Publications

Publications

2018

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.
Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD.
Nucleic acids research Volume 46 (2018) p.D221-D228
DOI: 10.1093/nar/gkx1031

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM.
Nucleic acids research Volume 46 (2018) p.D618-D623
DOI: 10.1093/nar/gkx1012

To what extent do structural changes in catalytic metal sites affect enzyme function?
Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C.
Journal of inorganic biochemistry Volume 179 (2018) p.40-53
DOI: 10.1016/j.jinorgbio.2017.11.002

Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D.
Nucleic acids research Volume 46 (2018) p.D1181-D1189
DOI: 10.1093/nar/gkx1111

Europe PMC in 2017.
Levchenko M, Gou Y, Graef F, Hamelers A, Huang Z, Ide-Smith M, Iyer A, Kilian O, Katuri J, Kim JH, Marinos N, Nambiar R, Parkin M, Pi X, Rogers F, Talo F, Vartak V, Venkatesan A, McEntyre J.
Nucleic acids research Volume 46 (2018) p.D1254-D1260
DOI: 10.1093/nar/gkx1005

Designing an intuitive web application for drug discovery scientists.
Karamanis N, Pignatelli M, Carvalho-Silva D, Rowland F, Cham JA, Dunham I.
Drug discovery today Volume (2018) p.
DOI: 10.1016/j.drudis.2018.01.032

The eukaryotic linear motif resource - 2018 update.
Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ.
Nucleic acids research Volume 46 (2018) p.D428-D434
DOI: 10.1093/nar/gkx1077

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD.
Nucleic acids research Volume 46 (2018) p.D624-D632
DOI: 10.1093/nar/gkx1134

Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient.
Brener J, Gall A, Hurst J, Batorsky R, Lavandier N, Chen F, Edwards A, Bolton C, Dsouza R, Allen T, Pybus OG, Kellam P, Matthews PC, Goulder PJR.
Retrovirology Volume 15 (2018) p.7
DOI: 10.1186/s12977-018-0390-9

ProForma: A Standard Proteoform Notation.
LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO.
Journal of proteome research Volume (2018) p.
DOI: 10.1021/acs.jproteome.7b00851

The Reactome Pathway Knowledgebase.
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.
Nucleic acids research Volume 46 (2018) p.D649-D655
DOI: 10.1093/nar/gkx1132

Subject-specific multi-poroelastic model for exploring the risk factors associated with the early stages of Alzheimer's disease.
Guo L, Vardakis JC, Lassila T, Mitolo M, Ravikumar N, Chou D, Lange M, Sarrami-Foroushani A, Tully BJ, Taylor ZA, Varma S, Venneri A, Frangi AF, Ventikos Y.
Interface focus Volume 8 (2018) p.20170019
DOI: 10.1098/rsfs.2017.0019

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S, Boland MA, Hunter FMI, Ten Hoopen P, Alako B, Amid C, Wilkinson DJ, Curtis TP, Cochrane G, Finn RD.
Nucleic acids research Volume 46 (2018) p.D726-D735
DOI: 10.1093/nar/gkx967

Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.
Armean IM, Lilley KS, Trotter MWB, Pilkington NCV, Holden SB.
Bioinformatics (Oxford, England) Volume (2018) p.
DOI: 10.1093/bioinformatics/btx803

StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites.
Akimov V, Olsen LCB, Hansen SVF, Barrio-Hernandez I, Puglia M, Jensen SS, Solov'yov IA, Kratchmarova I, Blagoev B.
Journal of proteome research Volume 17 (2018) p.296-304
DOI: 10.1021/acs.jproteome.7b00566

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD.
Genome research Volume 28 (2018) p.203-213
DOI: 10.1101/gr.225615.117

Expression Atlas: gene and protein expression across multiple studies and organisms.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R.
Nucleic acids research Volume 46 (2018) p.D246-D251
DOI: 10.1093/nar/gkx1158

Reactome graph database: Efficient access to complex pathway data.
Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H.
PLoS computational biology Volume 14 (2018) p.e1005968
DOI: 10.1371/journal.pcbi.1005968

