17230-17235

Peroxidase gene discovery from the horseradish transcriptome.
Näätsaari L, Krainer FW, Schubert M, Glieder A, Thallinger GG.
BMC genomics Volume 15 (2014) p.227

Overview of the gene ontology task at BioCreative IV.
Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z.
Database : the journal of biological databases and curation Volume 2014 (2014) p.

A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium 2, Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Arranz MJ, Bakker S, Bender S, Bruggeman R, Cahn W, Chandler D, Collier DA, Crespo-Facorro B, Dazzan P, de Haan L, Di Forti M, Dragović M, Giegling I, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Kravariti E, Lawrie S, Linszen DH, Mata I, McDonald C, McIntosh A, Myin-Germeys I, Ophoff RA, Pariante CM, Paunio T, Picchioni M, Psychiatric Genomics Consortium, Ripke S, Rujescu D, Sauer H, Shaikh M, Sussmann J, Suvisaari J, Tosato S, Toulopoulou T, Van Os J, Walshe M, Weisbrod M, Whalley H, Wiersma D, Blackwell JM, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Wood NW, Barroso I, Peltonen L, Lewis CM, Murray RM, Donnelly P, Powell J, Spencer CC.
Biological psychiatry Volume 75 (2014) p.386-397

InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1236-1240

BC4GO: a full-text corpus for the BioCreative IV GO task.
Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z.
Database : the journal of biological databases and curation Volume 2014 (2014) p.

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.
Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T.
Journal of the American Society of Nephrology : JASN Volume 25 (2014) p.1509-1522

The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.
Courtot M, Brinkman RR, Ruttenberg A.
PloS one Volume 9 (2014) p.e92632

Activities at the Universal Protein Resource (UniProt).

Nucleic acids research Volume 42 (2014) p.7486-7486

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Cejuela JM, McQuilton P, Ponting L, Marygold SJ, Stefancsik R, Millburn GH, Rost B, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau033

Characterizing genetic variants for clinical action.
Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJ, Jarvik GP, O'Donnell C, Sherry ST, Aronson N, Biesecker LG, Blumberg B, Calonge N, Colhoun HM, Epstein RS, Flicek P, Gordon ES, Green ED, Green RC, Hurles M, Kawamoto K, Knaus W, Ledbetter DH, Levy HP, Lyon E, Maglott D, McLeod HL, Rahman N, Randhawa G, Wicklund C, Manolio TA, Chisholm RL, Williams MS.
American journal of medical genetics. Part C, Seminars in medical genetics Volume 166C (2014) p.93-104

PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.
Lucas JM, Muffato M, Roest Crollius H.
BMC bioinformatics Volume 15 (2014) p.268

A promoter-level mammalian expression atlas.
FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.
Nature Volume 507 (2014) p.462-470

Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
Nayduch D, Cohnstaedt LW, Saski C, Lawson D, Kersey P, Fife M, Carpenter S.
Virus research Volume 182 (2014) p.43-49

Protection against colitis by CD100-dependent modulation of intraepithelial γδ T lymphocyte function.
Meehan TF, Witherden DA, Kim CH, Sendaydiego K, Ye I, Garijo O, Komori HK, Kumanogoh A, Kikutani H, Eckmann L, Havran WL.
Mucosal immunology Volume 7 (2014) p.134-142

Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.
Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I.
Medical mycology Volume 52 (2014) p.472-481

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.
Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR, FANTOM Consortium, Suzuki H.
Scientific reports Volume 4 (2014) p.5228

KEGGViewer, a BioJS component to visualize KEGG Pathways.
Villaveces JM, Jimenez RC, Habermann BH.
F1000Research Volume 3 (2014) p.43

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers.
Villaveces JM, Jimenez RC, Habermann BH.
F1000Research Volume 3 (2014) p.44

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

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ.
BMC bioinformatics Volume 15 (2014) p.155

Smoothing 3D protein structure motifs through graph mining and amino acid similarities.
Dhifli W, Saidi R, Nguifo EM.
Journal of computational biology : a journal of computational molecular cell biology Volume 21 (2014) p.162-172

Sequence, a BioJS component for visualising sequences.
Gomez J, Jimenez R.
F1000Research Volume 3 (2014) p.52

Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR, Apweiler R, Ping P.
Journal of proteome research Volume 13 (2014) p.433-446

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.
Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H.
Proteomics Volume 14 (2014) p.2363-2368

Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D (1)H-NMR data.
Gómez J, Brezmes J, Mallol R, Rodríguez MA, Vinaixa M, Salek RM, Correig X, Cañellas N.
Analytical and bioanalytical chemistry Volume 406 (2014) p.7967-7976

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C.
Methods in molecular biology (Clifton, N.J.) Volume 1079 (2014) p.59-73

Genome sequencing of normal cells reveals developmental lineages and mutational processes.
Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M, Cuppen E, Clevers H, Stratton MR.
Nature Volume 513 (2014) p.422-425

Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b.
Toribio AL, Pickard D, Cerdeño-Tárraga AM, Petty NK, Thomson N, Salmond G, Dougan G.
Genome announcements Volume 2 (2014) p.

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler TJ, Clements J, Finn RD.
BMC bioinformatics Volume 15 (2014) p.7

Ten simple rules for running interactive workshops.
Pavelin K, Pundir S, Cham JA.
PLoS computational biology Volume 10 (2014) p.e1003485

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

Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM.
Nature methods Volume 11 (2014) p.171-174

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D802-9

The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.
Current opinion in structural biology Volume 26 (2014) p.121-130

CLO: The cell line ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.
Journal of biomedical semantics Volume 5 (2014) p.37

Exploring the biological and chemical complexity of the ligases.
Holliday GL, Rahman SA, Furnham N, Thornton JM.
Journal of molecular biology Volume 426 (2014) p.2098-2111

Large-scale identification of phosphorylation sites for profiling protein kinase selectivity.
Imamura H, Sugiyama N, Wakabayashi M, Ishihama Y.
Journal of proteome research Volume 13 (2014) p.3410-3419

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange.
Beer R, Herbst K, Ignatiadis N, Kats I, Adlung L, Meyer H, Niopek D, Christiansen T, Georgi F, Kurzawa N, Meichsner J, Rabe S, Riedel A, Sachs J, Schessner J, Schmidt F, Walch P, Niopek K, Heinemann T, Eils R, Di Ventura B.
Molecular bioSystems Volume 10 (2014) p.1709-1718

High-resolution genome screen for bone mineral density in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T.
Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Volume 29 (2014) p.1619-1626

Chemical, target, and bioactive properties of allosteric modulation.
van Westen GJ, Gaulton A, Overington JP.
PLoS computational biology Volume 10 (2014) p.e1003559

Genomic standards consortium projects.
Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.
Standards in genomic sciences Volume 9 (2014) p.599-601

The architecture of parent-of-origin effects in mice.
Mott R, Yuan W, Kaisaki P, Gan X, Cleak J, Edwards A, Baud A, Flint J.
Cell Volume 156 (2014) p.332-342

Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat.
Falak S, Schafer S, Baud A, Hummel O, Schulz H, Gauguier D, Hubner N, Osborne-Pellegrin M.
Physiological genomics Volume 46 (2014) p.418-428

Transporter taxonomy - a comparison of different transport protein classification schemes.
Viereck M, Gaulton A, Digles D, Ecker GF.
Drug discovery today. Technologies Volume 12 (2014) p.e37-46

Transporter assays and assay ontologies: useful tools for drug discovery.
Zdrazil B, Chichester C, Zander Balderud L, Engkvist O, Gaulton A, Overington JP.
Drug discovery today. Technologies Volume 12 (2014) p.e47-54

UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers.
Chambers J, Davies M, Gaulton A, Papadatos G, Hersey A, Overington JP.
Journal of cheminformatics Volume 6 (2014) p.43

Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat.
Tuncel J, Haag S, Yau AC, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, EURATRANS Consortium, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R.
PLoS genetics Volume 10 (2014) p.e1004151

Genomes and phenomes of a population of outbred rats and its progenitors.
Baud A, Guryev V, Hummel O, Johannesson M, Rat Genome Sequencing and Mapping Consortium, Flint J.
Scientific data Volume 1 (2014) p.140011

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y, Mashima J, Nakamura Y, Cochrane G, Karsch-Mizrachi I.
Standards in genomic sciences Volume 9 (2014) p.1275-1277

