Publications for 2015

2015

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.
Chiang Z, Vastermark A, Punta M, Coggill PC, Mistry J, Finn RD, Saier MH.
Briefings in bioinformatics Volume 16 (2015) p.865-872

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.
Ten Hoopen P, Pesant S, Kottmann R, Kopf A, Bicak M, Claus S, Deneudt K, Borremans C, Thijsse P, Dekeyzer S, Schaap DM, Bowler C, Glöckner FO, Cochrane G.
Standards in genomic sciences Volume 10 (2015) p.20

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.
Whelan S, Allen JE, Blackburne BP, Talavera D.
Systematic biology Volume 64 (2015) p.42-55

The European Genome-phenome Archive of human data consented for biomedical research.
Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P.
Nature genetics Volume 47 (2015) p.692-695

A gene expression resource generated by genome-wide lacZ profiling in the mouse.
Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H, Carragher DM, Karp NA, Smedley D, Adams NC, Sanger Institute Mouse Genetics Project, Bussell JN, Adams DJ, Ramírez-Solis R, Steel KP, Galli A, White JK.
Disease models & mechanisms Volume 8 (2015) p.1467-1478

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 15 (2015) p.930-949

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.
Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, METABRIC Group, Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C.
Molecular Oncology Volume 9 (2015) p.115-127

Applying the ARRIVE Guidelines to an In Vivo Database.
Karp NA, Meehan TF, Morgan H, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott RF, Iyer V, Matthews P, Melvin DG, Wells S, Flenniken AM, Masuya H, Wakana S, White JK, Lloyd KC, Reynolds CL, Paylor R, West DB, Svenson KL, Chesler EJ, de Angelis MH, Tocchini-Valentini GP, Sorg T, Herault Y, Parkinson H, Mallon AM, Brown SD.
PLoS biology Volume 13 (2015) p.e1002151

Erratum for Rahman et al., Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis.
Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE.
mBio Volume 6 (2015) p.

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage.
Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO, FANTOM consortium, Okada-Hatakeyama M, Mar JC.
PloS one Volume 10 (2015) p.e0144176

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.
Yoshihara M, Ohmiya H, Hara S, Kawasaki S, FANTOM consortium, Hayashizaki Y, Itoh M, Kawaji H, Tsujikawa M, Nishida K.
PloS one Volume 10 (2015) p.e0117581

Reply to '"Mycobacterium indicus pranii" is a strain of Mycobacterium intracellulare': "M. indicus pranii" is a distinct strain, not derived from M. intracellulare, and is an organism at an evolutionary transition point between a fast grower and slow grower.
Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE.
mBio Volume 6 (2015) p.

INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.
INFRAFRONTIER Consortium.
Nucleic Acids Research Volume 43 (2015) p.D1171-5

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.
Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, Gannon V, Allison LJ, Hanson MF, Dallman T, Ashton P, Franz E, van Hoek AH, French NP, George T, Biggs PJ, Forbes KJ.
Scientific reports Volume 5 (2015) p.14145

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

Gateways to the FANTOM5 promoter level mammalian expression atlas.
Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H, FANTOM consortium.
Genome biology Volume 16 (2015) p.22

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.
Liang C, FANTOM Consortium, Forrest AR, Wagner GP.
Nature communications Volume 6 (2015) p.6066

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM.
Nucleic acids research Volume 43 (2015) p.D1071-8

Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters.
Li P, Seneviratne CJ, Alpi E, Vizcaino JA, Jin L.
Antimicrobial agents and chemotherapy Volume 59 (2015) p.6101-6112

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN.
American journal of human genetics Volume 97 (2015) p.111-124

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.
Science (New York, N.Y.) Volume 347 (2015) p.1010-1014

Precision medicine: Look to the mice.
Lloyd KC, Meehan T, Beaudet A, Murray S, Svenson K, McKerlie C, West D, Morse I, Parkinson H, Brown S, Mallon AM, Moore M.
Science (New York, N.Y.) Volume 349 (2015) p.390

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.
Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P, Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS.
Nature genetics Volume 47 (2015) p.381-386

CATH: comprehensive structural and functional annotations for genome sequences.
Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA.
Nucleic acids research Volume 43 (2015) p.D376-81

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

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N.
CPT: pharmacometrics & systems pharmacology Volume 4 (2015) p.316-319

Introducing the PRIDE Archive RESTful web services.
Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA.
Nucleic acids research Volume 43 (2015) p.W599-604

The evolution of standards and data management practices in systems biology.
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.
Molecular systems biology Volume 11 (2015) p.851

Human genomics: The end of the start for population sequencing.
Birney E, Soranzo N.
Nature Volume 526 (2015) p.52-53

Using human genetics to make new medicines.
Barrett JC, Dunham I, Birney E.
Nature reviews. Genetics Volume 16 (2015) p.561-562

Harnessing the heart of big data.
Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR, Lindsey ML, Ping P.
Circulation research Volume 116 (2015) p.1115-1119

Open source libraries and frameworks for biological data visualisation: a guide for developers.
Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.
Proteomics Volume 15 (2015) p.1356-1374

The cardiovascular gene annotation initiative: Impact on data analysis
Lovering RC, Rodriguez-Lopez M, Campbell NH, Huntley RP, Sawford T, O’Donovan C, Orchard S, Hermjakob H, Martin M, Mayr M, Humphries SE, Talmud PJ.
Atherosclerosis Volume 241 (2015) p.e37

Identifying novel biomarkers through data mining-a realistic scenario?
Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.
Proteomics. Clinical applications Volume 9 (2015) p.437-443

Progress in Medicine: Experts Take Stock.
PLOS Medicine Editors, Beck A, Birney E, Graeber M, Tumwine J, Hay P, Ahn HS, Patel A, du Cros P, von Seidlein L, Wareham N, Low N.
PLoS medicine Volume 12 (2015) p.e1001933

Genome3D: exploiting structure to help users understand their sequences.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.
Nucleic acids research Volume 43 (2015) p.D382-6

A public repository for mass spectrometry imaging data.
Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA.
Analytical and bioanalytical chemistry Volume 407 (2015) p.2027-2033

Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae.
Redmond SN, Eiglmeier K, Mitri C, Markianos K, Guelbeogo WM, Gneme A, Isaacs AT, Coulibaly B, Brito-Fravallo E, Maslen G, Mead D, Niare O, Traore SF, Sagnon N, Kwiatkowski D, Riehle MM, Vernick KD.
BMC genomics Volume 16 (2015) p.779