Ensembl 2018.
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P.
Nucleic acids research Volume 46 (2018) p.D754-D761
DOI: 10.1093/nar/gkx1098

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Kersey PJ, Allen JE, Allot A, Barba M, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Grabmueller C, Kumar N, Liu Z, Maurel T, Moore B, McDowall MD, Maheswari U, Naamati G, Newman V, Ong CK, Paulini M, Pedro H, Perry E, Russell M, Sparrow H, Tapanari E, Taylor K, Vullo A, Williams G, Zadissia A, Olson A, Stein J, Wei S, Tello-Ruiz M, Ware D, Luciani A, Potter S, Finn RD, Urban M, Hammond-Kosack KE, Bolser DM, De Silva N, Howe KL, Langridge N, Maslen G, Staines DM, Yates A.
Nucleic acids research Volume 46 (2018) p.D802-D808
DOI: 10.1093/nar/gkx1011

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.
Pratas MI, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP.
Scientific reports Volume 8 (2018) p.1717
DOI: 10.1038/s41598-018-19820-1

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI.
Nucleic acids research Volume 46 (2018) p.D335-D342
DOI: 10.1093/nar/gkx1038

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S.
Analytical chemistry Volume 90 (2018) p.649-656
DOI: 10.1021/acs.analchem.7b02795

A systematic atlas of chaperome deregulation topologies across the human cancer landscape.
Hadizadeh Esfahani A, Sverchkova A, Saez-Rodriguez J, Schuppert AA, Brehme M.
PLoS computational biology Volume 14 (2018) p.e1005890
DOI: 10.1371/journal.pcbi.1005890

Perturbation-response genes reveal signaling footprints in cancer gene expression.
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J.
Nature communications Volume 9 (2018) p.20
DOI: 10.1038/s41467-017-02391-6

The European Bioinformatics Institute in 2017: data coordination and integration.
Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E.
Nucleic acids research Volume 46 (2018) p.D21-D29
DOI: 10.1093/nar/gkx1154

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.
Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP.
Circulation. Genomic and precision medicine Volume 11 (2018) p.e001813
DOI: 10.1161/circgen.117.001813

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.
Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J.
Metabolic engineering Volume 45 (2018) p.149-157
DOI: 10.1016/j.ymben.2017.11.011

NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.
Gaude E, Schmidt C, Gammage PA, Dugourd A, Blacker T, Chew SP, Saez-Rodriguez J, O'Neill JS, Szabadkai G, Minczuk M, Frezza C.
Molecular cell Volume 69 (2018) p.581-593.e7
DOI: 10.1016/j.molcel.2018.01.034

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.
Wirbel J, Cutillas P, Saez-Rodriguez J.
Methods in molecular biology (Clifton, N.J.) Volume 1711 (2018) p.103-132
DOI: 10.1007/978-1-4939-7493-1_6

Exploring autophagy with Gene Ontology.
Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P.
Autophagy Volume (2018) p.1-18
DOI: 10.1080/15548627.2017.1415189

The SysteMHC Atlas project.
Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.
Nucleic acids research Volume 46 (2018) p.D1237-D1247
DOI: 10.1093/nar/gkx664

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P.
Nature ecology & evolution Volume 2 (2018) p.152-163
DOI: 10.1038/s41559-017-0377-2

Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution.
Halewood M, Chiurugwi T, Sackville Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron N, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, Powell W.
The New phytologist Volume 217 (2018) p.1407-1419
DOI: 10.1111/nph.14993

DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels: a systematic review and replication in a case-control sample of the Lifelines study.
Walaszczyk E, Luijten M, Spijkerman AMW, Bonder MJ, Lutgers HL, Snieder H, Wolffenbuttel BHR, van Vliet-Ostaptchouk JV.
Diabetologia Volume 61 (2018) p.354-368
DOI: 10.1007/s00125-017-4497-7

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.
Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK.
Gut Volume 67 (2018) p.108-119
DOI: 10.1136/gutjnl-2016-312135