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F.
PLoS computational biology Volume 10 (2014) p.e1003535

The EBI RDF platform: linked open data for the life sciences.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1338-1339

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.
Biochimica et biophysica acta Volume 1844 (2014) p.98-107

BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
Kim JK, Cho Y, Laskowski RA, Ryu SE, Sugihara K, Kim DS.
Proteins Volume 82 (2014) p.1829-1849

Data standardization and sharing-the work of the HUPO-PSI.
Orchard S.
Biochimica et biophysica acta Volume 1844 (2014) p.82-87

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

DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.
Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S.
Genomics Volume 103 (2014) p.1-10

BioJS: an open source standard for biological visualisation - its status in 2014.
Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H.
F1000Research Volume 3 (2014) p.55

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

Big data and other challenges in the quest for orthologs.
Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs consortium.
Bioinformatics (Oxford, England) Volume 30 (2014) p.2993-2998

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.
Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I, UniProt Consortium.
Human mutation Volume 35 (2014) p.927-935

Computational approaches to interpreting genomic sequence variation.
Ritchie GR, Flicek P.
Genome medicine Volume 6 (2014) p.87

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA.
Proteomics Volume 14 (2014) p.2233-2241

Enly: Improving Draft Genomes through Reads Recycling.
Fondi M, Orlandini V, Corti G, Severgnini M, Galardini M, Pietrelli A, Fuligni F, Iacono M, Rizzi E, De Bellis G, Fani R.
Journal of genomics Volume 2 (2014) p.89-93

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.
Nature biotechnology Volume 32 (2014) p.223-226

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
Nucleic acids research Volume 42 (2014) p.D485-9

Maximum likelihood inference of small trees in the presence of long branches.
Parks SL, Goldman N.
Systematic biology Volume 63 (2014) p.798-811

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Kultys M, Nicholas L, Schwarz R, Goldman N, King J.
BMC Proceedings Volume 8 (2014) p.S8

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
Papatheodorou I, Petrovs R, Thornton JM.
Bioinformatics (Oxford, England) Volume 30 (2014) p.2999-3003

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.
Journal of biomedical semantics Volume 5 (2014) p.25

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.
Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D.
Aging Volume 6 (2014) p.98-117

PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA.
Nucleic acids research Volume 42 (2014) p.D292-6

qcML: an exchange format for quality control metrics from mass spectrometry experiments.
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.
Molecular & cellular proteomics : MCP Volume 13 (2014) p.1905-1913

Biomarkers in autism spectrum disorder: the old and the new.
Ruggeri B, Sarkans U, Schumann G, Persico AM.
Psychopharmacology Volume 231 (2014) p.1201-1216

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

EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.
Nature methods Volume 11 (2014) p.171-174

Mining Molecular Pharmacological Effects from Biomedical Text: a Case Study for Eliciting Anti-Obesity/Diabetes Effects of Chemical Compounds.
Dura E, Muresan S, Engkvist O, Blomberg N, Chen H.
Molecular informatics Volume 33 (2014) p.332-342

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.
Genome research Volume 24 (2014) p.1797-1807

Innate immunity. A Spaetzle-like role for nerve growth factor β in vertebrate immunity to Staphylococcus aureus.
Hepburn L, Prajsnar TK, Klapholz C, Moreno P, Loynes CA, Ogryzko NV, Brown K, Schiebler M, Hegyi K, Antrobus R, Hammond KL, Connolly J, Ochoa B, Bryant C, Otto M, Surewaard B, Seneviratne SL, Grogono DM, Cachat J, Ny T, Kaser A, Török ME, Peacock SJ, Holden M, Blundell T, Wang L, Ligoxygakis P, Minichiello L, Woods CG, Foster SJ, Renshaw SA, Floto RA.
Science (New York, N.Y.) Volume 346 (2014) p.641-646

ECCB 2014: The 13th European Conference on Computational Biology.
Devignes MD, Moreau Y.
Bioinformatics (Oxford, England) Volume 30 (2014) p.i345-8

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

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.
Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest AR, Hayashizaki Y, Carloni P, Ferrer I, Lodovichi C, Plessy C, FANTOM Consortium, Carninci P, Gustincich S.
BMC genomics Volume 15 (2014) p.729