Improving the Sequence Ontology terminology for genomic variant annotation.
Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K.
Journal of biomedical semantics Volume 6 (2015) p.32

SPARQL-enabled identifier conversion with Identifiers.org.
Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1875-1877

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

Glucose-6-phosphate dehydrogenase deficiency and the risk of malaria and other diseases in children in Kenya: a case-control and a cohort study.
Uyoga S, Ndila CM, Macharia AW, Nyutu G, Shah S, Peshu N, Clarke GM, Kwiatkowski DP, Rockett KA, Williams TN, MalariaGEN Consortium.
The Lancet. Haematology Volume 2 (2015) p.e437-44

Proteomics data visualisation.
Vizcaíno JA, Barsnes H, Hermjakob H.
Proteomics Volume 15 (2015) p.1339-1340

A mouse informatics platform for phenotypic and translational discovery.
Ring N, Meehan TF, Blake A, Brown J, Chen CK, Conte N, Di Fenza A, Fiegel T, Horner N, Jacobsen JO, Karp N, Lawson T, Mason JC, Matthews P, Morgan H, Relac M, Santos L, Smedley D, Sneddon D, Pengelly A, Tudose I, Warren JW, Westerberg H, Yaikhom G, Parkinson H, Mallon AM.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 26 (2015) p.413-421

Shared resources, shared costs--leveraging biocuration resources.
Orchard S, Hermjakob H.
Database : the journal of biological databases and curation Volume 2015 (2015) p.

Correction: 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 11 (2015) p.e1005177

The ocean sampling day consortium.
Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO.
GigaScience Volume 4 (2015) p.27

Acellular approaches for regenerative medicine: on the verge of clinical trials with extracellular membrane vesicles?
Fuster-Matanzo A, Gessler F, Leonardi T, Iraci N, Pluchino S.
Stem cell research & therapy Volume 6 (2015) p.227

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, Rayner NW, Robertson N, Scott RA, Prokopenko I, Scott LJ, Green T, Sparso T, Thuillier D, Yengo L, Grallert H, Wahl S, Frånberg M, Strawbridge RJ, Kestler H, Chheda H, Eisele L, Gustafsson S, Steinthorsdottir V, Thorleifsson G, Qi L, Karssen LC, van Leeuwen EM, Willems SM, Li M, Chen H, Fuchsberger C, Kwan P, Ma C, Linderman M, Lu Y, Thomsen SK, Rundle JK, Beer NL, van de Bunt M, Chalisey A, Kang HM, Voight BF, Abecasis GR, Almgren P, Baldassarre D, Balkau B, Benediktsson R, Blüher M, Boeing H, Bonnycastle LL, Bottinger EP, Burtt NP, Carey J, Charpentier G, Chines PS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Doney AS, Dorkhan M, Edkins S, Eriksson JG, Esko T, Eury E, Fadista J, Flannick J, Fontanillas P, Fox C, Franks PW, Gertow K, Gieger C, Gigante B, Gottesman O, Grant GB, Grarup N, Groves CJ, Hassinen M, Have CT, Herder C, Holmen OL, Hreidarsson AB, Humphries SE, Hunter DJ, Jackson AU, Jonsson A, Jørgensen ME, Jørgensen T, Kao WH, Kerrison ND, Kinnunen L, Klopp N, Kong A, Kovacs P, Kraft P, Kravic J, Langford C, Leander K, Liang L, Lichtner P, Lindgren CM, Lindholm E, Linneberg A, Liu CT, Lobbens S, Luan J, Lyssenko V, Männistö S, McLeod O, Meyer J, Mihailov E, Mirza G, Mühleisen TW, Müller-Nurasyid M, Navarro C, Nöthen MM, Oskolkov NN, Owen KR, Palli D, Pechlivanis S, Peltonen L, Perry JR, Platou CG, Roden M, Ruderfer D, Rybin D, van der Schouw YT, Sennblad B, Sigurðsson G, Stančáková A, Steinbach G, Storm P, Strauch K, Stringham HM, Sun Q, Thorand B, Tikkanen E, Tonjes A, Trakalo J, Tremoli E, Tuomi T, Wennauer R, Wiltshire S, Wood AR, Zeggini E, Dunham I, Birney E, Pasquali L, Ferrer J, Loos RJ, Dupuis J, Florez JC, Boerwinkle E, Pankow JS, van Duijn C, Sijbrands E, Meigs JB, Hu FB, Thorsteinsdottir U, Stefansson K, Lakka TA, Rauramaa R, Stumvoll M, Pedersen NL, Lind L, Keinanen-Kiukaanniemi SM, Korpi-Hyövälti E, Saaristo TE, Saltevo J, Kuusisto J, Laakso M, Metspalu A, Erbel R, Jöcke KH, Moebus S, Ripatti S, Salomaa V, Ingelsson E, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Koistinen H, Tuomilehto J, Hveem K, Njølstad I, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, de Faire U, Hamsten A, Illig T, Peters A, Cauchi S, Sladek R, Froguel P, Hansen T, Pedersen O, Morris AD, Palmer CN, Kathiresan S, Melander O, Nilsson PM, Groop LC, Barroso I, Langenberg C, Wareham NJ, O'Callaghan CA, Gloyn AL, Altshuler D, Boehnke M, Teslovich TM, McCarthy MI, Morris AP, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.
Nature genetics Volume 47 (2015) p.1415-1425

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

Whole-genome sequence-based analysis of thyroid function.
Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Davey Smith G, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG, UK0K Consortium.
Nature communications Volume 6 (2015) p.5681

The UK10K project identifies rare variants in health and disease.
UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CM, Timpson NJ, Durbin R, Soranzo N.
Nature Volume 526 (2015) p.82-90

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

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.
Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira PG, Asher CL, Jurkowski TP, Segonds-Pichon A, Bachman M, González-Navarrete I, Minoche AE, Krueger F, Lowy E, Marcet-Houben M, Rodriguez-Ales JL, Nascimento FS, Balasubramanian S, Gabaldon T, Tarver JE, Andrews S, Himmelbauer H, Hughes WO, Guigó R, Reik W, Sumner S.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.13970-13975