Evolution, dynamics and dysregulation of kinase signalling.
Ochoa D, Bradley D, Beltrao P.
Current opinion in structural biology Volume 48 (2018) p.133-140
DOI: 10.1016/j.sbi.2017.12.008

JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure.
Troshin PV, Procter JB, Sherstnev A, Barton DL, Madeira F, Barton GJ.
Bioinformatics (Oxford, England) Volume (2018) p.
DOI: 10.1093/bioinformatics/bty045

ChannelsDB: database of biomacromolecular tunnels and pores.
Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J.
Nucleic acids research Volume 46 (2018) p.D399-D405
DOI: 10.1093/nar/gkx868

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA.
Genome biology Volume 19 (2018) p.12
DOI: 10.1186/s13059-017-1377-x

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.
Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC.
Nature cell biology Volume 20 (2018) p.127-134
DOI: 10.1038/s41556-017-0013-z

DISNOR: a disease network open resource.
Lo Surdo P, Calderone A, Iannuccelli M, Licata L, Peluso D, Castagnoli L, Cesareni G, Perfetto L.
Nucleic acids research Volume 46 (2018) p.D527-D534
DOI: 10.1093/nar/gkx876

Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J.
Cancer research Volume 78 (2018) p.769-780
DOI: 10.1158/0008-5472.can-17-1679

PDBsum: Structural summaries of PDB entries.
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM.
Protein science : a publication of the Protein Society Volume 27 (2018) p.129-134
DOI: 10.1002/pro.3289

AmyPro: a database of proteins with validated amyloidogenic regions.
Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R.
Nucleic acids research Volume 46 (2018) p.D387-D392
DOI: 10.1093/nar/gkx950

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.
Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH.
Stem cell reports Volume 10 (2018) p.1-6
DOI: 10.1016/j.stemcr.2017.12.002

Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
Bonàs-Guarch S, Guindo-Martínez M, Miguel-Escalada I, Grarup N, Sebastian D, Rodriguez-Fos E, Sánchez F, Planas-Fèlix M, Cortes-Sánchez P, González S, Timshel P, Pers TH, Morgan CC, Moran I, Atla G, González JR, Puiggros M, Martí J, Andersson EA, Díaz C, Badia RM, Udler M, Leong A, Kaur V, Flannick J, Jørgensen T, Linneberg A, Jørgensen ME, Witte DR, Christensen C, Brandslund I, Appel EV, Scott RA, Luan J, Langenberg C, Wareham NJ, Pedersen O, Zorzano A, Florez JC, Hansen T, Ferrer J, Mercader JM, Torrents D.
Nature communications Volume 9 (2018) p.321
DOI: 10.1038/s41467-017-02380-9

Integrated omics dissection of proteome dynamics during cardiac remodeling.
Lau E, Cao Q, Lam MPY, Wang J, Ng DCM, Bleakley BJ, Lee JM, Liem DA, Wang D, Hermjakob H, Ping P.
Nature communications Volume 9 (2018) p.120
DOI: 10.1038/s41467-017-02467-3

Identification of genetic elements in metabolism by high-throughput mouse phenotyping.
Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H, IMPC Consortium, Hough T, Mallon AM, Wells S, Santos L, Lelliott CJ, White JK, Sorg T, Champy MF, Bower LR, Reynolds CL, Flenniken AM, Murray SA, Nutter LMJ, Svenson KL, West D, Tocchini-Valentini GP, Beaudet AL, Bosch F, Braun RB, Dobbie MS, Gao X, Herault Y, Moshiri A, Moore BA, Kent Lloyd KC, McKerlie C, Masuya H, Tanaka N, Flicek P, Parkinson HE, Sedlacek R, Seong JK, Wang CL, Moore M, Brown SD, Tschöp MH, Wurst W, Klingenspor M, Wolf E, Beckers J, Machicao F, Peter A, Staiger H, Häring HU, Grallert H, Campillos M, Maier H, Fuchs H, Gailus-Durner V, Werner T, Hrabe de Angelis M.
Nature communications Volume 9 (2018) p.288
DOI: 10.1038/s41467-017-01995-2