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
Huntley RP, Sawford T, Martin MJ, O'Donovan C.
GigaScience Volume 3 (2014) p.4

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression.
Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AE, Wardle FC.
BMC biology Volume 12 (2014) p.81

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.
Barrera A, Alastruey-Izquierdo A, Martín MJ, Cuesta I, Vizcaíno JA.
PLoS computational biology Volume 10 (2014) p.e1003733

Practical aspects of protein co-evolution.
Ochoa D, Pazos F.
Frontiers in cell and developmental biology Volume 2 (2014) p.14

The Nucleic Acid Database: new features and capabilities.
Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM.
Nucleic acids research Volume 42 (2014) p.D114-22

The common marmoset genome provides insight into primate biology and evolution.
Marmoset Genome Sequencing and Analysis Consortium.
Nature genetics Volume 46 (2014) p.850-857

A formal re-description of the cockroach Hebardina concinna anchored on DNA Barcodes confirms wing polymorphism and identifies morphological characters for field identification.
Yue Q, Wu K, Qiu D, Hu J, Liu D, Wei X, Chen J, Cook CE.
PloS one Volume 9 (2014) p.e106789

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

Dissecting the transcriptional phenotype of ribosomal protein deficiency: implications for Diamond-Blackfan Anemia.
Aspesi A, Pavesi E, Robotti E, Crescitelli R, Boria I, Avondo F, Moniz H, Da Costa L, Mohandas N, Roncaglia P, Ramenghi U, Ronchi A, Gustincich S, Merlin S, Marengo E, Ellis SR, Follenzi A, Santoro C, Dianzani I.
Gene Volume 545 (2014) p.282-289

Representing kidney development using the gene ontology.
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP.
PloS one Volume 9 (2014) p.e99864

Updates to BioSamples database at European Bioinformatics Institute.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D50-2

PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Nucleic acids research Volume 42 (2014) p.D285-91

Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z.
PLoS genetics Volume 10 (2014) p.e1004132

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.
Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J.
Molecular cancer Volume 13 (2014) p.28

Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.
Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH.
Structure (London, England : 1993) Volume 22 (2014) p.1862-1874

Proceedings of the 13th European Conference on Computational Biology (ECCB’14), September 7-10, 2014, Strasbourg, France.

Bioinformatics (Oxford, England) Volume 30 (2014) p.i341-645

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

gitter: a robust and accurate method for quantification of colony sizes from plate images.
Wagih O, Parts L.
G3 (Bethesda, Md.) Volume 4 (2014) p.547-552

Relationship between genome and epigenome--challenges and requirements for future research.
Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.
BMC genomics Volume 15 (2014) p.487

An overview of tools for the validation of protein NMR structures.
Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A.
Journal of biomolecular NMR Volume 58 (2014) p.259-285

Do climatic conditions affect host and parasite phenotypes differentially? A case study of magpies and great spotted cuckoos.
Soler JJ, De Neve L, Martín-Gálvez D, Molina-Morales M, Pérez-Contreras T, Ruiz-Rodríguez M.
Oecologia Volume 174 (2014) p.327-338

Eavesdropping cuckoos: further insights on great spotted cuckoo preference by magpie nests and egg colour.
Soler JJ, Avilés JM, Martín-Gálvez D, de Neve L, Soler M.
Oecologia Volume 175 (2014) p.105-115

Cuckoo hosts shift from accepting to rejecting parasitic eggs across their lifetime.
Molina-Morales M, Martínez JG, Martín-Gálvez D, Dawson DA, Burke T, Avilés JM.
Evolution; international journal of organic evolution Volume 68 (2014) p.3020-3029

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium.
Nature biotechnology Volume 32 (2014) p.903-914

Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi N, Lippert C, Lawrence ND, Stegle O.
Nature communications Volume 5 (2014) p.4890

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C.
Angewandte Chemie (International ed. in English) Volume 53 (2014) p.6720-6723

Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL.
Developmental cell Volume 28 (2014) p.351-365

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw.
Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS.
Biotechnology for biofuels Volume 7 (2014) p.495

On best practices in the development of bioinformatics software.
Leprevost Fda V, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC.
Frontiers in genetics Volume 5 (2014) p.199