Applying extracellular vesicles based therapeutics in clinical trials - an ISEV position paper.
Lener T, Gimona M, Aigner L, Börger V, Buzas E, Camussi G, Chaput N, Chatterjee D, Court FA, Del Portillo HA, O'Driscoll L, Fais S, Falcon-Perez JM, Felderhoff-Mueser U, Fraile L, Gho YS, Görgens A, Gupta RC, Hendrix A, Hermann DM, Hill AF, Hochberg F, Horn PA, de Kleijn D, Kordelas L, Kramer BW, Krämer-Albers EM, Laner-Plamberger S, Laitinen S, Leonardi T, Lorenowicz MJ, Lim SK, Lötvall J, Maguire CA, Marcilla A, Nazarenko I, Ochiya T, Patel T, Pedersen S, Pocsfalvi G, Pluchino S, Quesenberry P, Reischl IG, Rivera FJ, Sanzenbacher R, Schallmoser K, Slaper-Cortenbach I, Strunk D, Tonn T, Vader P, van Balkom BW, Wauben M, Andaloussi SE, Théry C, Rohde E, Giebel B.
Journal of extracellular vesicles Volume 4 (2015) p.30087

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

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

Extracellular vesicles and their synthetic analogues in aging and age-associated brain diseases.
Smith JA, Leonardi T, Huang B, Iraci N, Vega B, Pluchino S.
Biogerontology Volume 16 (2015) p.147-185

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF, UK10K Consortium, Gambaro G, Richards JB, Durbin R, Timpson NJ, Marchini J, Soranzo N.
Nature communications Volume 6 (2015) p.8111

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2903-2905

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.
Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F.
Nucleic acids research Volume 43 (2015) p.D637-44

Development of data representation standards by the human proteome organization proteomics standards initiative.
Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.
Journal of the American Medical Informatics Association : JAMIA Volume 22 (2015) p.495-506

MinION Analysis and Reference Consortium: Phase 1 data release and analysis.
Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE, MinION Analysis and Reference Consortium.
F1000Research Volume 4 (2015) p.1075

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H.
Database : the journal of biological databases and curation Volume 2015 (2015) p.

Section level search functionality in Europe PMC.
Kafkas Ş, Pi X, Marinos N, Talo' F, Morrison A, McEntyre JR.
Journal of biomedical semantics Volume 6 (2015) p.7

Where Next for Genetics and Genomics?
Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M, McVean G.
PLoS Biology Volume 13 (2015) p.e1002216

BioModels: Content, Features, Functionality, and Use.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.
CPT: Pharmacometrics & Systems Pharmacology Volume 4 (2015) p.e3

Linking gene expression to phenotypes via pathway information.
Papatheodorou I, Oellrich A, Smedley D.
Journal of biomedical semantics Volume 6 (2015) p.17

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.
Journal of integrative bioinformatics Volume 12 (2015) p.271

Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP.
PloS one Volume 10 (2015) p.e0126138

Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.
Debette S, Ibrahim Verbaas CA, Bressler J, Schuur M, Smith A, Bis JC, Davies G, Wolf C, Gudnason V, Chibnik LB, Yang Q, deStefano AL, de Quervain DJ, Srikanth V, Lahti J, Grabe HJ, Smith JA, Priebe L, Yu L, Karbalai N, Hayward C, Wilson JF, Campbell H, Petrovic K, Fornage M, Chauhan G, Yeo R, Boxall R, Becker J, Stegle O, Mather KA, Chouraki V, Sun Q, Rose LM, Resnick S, Oldmeadow C, Kirin M, Wright AF, Jonsdottir MK, Au R, Becker A, Amin N, Nalls MA, Turner ST, Kardia SL, Oostra B, Windham G, Coker LH, Zhao W, Knopman DS, Heiss G, Griswold ME, Gottesman RF, Vitart V, Hastie ND, Zgaga L, Rudan I, Polasek O, Holliday EG, Schofield P, Choi SH, Tanaka T, An Y, Perry RT, Kennedy RE, Sale MM, Wang J, Wadley VG, Liewald DC, Ridker PM, Gow AJ, Pattie A, Starr JM, Porteous D, Liu X, Thomson R, Armstrong NJ, Eiriksdottir G, Assareh AA, Kochan NA, Widen E, Palotie A, Hsieh YC, Eriksson JG, Vogler C, van Swieten JC, Shulman JM, Beiser A, Rotter J, Schmidt CO, Hoffmann W, Nöthen MM, Ferrucci L, Attia J, Uitterlinden AG, Amouyel P, Dartigues JF, Amieva H, Räikkönen K, Garcia M, Wolf PA, Hofman A, Longstreth WT, Psaty BM, Boerwinkle E, DeJager PL, Sachdev PS, Schmidt R, Breteler MM, Teumer A, Lopez OL, Cichon S, Chasman DI, Grodstein F, Müller-Myhsok B, Tzourio C, Papassotiropoulos A, Bennett DA, Ikram MA, Deary IJ, van Duijn CM, Launer L, Fitzpatrick AL, Seshadri S, Mosley TH, Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium.
Biological psychiatry Volume 77 (2015) p.749-763

Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
Brage S, Westgate K, Franks PW, Stegle O, Wright A, Ekelund U, Wareham NJ.
PLoS ONE Volume 10 (2015) p.e0137206

Predicting malignancy from mammography findings and image-guided core biopsies.
Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.
International journal of data mining and bioinformatics Volume 11 (2015) p.257-276

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

Identification of artesunate as a specific activator of ferroptosis in pancreatic cancer cells.
Eling N, Reuter L, Hazin J, Hamacher-Brady A, Brady NR.
Oncoscience Volume 2 (2015) p.517-532

Emerging Drug Target In Pancreatic Cancer: Placing Sirtuin 1 on the Canvas.
Giry-Laterriere M, Pinho AV, Eling N, Chantrill L, Rooman I.
Current cancer drug targets Volume 15 (2015) p.463-468

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

Efficient set tests for the genetic analysis of correlated traits.
Casale FP, Rakitsch B, Lippert C, Stegle O.
Nature methods Volume 12 (2015) p.755-758

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage.
Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D.
PLoS genetics Volume 11 (2015) p.e1004920

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.44-55

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.
Reimand J, Wagih O, Bader GD.
PLoS genetics Volume 11 (2015) p.e1004919

Genetic Interaction Scoring Procedure for Bacterial Species.
Wagih O, Parts L.
Advances in experimental medicine and biology Volume 883 (2015) p.169-185

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.342-346

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

A random forest approach to capture genetic effects in the presence of population structure.
Stephan J, Stegle O, Beyer A.
Nature communications Volume 6 (2015) p.7432

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M.
eLife Volume 4 (2015) p.e05255

Searching and Navigating UniProt Databases.
Pundir S, Magrane M, Martin MJ, O'Donovan C, UniProt Consortium.
Current protocols in bioinformatics Volume 50 (2015) p.1.27.1-10

A quick guide for building a successful bioinformatics community.
Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N.
PLoS computational biology Volume 11 (2015) p.e1003972

The ELIXIR channel in F1000Research.
Blomberg N, Oliveira A, Mons B, Persson B, Jonassen I.
F1000Research Volume 4 (2015) p.