The BioStudies database-one stop shop for all data supporting a life sciences study.
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J.
Nucleic acids research Volume 46 (2018) p.D1266-D1270
DOI: 10.1093/nar/gkx965

Interleukins and their signaling pathways in the Reactome biological pathway database.
Jupe S, Ray K, Duenas Roca C, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H.
The Journal of allergy and clinical immunology Volume (2018) p.
DOI: 10.1016/j.jaci.2017.12.992

The international nucleotide sequence database collaboration.
Karsch-Mizrachi I, Takagi T, Cochrane G, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 46 (2018) p.D48-D51
DOI: 10.1093/nar/gkx1097

Whole Exome Sequencing allows the identification of two novel groups of Xeroderma pigmentosum in Tunisia, XP-D and XP-E: Impact on molecular diagnosis.
Ben Rekaya M, Naouali C, Messaoud O, Jones M, Bouyacoub Y, Nagara M, Pippucci T, Jmel H, Chargui M, Jerbi M, Alibi M, Dallali H, Bashamboo A, McElreavey K, Romeo G, Barakat A, Zghal M, Yacoub-Youssef H, Abdelhak S.
Journal of dermatological science Volume 89 (2018) p.172-180
DOI: 10.1016/j.jdermsci.2017.10.015

WormBase 2017: molting into a new stage.
Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C, Kishore R, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers F, Russell M, Schindelman G, Tuli MA, Van Auken K, Wang Q, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW.
Nucleic acids research Volume 46 (2018) p.D869-D874
DOI: 10.1093/nar/gkx998

The European Nucleotide Archive in 2017.
Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 46 (2018) p.D36-D40
DOI: 10.1093/nar/gkx1125

A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.
Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J.
Archives of toxicology Volume 92 (2018) p.553-555
DOI: 10.1007/s00204-017-2041-7

Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping.
Quan TP, Bawa Z, Foster D, Walker T, Del Ojo Elias C, Rathod P, MMM Informatics Group, Iqbal Z, Bradley P, Mowbray J, Walker AS, Crook DW, Wyllie DH, Peto TEA, Smith EG.
Journal of clinical microbiology Volume 56 (2018) p.
DOI: 10.1128/jcm.01480-17

Three-dimensional cardiovascular imaging-genetics: a mass univariate framework.
Biffi C, de Marvao A, Attard MI, Dawes TJW, Whiffin N, Bai W, Shi W, Francis C, Meyer H, Buchan R, Cook SA, Rueckert D, O'Regan DP.
Bioinformatics (Oxford, England) Volume 34 (2018) p.97-103
DOI: 10.1093/bioinformatics/btx552

BioModels: expanding horizons to include more modelling approaches and formats.
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H.
Nucleic acids research Volume 46 (2018) p.D1248-D1253
DOI: 10.1093/nar/gkx1023

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S.
Nucleic acids research Volume 46 (2018) p.D486-D492
DOI: 10.1093/nar/gkx1070

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog.
Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL.
Genome biology Volume 19 (2018) p.21
DOI: 10.1186/s13059-018-1396-2

2017

LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs.
Hong S, Freeberg MA, Han T, Kamath A, Yao Y, Fukuda T, Suzuki T, Kim JK, Inoki K.
eLife Volume 6 (2017) p.
DOI: 10.7554/elife.25237

First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151.
Marquez-Ortiz RA, Haggerty L, Sim EM, Duarte C, Castro-Cardozo BE, Beltran M, Saavedra S, Vanegas N, Escobar-Perez J, Petty NK.
Genome announcements Volume 5 (2017) p.
DOI: 10.1128/genomea.01472-16

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.
Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB.
Nature genetics Volume 49 (2017) p.1714-1721
DOI: 10.1038/ng.3959