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
Greger L, Su J, Rung J, Ferreira PG, Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.
PloS one Volume 9 (2014) p.e104567

Ensembl 2014.
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Yates A, Zerbino DR, Searle SM.
Nucleic acids research Volume 42 (2014) p.D749-55

PIP₃ induces the recycling of receptor tyrosine kinases.
Laketa V, Zarbakhsh S, Traynor-Kaplan A, Macnamara A, Subramanian D, Putyrski M, Mueller R, Nadler A, Mentel M, Saez-Rodriguez J, Pepperkok R, Schultz C.
Science signaling Volume 7 (2014) p.ra5

A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.
Nature biotechnology Volume 32 (2014) p.1202-1212

Serum levels of mature microRNAs in DICER1-mutated pleuropulmonary blastoma.
Murray MJ, Bailey S, Raby KL, Saini HK, de Kock L, Burke GA, Foulkes WD, Enright AJ, Coleman N, Tischkowitz M.
Oncogenesis Volume 3 (2014) p.e87

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau016

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

Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation.
Billis K, Billini M, Tripp HJ, Kyrpides NC, Mavromatis K.
PloS one Volume 9 (2014) p.e109738

Gramene 2013: comparative plant genomics resources.
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
Nucleic acids research Volume 42 (2014) p.D1193-9

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N, UK1OK Consortium Members, UK1OK Consortium Members.
Nature communications Volume 5 (2014) p.4871

Visualisation of BioPAX Networks using BioLayout Express (3D).
Wright DW, Angus T, Enright AJ, Freeman TC.
F1000Research Volume 3 (2014) p.246

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic acids research Volume 42 (2014) p.D926-32

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

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.
BMC Bioinformatics Volume 15 (2014) p.136

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

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

Posterior localization of ApVas1 positions the preformed germ plasm in the sexual oviparous pea aphid Acyrthosiphon pisum.
Lin GW, Cook CE, Miura T, Chang CC.
EvoDevo Volume 5 (2014) p.18

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA.
Journal of biomedical semantics Volume 5 (2014) p.34

Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats.
Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C, Jobling MA.
Human mutation Volume 35 (2014) p.609-617

IMG/M 4 version of the integrated metagenome comparative analysis system.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC.
Nucleic acids research Volume 42 (2014) p.D568-73

IMG 4 version of the integrated microbial genomes comparative analysis system.
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC.
Nucleic acids research Volume 42 (2014) p.D560-7

Transcriptional diversity during lineage commitment of human blood progenitors.
Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium B, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HHD, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A.
Science (New York, N.Y.) Volume 345 (2014) p.1251033

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.
Molecular & cellular proteomics : MCP Volume 13 (2014) p.2765-2775

A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region.
Kraaijenbrink T, van der Gaag KJ, Zuniga SB, Xue Y, Carvalho-Silva DR, Tyler-Smith C, Jobling MA, Parkin EJ, Su B, Shi H, Xiao CJ, Tang WR, Kashyap VK, Trivedi R, Sitalaximi T, Banerjee J, Karma Tshering of Gaselô, Tuladhar NM, Opgenort JR, van Driem GL, Barbujani G, de Knijff P.
PloS one Volume 9 (2014) p.e91534

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

A long-term experimental study demonstrates the costs of begging that were not found over the short term.
Soler M, Ruiz-Raya F, Carra LG, Medina-Molina E, Ibáñez-Álamo JD, Martín-Gálvez D.
PloS one Volume 9 (2014) p.e111929

Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M.
Nucleic acids research Volume 42 (2014) p.D222-30

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.
Nucleic acids research Volume 42 (2014) p.D358-63

Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes.
Colombo M, Laayouni H, Invergo BM, Bertranpetit J, Montanucci L.
Evolution; international journal of organic evolution Volume 68 (2014) p.605-613

A 3D cellular context for the macromolecular world.
Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ.
Nature structural & molecular biology Volume 21 (2014) p.841-845

A molecular fragment cheminformatics roadmap for mesoscopic simulation.
Truszkowski A, Daniel M, Kuhn H, Neumann S, Steinbeck C, Zielesny A, Epple M.
Journal of Cheminformatics Volume 6 (2014) p.45

Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.6131-6138

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 42 (2014) p.D191-8

A survey of molecular descriptors used in mass spectrometry based proteomics.
Audain E, Sanchez A, Vizcaíno JA, Perez-Riverol Y.
Current topics in medicinal chemistry Volume 14 (2014) p.388-397

Bioinformatics tools for the functional interpretation of quantitative proteomics results.
Villavicencio-Diaz TN, Rodriguez-Ulloa A, Guirola-Cruz O, Perez-Riverol Y.
Current topics in medicinal chemistry Volume 14 (2014) p.435-449

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D1001-6

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1008-1009

Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription.
García P, Paulo E, Gao J, Wahls WP, Ayté J, Lowy E, Hidalgo E.
Nucleic acids research Volume 42 (2014) p.10351-10359

A unifying model of genome evolution under parsimony.
Paten B, Zerbino DR, Hickey G, Haussler D.
BMC bioinformatics Volume 15 (2014) p.206

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.
Bio Systems Volume 124 (2014) p.26-38

The sheep genome illuminates biology of the rumen and lipid metabolism.
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP.
Science (New York, N.Y.) Volume 344 (2014) p.1168-1173

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

Turtle ghrelin.
Pascual-Anaya J, Zaddissa A, Aken B, Zhang G, Irie N.
Nature genetics Volume 46 (2014) p.526

Efficient ring perception for the Chemistry Development Kit.
May JW, Steinbeck C.
Journal of Cheminformatics Volume 6 (2014) p.3

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

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L.
Science (New York, N.Y.) Volume 345 (2014) p.1074-1079

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.
Beisken S, Earll M, Portwood D, Seymour M, Steinbeck C.
Molecular informatics Volume 33 (2014) p.307-310

A comprehensive model of the phototransduction cascade in mouse rod cells.
Invergo BM, Dell'Orco D, Montanucci L, Koch KW, Bertranpetit J.
Molecular bioSystems Volume 10 (2014) p.1481-1489

Gibbon genome and the fast karyotype evolution of small apes.
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.
Nature Volume 513 (2014) p.195-201

The genomic substrate for adaptive radiation in African cichlid fish.
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F.
Nature Volume 513 (2014) p.375-381

Current status and new features of the Consensus Coding Sequence database.
Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD.
Nucleic acids research Volume 42 (2014) p.D865-72

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.
Jayaseelan KV, Steinbeck C.
BMC bioinformatics Volume 15 (2014) p.234

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P.
PloS one Volume 9 (2014) p.e96855

Ten recommendations for software engineering in research.
Hastings J, Haug K, Steinbeck C.
GigaScience Volume 3 (2014) p.31

The Reactome pathway knowledgebase.
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
Nucleic acids research Volume 42 (2014) p.D472-7

Bioinformatics curriculum guidelines: toward a definition of core competencies.
Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV.
PLoS computational biology Volume 10 (2014) p.e1003496

Evolution of transcription factor binding in metazoans - mechanisms and functional implications.
Villar D, Flicek P, Odom DT.
Nature reviews. Genetics Volume 15 (2014) p.221-233

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

Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.
Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C.
Scientific data Volume 1 (2014) p.140029

The cavefish genome reveals candidate genes for eye loss.
McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC.
Nature communications Volume 5 (2014) p.5307

A standardized framing for reporting protein identifications in mzIdentML 1.2.
Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR.
Proteomics Volume 14 (2014) p.2389-2399

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

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.
Marguerat S, Lawler K, Brazma A, Bähler J.
RNA biology Volume 11 (2014) p.702-714

ISMB 2014 Proceedings Papers Committee.

Bioinformatics (Oxford, England) Volume 30 (2014) p.i3-i8

Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM.
Nucleic acids research Volume 42 (2014) p.D546-52

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.
Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A.
PLoS genetics Volume 10 (2014) p.e1004120

The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.
Nucleic acids research Volume 42 (2014) p.D18-25

Editorial: Genomics and proteomics behind drug design.
Perez-Riverol Y, Carvalho PC.
Current topics in medicinal chemistry Volume 14 (2014) p.343

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F.
Nucleic acids research Volume 42 (2014) p.D873-8

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G.
Nature methods Volume 11 (2014) p.817-820