Cancer evolution: mathematical models and computational inference.
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.
Systematic biology Volume 64 (2015) p.e1-25

Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ.
Science (New York, N.Y.) Volume 348 (2015) p.880-886

Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes.
Gerstung M, Pellagatti A, Malcovati L, Giagounidis A, Porta MG, Jädersten M, Dolatshad H, Verma A, Cross NC, Vyas P, Killick S, Hellström-Lindberg E, Cazzola M, Papaemmanuil E, Campbell PJ, Boultwood J.
Nature Communications Volume 6 (2015) p.5901

UniProt: a hub for protein information.
UniProt Consortium.
Nucleic acids research Volume 43 (2015) p.D204-12

Computational approaches for inferring the functions of intrinsically disordered proteins.
Varadi M, Vranken W, Guharoy M, Tompa P.
Frontiers in Molecular Biosciences Volume 2 (2015) p.45

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.
Varadi M, Zsolyomi F, Guharoy M, Tompa P.
PloS one Volume 10 (2015) p.e0139731

DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder.
Varadi M, Guharoy M, Zsolyomi F, Tompa P.
BMC bioinformatics Volume 16 (2015) p.153

The Protein Ensemble Database.
Varadi M, Tompa P.
Advances in experimental medicine and biology Volume 870 (2015) p.335-349

Subclonal diversification of primary breast cancer revealed by multiregion sequencing.
Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, Aas T, Alexandrov LB, Larsimont D, Davies H, Li Y, Ju YS, Ramakrishna M, Haugland HK, Lilleng PK, Nik-Zainal S, McLaren S, Butler A, Martin S, Glodzik D, Menzies A, Raine K, Hinton J, Jones D, Mudie LJ, Jiang B, Vincent D, Greene-Colozzi A, Adnet PY, Fatima A, Maetens M, Ignatiadis M, Stratton MR, Sotiriou C, Richardson AL, Lønning PE, Wedge DC, Campbell PJ.
Nature medicine Volume 21 (2015) p.751-759

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers.
Shlien A, Campbell BB, de Borja R, Alexandrov LB, Merico D, Wedge D, Van Loo P, Tarpey PS, Coupland P, Behjati S, Pollett A, Lipman T, Heidari A, Deshmukh S, Avitzur N, Meier B, Gerstung M, Hong Y, Merino DM, Ramakrishna M, Remke M, Arnold R, Panigrahi GB, Thakkar NP, Hodel KP, Henninger EE, Göksenin AY, Bakry D, Charames GS, Druker H, Lerner-Ellis J, Mistry M, Dvir R, Grant R, Elhasid R, Farah R, Taylor GP, Nathan PC, Alexander S, Ben-Shachar S, Ling SC, Gallinger S, Constantini S, Dirks P, Huang A, Scherer SW, Grundy RG, Durno C, Aronson M, Gartner A, Meyn MS, Taylor MD, Pursell ZF, Pearson CE, Malkin D, Futreal PA, Stratton MR, Bouffet E, Hawkins C, Campbell PJ, Tabori U, Biallelic Mismatch Repair Deficiency Consortium.
Nature genetics Volume 47 (2015) p.257-262

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.
Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E99-100

A new system for profiling drug-induced calcium signal perturbation in human embryonic stem cell-derived cardiomyocytes.
Lewis KJ, Silvester NC, Barberini-Jammaers S, Mason SA, Marsh SA, Lipka M, George CH.
Journal of biomolecular screening Volume 20 (2015) p.330-340

Known Allergen Structures Predict Schistosoma mansoni IgE-Binding Antigens in Human Infection.
Farnell EJ, Tyagi N, Ryan S, Chalmers IW, Pinot de Moira A, Jones FM, Wawrzyniak J, Fitzsimmons CM, Tukahebwa EM, Furnham N, Maizels RM, Dunne DW.
Frontiers in immunology Volume 6 (2015) p.26

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.
Lowe R, Slodkowicz G, Goldman N, Rakyan VK.
Epigenetics Volume 10 (2015) p.274-281

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.
Database : the journal of biological databases and curation Volume 2015 (2015) p.bav043

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.
Ju YS, Tubio JM, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group, ICGC Breast Cancer Working Group, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MT, van't Veer LJ, Tan BK, Aparicio S, Span PN, Martens JW, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova SG, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR.
Genome research Volume 25 (2015) p.814-824

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

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Wagih O, Reimand J, Bader GD.
Nature methods Volume 12 (2015) p.531-533

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P.
PLoS computational biology Volume 11 (2015) p.e1004362

Expression change in Angiopoietin-1 underlies change in relative brain size in fish.
Chen YC, Harrison PW, Kotrschal A, Kolm N, Mank JE, Panula P.
Proceedings. Biological sciences Volume 282 (2015) p.

Data integration in biological research: an overview.
Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV.
Journal of biological research (Thessalonike, Greece) Volume 22 (2015) p.9

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.
Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB.
Frontiers in genetics Volume 6 (2015) p.197

Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution.
Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE.
Molecular ecology Volume 24 (2015) p.1218-1235

Sexual selection drives evolution and rapid turnover of male gene expression.
Harrison PW, Wright AE, Zimmer F, Dean R, Montgomery SH, Pointer MA, Mank JE.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.4393-4398

Differential genetic interactions of yeast stress response MAPK pathways.
Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ.
Molecular Systems Biology Volume 11 (2015) p.800

Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation.
Wright AE, Zimmer F, Harrison PW, Mank JE.
Genetics Volume 201 (2015) p.587-598

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.
Dean R, Harrison PW, Wright AE, Zimmer F, Mank JE.
Molecular biology and evolution Volume 32 (2015) p.2646-2656

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.
Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK.
Bioinformatics (Oxford, England) Volume 31 (2015) p.140-142

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.
Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS.
Metabolomics : Official journal of the Metabolomic Society Volume 11 (2015) p.872-894

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.
Hostaš J, Jakubec D, Laskowski RA, Gnanasekaran R, Řezáč J, Vondrášek J, Hobza P.
Journal of chemical theory and computation Volume 11 (2015) p.4086-4092

Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.
Jakubec D, Hostas J, Laskowski RA, Hobza P, Vondrásek J.
Journal of chemical theory and computation Volume 11 (2015) p.1939-1948

BetaCavityWeb: a webserver for molecular voids and channels.
Kim JK, Cho Y, Lee M, Laskowski RA, Ryu SE, Sugihara K, Kim DS.
Nucleic acids research Volume 43 (2015) p.W413-8

ISMB/ECCB 2015 Proceedings Papers Committee.

Bioinformatics (Oxford, England) Volume 31 (2015) p.i3-i8

ISMB/ECCB 2015.
Moreau Y, Beerenwinkel N.
Bioinformatics (Oxford, England) Volume 31 (2015) p.i1-2

Behavioural and molecular endophenotypes in psychotic disorders reveal heritable abnormalities in glutamatergic neurotransmission.
Scoriels L, Salek RM, Goodby E, Grainger D, Dean AM, West JA, Griffin JL, Suckling J, Nathan PJ, Lennox BR, Murray GK, Bullmore ET, Jones PB.
Translational psychiatry Volume 5 (2015) p.e540

Getting the right answers: understanding metabolomics challenges.
Beisken S, Eiden M, Salek RM.
Expert review of molecular diagnostics Volume 15 (2015) p.97-109

A contribution to the rational design of Ru(CO)3Cl2L complexes for in vivo delivery of CO.
Seixas JD, Santos MF, Mukhopadhyay A, Coelho AC, Reis PM, Veiros LF, Marques AR, Penacho N, Gonçalves AM, Romão MJ, Bernardes GJ, Santos-Silva T, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 44 (2015) p.5058-5075

Towards the computational design of protein post-translational regulation.
Strumillo M, Beltrao P.
Bioorganic & medicinal chemistry Volume 23 (2015) p.2877-2882

App for the calculation of blood lactate markers.
Newell J, Korir P, Moore B, Pedlar C.
Journal of sports sciences Volume 33 (2015) p.568-569

Enhancer evolution across 20 mammalian species.
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT.
Cell Volume 160 (2015) p.554-566

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.
Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B.
Genome research Volume 25 (2015) p.41-56

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M.
Genome research Volume 25 (2015) p.504-513

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.
Raposo AA, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DL, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS.
Cell reports Volume (2015) p.

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.
Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HHD, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RAF, Martens JHA, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B.
Nature genetics Volume 47 (2015) p.1316-1325

Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism.
Patel S, Roncaglia P, Lovering RC.
BMC bioinformatics Volume 16 (2015) p.186

Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.
Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S.
BMC genomics Volume 16 (2015) p.876

Operon and non-operon gene clusters in the C. elegans genome.
Blumenthal T, Davis P, Garrido-Lecca A.
WormBook : the online review of C. elegans biology Volume (2015) p.1-20

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C.
BMC Bioinformatics Volume 16 (2015) p.56

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

Structural and functional basis for p38-MK2-activated Rsk signaling in toll-like receptor-stimulated dendritic cells.
Zaru R, Edgar AJ, Hanauer A, Watts C.
Molecular and cellular biology Volume 35 (2015) p.132-140

Towards recommendations for metadata and data handling in plant phenotyping.
Krajewski P, Chen D, Ćwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.
Journal of experimental botany Volume 66 (2015) p.5417-5427

Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK, Geeleher P, Seoighe C.
BMC bioinformatics Volume 16 (2015) p.286

The PDK1-Rsk Signaling Pathway Controls Langerhans Cell Proliferation and Patterning.
Zaru R, Matthews SP, Edgar AJ, Prescott AR, Gomez-Nicola D, Hanauer A, Watts C.
Journal of immunology (Baltimore, Md. : 1950) Volume 195 (2015) p.4264-4272

Nomenclature of Toso, Fas apoptosis inhibitory molecule 3, and IgM FcR.
Kubagawa H, Carroll MC, Jacob CO, Lang KS, Lee KH, Mak T, McAndrews M, Morse HC, Nolan GP, Ohno H, Richter GH, Seal R, Wang JY, Wiestner A, Coligan JE.
Journal of immunology (Baltimore, Md. : 1950) Volume 194 (2015) p.4055-4057

Epigenome data release: a participant-centered approach to privacy protection.
Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T.
Genome biology Volume 16 (2015) p.142

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL.
BMC genomics Volume 16 (2015) p.982

Transcriptional profiling of chronic clinical hepatic schistosomiasis japonica indicates reduced metabolism and immune responses.
Gobert GN, Burke ML, McManus DP, Ellis MK, Chuah C, Ramm GA, Wang Y, Li Y.
Parasitology Volume 142 (2015) p.1453-1468

Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.
Meex RC, Hoy AJ, Morris A, Brown RD, Lo JC, Burke M, Goode RJ, Kingwell BA, Kraakman MJ, Febbraio MA, Greve JW, Rensen SS, Molloy MP, Lancaster GI, Bruce CR, Watt MJ.
Cell metabolism Volume 22 (2015) p.1078-1089

HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.
Nucleic acids research Volume 43 (2015) p.W30-8

Prediction of human population responses to toxic compounds by a collaborative competition.
Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J.
Nature biotechnology Volume 33 (2015) p.933-940

Cooperative development of logical modelling standards and tools with CoLoMoTo.
Naldi A, Monteiro PT, Müssel C, Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1154-1159

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

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS.
Journal of proteome research Volume 14 (2015) p.3415-3431

Testing the mean matrix in high-dimensional transposable data.
Touloumis A, Tavaré S, Marioni JC.
Biometrics Volume 71 (2015) p.157-166

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.
Nature communications Volume 6 (2015) p.8687

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW.
Scientific reports Volume 5 (2015) p.11487

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.
Kotelnikova E, Bernardo-Faura M, Silberberg G, Kiani NA, Messinis D, Melas IN, Artigas L, Schwartz E, Mazo I, Masso M, Alexopoulos LG, Mas JM, Olsson T, Tegner J, Martin R, Zamora A, Paul F, Saez-Rodriguez J, Villoslada P.
Multiple sclerosis (Houndmills, Basingstoke, England) Volume 21 (2015) p.138-146

Prospective derivation of a living organoid biobank of colorectal cancer patients.
van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.
Cell Volume 161 (2015) p.933-945

Integrative approaches for signalling and metabolic networks.
Hatzimanikatis V, Saez-Rodriguez J.
Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.844-845

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.
Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP.
Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.904-920

Modeling Signaling Networks to Advance New Cancer Therapies.
Saez-Rodriguez J, MacNamara A, Cook S.
Annual review of biomedical engineering Volume 17 (2015) p.143-163

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J.
Nature communications Volume 6 (2015) p.8033

Designing Experiments to Discriminate Families of Logic Models.
Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C.
Frontiers in bioengineering and biotechnology Volume 3 (2015) p.131

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.
BMC systems biology Volume 9 (2015) p.8

DREAMTools: a Python package for scoring collaborative challenges.
Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J.
F1000Research Volume 4 (2015) p.1030

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM.
PLoS ONE Volume 10 (2015) p.e0139446

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.
Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW.
Scientific Reports Volume 5 (2015) p.18178

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA.
Cell stem cell Volume 17 (2015) p.471-485

The Classification and Evolution of Enzyme Function.
Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM.
Biophysical Journal Volume 109 (2015) p.1082-1086

Longevity GWAS Using the Drosophila Genetic Reference Panel.
Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM.
The journals of gerontology. Series A, Biological sciences and medical sciences Volume 70 (2015) p.1470-1478

PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.
Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA.
PLoS ONE Volume 10 (2015) p.e0131274

SurvCurv database and online survival analysis platform update.
Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3878-3880

The history of the CATH structural classification of protein domains.
Sillitoe I, Dawson N, Thornton J, Orengo C.
Biochimie Volume 119 (2015) p.209-217

What you need to know to make the most of big data in biology.
Thornton J.
Lancet (London, England) Volume 385 Suppl 1 (2015) p.S5-6

Proteins: interaction at a distance.
Laskowski RA, Thornton JM.
IUCrJ Volume 2 (2015) p.609-610

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.
Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N.
PLoS Computational Biology Volume 11 (2015) p.e1004546

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.
Kafkas Ş, Kim JH, Pi X, McEntyre JR.
Journal of biomedical semantics Volume 6 (2015) p.1

Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F.
Methods (San Diego, Calif.) Volume 85 (2015) p.54-61

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

Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC.
Nature reviews. Genetics Volume 16 (2015) p.133-145

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR.
Genome biology Volume 16 (2015) p.201

The technology and biology of single-cell RNA sequencing.
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA.
Molecular cell Volume 58 (2015) p.610-620

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC.
Nature biotechnology Volume 33 (2015) p.503-509

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O.
Nature biotechnology Volume 33 (2015) p.155-160

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S.
PLoS computational biology Volume 11 (2015) p.e1004333

Empirical inference of circuitry and plasticity in a kinase signaling network.
Wilkes EH, Terfve C, Gribben JG, Saez-Rodriguez J, Cutillas PR.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.7719-7724

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziołowski C, Klamt S.
BMC Bioinformatics Volume 16 (2015) p.345

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.
Bacci G, Ceccherini MT, Bani A, Bazzicalupo M, Castaldini M, Galardini M, Giovannetti L, Mocali S, Pastorelli R, Pantani OL, Arfaioli P, Pietramellara G, Viti C, Nannipieri P, Mengoni A.
Antonie van Leeuwenhoek Volume 107 (2015) p.785-797

The Ensembl REST API: Ensembl Data for Any Language.
Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GR, Ruffier M, Taylor K, Vullo A, Flicek P.
Bioinformatics (Oxford, England) Volume 31 (2015) p.143-145

Molecular disease presentation in diabetic nephropathy.
Heinzel A, Mühlberger I, Stelzer G, Lancet D, Oberbauer R, Martin M, Perco P.
Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association Volume 30 Suppl 4 (2015) p.iv17-25

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A.
PLoS computational biology Volume 11 (2015) p.e1004478

From pangenome to panphenome and back.
Galardini M, Mengoni A, Mocali S.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.257-270

Preface. Bacterial pangenomics.
Mengoni A, Fondi M, Galardini M.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.v-vi

MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2443-2451

Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.
Golanowska M, Galardini M, Bazzicalupo M, Hugouvieux-Cotte-Pattat N, Mengoni A, Potrykus M, Slawiak M, Lojkowska E.
Genome announcements Volume 3 (2015) p.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.
Laird MR, Langille MG, Brinkman FS.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3348-3349

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.
Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS.
Nucleic acids research Volume 43 (2015) p.W104-8

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C.
Systematic biology Volume 64 (2015) p.778-791

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T, Quest for Orthologs Species Tree Working Group.
Genome Biology and Evolution Volume 7 (2015) p.1988-1999

flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1337-1339

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

The 3D organization of chromatin explains evolutionary fragile genomic regions.
Berthelot C, Muffato M, Abecassis J, Roest Crollius H.
Cell reports Volume 10 (2015) p.1913-1924

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.
Structure (London, England : 1993) Volume 23 (2015) p.1156-1167

NMR Exchange Format: a unified and open standard for representation of NMR restraint data.
Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW.
Nature structural & molecular biology Volume 22 (2015) p.433-434

High-throughput phenomics.
Viti C, Decorosi F, Marchi E, Galardini M, Giovannetti L.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.99-123

Mapping contigs using CONTIGuator.
Galardini M, Mengoni A, Bazzicalupo M.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.163-176

Gene Ontology Consortium: going forward.
Gene Ontology Consortium.
Nucleic acids research Volume 43 (2015) p.D1049-56

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.
Journal of integrative bioinformatics Volume 12 (2015) p.270

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ.
Journal of integrative bioinformatics Volume 12 (2015) p.266

The Importance of Biological Databases in Biological Discovery.
Baxevanis AD, Bateman A.
Current protocols in bioinformatics Volume 50 (2015) p.1.1.1-8

Domain atrophy creates rare cases of functional partial protein domains.
Prakash A, Bateman A.
Genome biology Volume 16 (2015) p.88

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Henriques D, Rocha M, Saez-Rodriguez J, Banga JR.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2999-3007

A single-cell model of PIP3 dynamics using chemical dimerization.
MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J.
Bioorganic & medicinal chemistry Volume 23 (2015) p.2868-2876

Pharmacogenomic agreement between two cancer cell line data sets.
Cancer Cell Line Encyclopedia Consortium, Genomics of Drug Sensitivity in Cancer Consortium.
Nature Volume 528 (2015) p.84-87

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F, NextGen Consortium.
Frontiers in genetics Volume 6 (2015) p.107

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H, FAANG Consortium.
Genome biology Volume 16 (2015) p.57

Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC.
Journal of Cheminformatics Volume 7 (2015) p.31

Ensembl 2015.
Cunningham F, 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 SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P.
Nucleic acids research Volume 43 (2015) p.D662-9

Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS.
Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A.
Journal of genomics Volume 3 (2015) p.36-39

Key challenges for the creation and maintenance of specialist protein resources.
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.
Proteins Volume 83 (2015) p.1005-1013

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

An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.
Nature Volume 526 (2015) p.75-81

RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium.
Nucleic Acids Research Volume 43 (2015) p.D123-9

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 370 (2015) p.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.
Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium, Huminiecki L.
PLoS biology Volume 13 (2015) p.e1002315

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

RSAT 2015: Regulatory Sequence Analysis Tools.
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.
Nucleic acids research Volume 43 (2015) p.W50-6

The BioMart community portal: an innovative alternative to large, centralized data repositories.
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.
Nucleic Acids Research Volume 43 (2015) p.W589-98

ADME SARfari: comparative genomics of drug metabolizing systems.
Davies M, Dedman N, Hersey A, Papadatos G, Hall MD, Cucurull-Sanchez L, Jeffrey P, Hasan S, Eddershaw PJ, Overington JP.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1695-1697

Extending reference assembly models.
Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P.
Genome biology Volume 16 (2015) p.13

Avianbase: a community resource for bird genomics.
Eöry L, Gilbert MT, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, Burt DW.
Genome biology Volume 16 (2015) p.21

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.
Database : the journal of biological databases and curation Volume 2015 (2015) p.bav063

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.
Science (New York, N.Y.) Volume 348 (2015) p.666-669

SpeckTackle: JavaScript charts for spectroscopy.
Beisken S, Conesa P, Haug K, Salek RM, Steinbeck C.
Journal of cheminformatics Volume 7 (2015) p.17

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.
Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G.
Nature genetics Volume 47 (2015) p.717-726

TNNI3K in cardiovascular disease and prospects for therapy.
Milano A, Lodder EM, Bezzina CR.
Journal of molecular and cellular cardiology Volume 82 (2015) p.167-173

The genome of the vervet (Chlorocebus aethiops sabaeus).
Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GW, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB.
Genome research Volume 25 (2015) p.1921-1933

The ensembl regulatory build.
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR.
Genome biology Volume 16 (2015) p.56

Chemical databases: curation or integration by user-defined equivalence?
Hersey A, Chambers J, Bellis L, Patrícia Bento A, Gaulton A, Overington JP.
Drug discovery today. Technologies Volume 14 (2015) p.17-24

Principles and application of LIMS in mouse clinics.
Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 26 (2015) p.467-481

Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B.
Journal of computational biology : a journal of computational molecular cell biology Volume 22 (2015) p.387-401

The complex portal--an encyclopaedia of macromolecular complexes.
Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.
Nucleic acids research Volume 43 (2015) p.D479-84

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC, WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY.
Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.
Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK.
Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.5437-5442

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.
PloS one Volume 10 (2015) p.e0137367

Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P.
Plant & cell physiology Volume 56 (2015) p.e3

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME.
Nature methods Volume 12 (2015) p.339-342

Expression data analysis with Reactome.
Jupe S, Fabregat A, Hermjakob H.
Current protocols in bioinformatics Volume 49 (2015) p.8.20.1-9

Identifying novel sequence variants of RNA 3D motifs.
Zirbel CL, Roll J, Sweeney BA, Petrov AI, Pirrung M, Leontis NB.
Nucleic acids research Volume 43 (2015) p.7504-7520

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N.
Nucleic acids research Volume 43 (2015) p.W15-23

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.
Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.
Journal of proteome research Volume 14 (2015) p.2988-2997

A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.
Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H.
Proteomics Volume 15 (2015) p.1390-1404

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

Collaborative computational project for electron cryo-microscopy.
Wood C, Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M.
Acta crystallographica. Section D, Biological crystallography Volume 71 (2015) p.123-126

Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M.
Data in brief Volume 4 (2015) p.468-473

The BioStudies database.
McEntyre J, Sarkans U, Brazma A.
Molecular systems biology Volume 11 (2015) p.847

Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M.
Journal of proteomics Volume 126 (2015) p.163-171

Chimira: analysis of small RNA sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3365-3367

High-density P300 enhancers control cell state transitions.
Witte S, Bradley A, Enright AJ, Muljo SA.
BMC genomics Volume 16 (2015) p.903

Cellular phenotype database: a repository for systems microscopy data.
Kirsanova C, Brazma A, Rustici G, Sarkans U.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2736-2740

Palmitoylation and palmitoyl-transferases in Plasmodium parasites.
Hodson N, Invergo B, Rayner JC, Choudhary JS.
Biochemical Society transactions Volume 43 (2015) p.240-245

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

Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins.
Invergo BM, Montanucci L, Bertranpetit J.
Proceedings of the Royal Society B: Biological Sciences Volume 282 (2015) p.20152215

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

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O.
Skeletal muscle Volume 5 (2015) p.35

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.
GigaScience Volume 4 (2015) p.38

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.
BMC genomics Volume 16 Suppl 8 (2015) p.S2

ChEMBL web services: streamlining access to drug discovery data and utilities.
Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP.
Nucleic acids research Volume 43 (2015) p.W612-20

A large-scale crop protection bioassay data set.
Gaulton A, Kale N, van Westen GJ, Bellis LJ, Bento AP, Davies M, Hersey A, Papadatos G, Forster M, Wege P, Overington JP.
Scientific data Volume 2 (2015) p.150032

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.
Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI.
Nature genetics Volume 47 (2015) p.746-756

Computational proteomics: Integrating mass spectral data into a biological context.
Carvalho PC, Padron G, Calvete JJ, Perez-Riverol Y.
Journal of proteomics Volume 129 (2015) p.1-2

Kinase-two-hybrid: towards the conditional interactome.
Ochoa D, Beltrao P.
Molecular systems biology Volume 11 (2015) p.798

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.
de Angelis MH, Nicholson G, Selloum M, White J, Morgan H, Ramirez-Solis R, Sorg T, Wells S, Fuchs H, Fray M, Adams DJ, Adams NC, Adler T, Aguilar-Pimentel A, Ali-Hadji D, Amann G, André P, Atkins S, Auburtin A, Ayadi A, Becker J, Becker L, Bedu E, Bekeredjian R, Birling MC, Blake A, Bottomley J, Bowl M, Brault V, Busch DH, Bussell JN, Calzada-Wack J, Cater H, Champy MF, Charles P, Chevalier C, Chiani F, Codner GF, Combe R, Cox R, Dalloneau E, Dierich A, Di Fenza A, Doe B, Duchon A, Eickelberg O, Esapa CT, El Fertak L, Feigel T, Emelyanova I, Estabel J, Favor J, Flenniken A, Gambadoro A, Garrett L, Gates H, Gerdin AK, Gkoutos G, Greenaway S, Glasl L, Goetz P, Da Cruz IG, Götz A, Graw J, Guimond A, Hans W, Hicks G, Hölter SM, Höfler H, Hancock JM, Hoehndorf R, Hough T, Houghton R, Hurt A, Ivandic B, Jacobs H, Jacquot S, Jones N, Karp NA, Katus HA, Kitchen S, Klein-Rodewald T, Klingenspor M, Klopstock T, Lalanne V, Leblanc S, Lengger C, le Marchand E, Ludwig T, Lux A, McKerlie C, Maier H, Mandel JL, Marschall S, Mark M, Melvin DG, Meziane H, Micklich K, Mittelhauser C, Monassier L, Moulaert D, Muller S, Naton B, Neff F, Nolan PM, Nutter LM, Ollert M, Pavlovic G, Pellegata NS, Peter E, Petit-Demoulière B, Pickard A, Podrini C, Potter P, Pouilly L, Puk O, Richardson D, Rousseau S, Quintanilla-Fend L, Quwailid MM, Racz I, Rathkolb B, Riet F, Rossant J, Roux M, Rozman J, Ryder E, Salisbury J, Santos L, Schäble KH, Schiller E, Schrewe A, Schulz H, Steinkamp R, Simon M, Stewart M, Stöger C, Stöger T, Sun M, Sunter D, Teboul L, Tilly I, Tocchini-Valentini GP, Tost M, Treise I, Vasseur L, Velot E, Vogt-Weisenhorn D, Wagner C, Walling A, Weber B, Wendling O, Westerberg H, Willershäuser M, Wolf E, Wolter A, Wood J, Wurst W, Yildirim AÖ, Zeh R, Zimmer A, Zimprich A, EUMODIC Consortium, Holmes C, Steel KP, Herault Y, Gailus-Durner V, Mallon AM, Brown SD.
Nature genetics Volume 47 (2015) p.969-978

Update of the human and mouse Fanconi anemia genes.
Dong H, Nebert DW, Bruford EA, Thompson DC, Joenje H, Vasiliou V.
Human genomics Volume 9 (2015) p.32

Updates in Rhea--a manually curated resource of biochemical reactions.
Morgat A, Axelsen KB, Lombardot T, Alcántara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A.
Nucleic Acids Research Volume 43 (2015) p.D459-64

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.
Squizzato S, Park YM, Buso N, Gur T, Cowley A, Li W, Uludag M, Pundir S, Cham JA, McWilliam H, Lopez R.
Nucleic acids research Volume 43 (2015) p.W585-8

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E.
Journal of biomedical semantics Volume 6 (2015) p.10

Fine mapping of bone structure and strength QTLs in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, 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.
Bone Volume 81 (2015) p.417-426

Eyeing the Cyr61/CTGF/NOV (CCN) group of genes in development and diseases: highlights of their structural likenesses and functional dissimilarities.
Krupska I, Bruford EA, Chaqour B.
Human genomics Volume 9 (2015) p.24

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.
Metabolomics : Official journal of the Metabolomic Society Volume 11 (2015) p.1587-1597

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.
Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Russiñol N, Queirós AC, Beekman R, Rodríguez-Madoz JR, San José-Enériz E, Fang F, Gutiérrez NC, García-Verdugo JM, Robson MI, Schirmer EC, Guruceaga E, Martens JH, Gut M, Calasanz MJ, Flicek P, Siebert R, Campo E, Miguel JF, Melnick A, Stunnenberg HG, Gut IG, Prosper F, Martín-Subero JI.
Genome research Volume 25 (2015) p.478-487

Finding our way through phenotypes.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.
PLoS Biology Volume 13 (2015) p.e1002033

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.
Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J.
BMC microbiology Volume 15 (2015) p.146

Detection of significant protein coevolution.
Ochoa D, Juan D, Valencia A, Pazos F.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2166-2173

Europe: Lifelong learning for all in biomedicine.
Brooksbank C, Johnson C.
Nature Volume 524 (2015) p.415

Devising a Consensus Framework for Validation of Novel Human Coding Loci.
Bruford EA, Lane L, Harrow J.
Journal of proteome research Volume 14 (2015) p.4945-4948

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.
Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW, GOBLET Consortium.
PLoS computational biology Volume 11 (2015) p.e1004143

The EMBL-EBI bioinformatics web and programmatic tools framework.
Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R.
Nucleic Acids Research Volume 43 (2015) p.W580-4

Activity, assay and target data curation and quality in the ChEMBL database.
Papadatos G, Gaulton A, Hersey A, Overington JP.
Journal of Computer-Aided Molecular Design Volume 29 (2015) p.885-896

Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.
Senger S, Bartek L, Papadatos G, Gaulton A.
Journal of cheminformatics Volume 7 (2015) p.49

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

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.
Kruger FA, Gaulton A, Nowotka M, Overington JP.
Bioinformatics (Oxford, England) Volume 31 (2015) p.776-778

A global reference for human genetic variation.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.
Nature Volume 526 (2015) p.68-74

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia.
De Fanti S, Barbieri C, Sarno S, Sevini F, Vianello D, Tamm E, Metspalu E, van Oven M, Hübner A, Sazzini M, Franceschi C, Pettener D, Luiselli D.
PloS one Volume 10 (2015) p.e0144391

Third Report on Chicken Genes and Chromosomes 2015.
Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.
Cytogenetic and genome research Volume 145 (2015) p.78-179

Inflammaging and cancer: a challenge for the Mediterranean diet.
Ostan R, Lanzarini C, Pini E, Scurti M, Vianello D, Bertarelli C, Fabbri C, Izzi M, Palmas G, Biondi F, Martucci M, Bellavista E, Salvioli S, Capri M, Franceschi C, Santoro A.
Nutrients Volume 7 (2015) p.2589-2621

Dynamics of Lgr6⁺ Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis.
Füllgrabe A, Joost S, Are A, Jacob T, Sivan U, Haegebarth A, Linnarsson S, Simons BD, Clevers H, Toftgård R, Kasper M.
Stem cell reports Volume 5 (2015) p.843-855

Roary: rapid large-scale prokaryote pan genome analysis.
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3691-3693