Societal challenges of precision medicine: Bringing order to chaos.
Salgado R, Moore H, Martens JWM, Lively T, Malik S, McDermott U, Michiels S, Moscow JA, Tejpar S, McKee T, Lacombe D, IBCD-Faculty.
European journal of cancer (Oxford, England : 1990) Volume 84 (2017) p.325-334
DOI: 10.1016/j.ejca.2017.07.028

A high-resolution mRNA expression time course of embryonic development in zebrafish.
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM.
eLife Volume 6 (2017) p.
DOI: 10.7554/elife.30860

eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis.
Armit C, Richardson L, Venkataraman S, Graham L, Burton N, Hill B, Yang Y, Baldock RA.
Developmental biology Volume 423 (2017) p.1-11
DOI: 10.1016/j.ydbio.2017.01.023

Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress.
Jin M, Fuller GG, Han T, Yao Y, Alessi AF, Freeberg MA, Roach NP, Moresco JJ, Karnovsky A, Baba M, Yates JR, Gitler AD, Inoki K, Klionsky DJ, Kim JK.
Cell reports Volume 20 (2017) p.895-908
DOI: 10.1016/j.celrep.2017.06.082

MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality.
Weiser NE, Yang DX, Feng S, Kalinava N, Brown KC, Khanikar J, Freeberg MA, Snyder MJ, Csankovszki G, Chan RC, Gu SG, Montgomery TA, Jacobsen SE, Kim JK.
Developmental cell Volume 41 (2017) p.408-423.e7
DOI: 10.1016/j.devcel.2017.04.023

Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.
Chojnacki S, Cowley A, Lee J, Foix A, Lopez R.
Nucleic acids research Volume 45 (2017) p.W550-W553
DOI: 10.1093/nar/gkx273

Open Targets: a platform for therapeutic target identification and validation.
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.
Nucleic acids research Volume 45 (2017) p.D985-D994
DOI: 10.1093/nar/gkw1055

ComplexViewer: visualization of curated macromolecular complexes.
Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J.
Bioinformatics (Oxford, England) Volume 33 (2017) p.3673-3675
DOI: 10.1093/bioinformatics/btx497

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
Lepik K, Annilo T, Kukuškina V, eQTLGen Consortium, Kisand K, Kutalik Z, Peterson P, Peterson H.
PLoS computational biology Volume 13 (2017) p.e1005766
DOI: 10.1371/journal.pcbi.1005766

BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.
Bioinformatics (Oxford, England) Volume 33 (2017) p.2580-2582
DOI: 10.1093/bioinformatics/btx192

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P.
Nature communications Volume 8 (2017) p.1092
DOI: 10.1038/s41467-017-01037-x

Genenames.org: the HGNC and VGNC resources in 2017.
Yates B, Braschi B, Gray KA, Seal RL, Tweedie S, Bruford EA.
Nucleic acids research Volume 45 (2017) p.D619-D625
DOI: 10.1093/nar/gkw1033

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota.
Imhann F, Vich Vila A, Bonder MJ, Lopez Manosalva AG, Koonen DPY, Fu J, Wijmenga C, Zhernakova A, Weersma RK.
Gut microbes Volume 8 (2017) p.351-358
DOI: 10.1080/19490976.2017.1284732

The Proteins API: accessing key integrated protein and genome information.
Nightingale A, Antunes R, Alpi E, Bursteinas B, Gonzales L, Liu W, Luo J, Qi G, Turner E, Martin M.
Nucleic acids research Volume 45 (2017) p.W539-W544
DOI: 10.1093/nar/gkx237

Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.
Wahl S, Drong A, Lehne B, Loh M, Scott WR, Kunze S, Tsai PC, Ried JS, Zhang W, Yang Y, Tan S, Fiorito G, Franke L, Guarrera S, Kasela S, Kriebel J, Richmond RC, Adamo M, Afzal U, Ala-Korpela M, Albetti B, Ammerpohl O, Apperley JF, Beekman M, Bertazzi PA, Black SL, Blancher C, Bonder MJ, Brosch M, Carstensen-Kirberg M, de Craen AJ, de Lusignan S, Dehghan A, Elkalaawy M, Fischer K, Franco OH, Gaunt TR, Hampe J, Hashemi M, Isaacs A, Jenkinson A, Jha S, Kato N, Krogh V, Laffan M, Meisinger C, Meitinger T, Mok ZY, Motta V, Ng HK, Nikolakopoulou Z, Nteliopoulos G, Panico S, Pervjakova N, Prokisch H, Rathmann W, Roden M, Rota F, Rozario MA, Sandling JK, Schafmayer C, Schramm K, Siebert R, Slagboom PE, Soininen P, Stolk L, Strauch K, Tai ES, Tarantini L, Thorand B, Tigchelaar EF, Tumino R, Uitterlinden AG, van Duijn C, van Meurs JB, Vineis P, Wickremasinghe AR, Wijmenga C, Yang TP, Yuan W, Zhernakova A, Batterham RL, Smith GD, Deloukas P, Heijmans BT, Herder C, Hofman A, Lindgren CM, Milani L, van der Harst P, Peters A, Illig T, Relton CL, Waldenberger M, Järvelin MR, Bollati V, Soong R, Spector TD, Scott J, McCarthy MI, Elliott P, Bell JT, Matullo G, Gieger C, Kooner JS, Grallert H, Chambers JC.
Nature Volume 541 (2017) p.81-86
DOI: 10.1038/nature20784

DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M.
American journal of human genetics Volume 101 (2017) p.888-902
DOI: 10.1016/j.ajhg.2017.09.028

Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes.
Mandaviya PR, Joehanes R, Aïssi D, Kühnel B, Marioni RE, Truong V, Stolk L, Beekman M, Bonder MJ, Franke L, Gieger C, Huan T, Ikram MA, Kunze S, Liang L, Lindemans J, Liu C, McRae AF, Mendelson MM, Müller-Nurasyid M, Peters A, Slagboom PE, Starr JM, Trégouët DA, Uitterlinden AG, van Greevenbroek MMJ, van Heemst D, van Iterson M, Wells PS, Yao C, Deary IJ, Gagnon F, Heijmans BT, Levy D, Morange PE, Waldenberger M, Heil SG, van Meurs JBJ, CHARGE Consortium Epigenetics group and BIOS Consortium.
PloS one Volume 12 (2017) p.e0182472
DOI: 10.1371/journal.pone.0182472

Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.
Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O.
Cell Reports Volume 21 (2017) p.2017-2029
DOI: 10.1016/j.celrep.2017.10.071

Disease variants alter transcription factor levels and methylation of their binding sites.
Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HE, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ, BIOS Consortium, Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MM, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JB, 't Hoen PA, Franke L, Heijmans BT.
Nature genetics Volume 49 (2017) p.131-138
DOI: 10.1038/ng.3721

Microbiology Managers: Managerial Training in the RItrain Project.
Paterson RRM, Lima N, Brooksbank C, Guarini E, Pasterk M, Lavitrano M, RItrain project consortium.
Trends in microbiology Volume 25 (2017) p.425-428
DOI: 10.1016/j.tim.2017.03.002

Mechanism-based biomarker discovery.
Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG.
Drug discovery today Volume 22 (2017) p.1209-1215
DOI: 10.1016/j.drudis.2017.04.013

Precision oncology for acute myeloid leukemia using a knowledge bank approach.
Gerstung M, Papaemmanuil E, Martincorena I, Bullinger L, Gaidzik VI, Paschka P, Heuser M, Thol F, Bolli N, Ganly P, Ganser A, McDermott U, Döhner K, Schlenk RF, Döhner H, Campbell PJ.
Nature genetics Volume 49 (2017) p.332-340
DOI: 10.1038/ng.3756

Gli1+ Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target.
Schneider RK, Mullally A, Dugourd A, Peisker F, Hoogenboezem R, Van Strien PMH, Bindels EM, Heckl D, Büsche G, Fleck D, Müller-Newen G, Wongboonsin J, Ventura Ferreira M, Puelles VG, Saez-Rodriguez J, Ebert BL, Humphreys BD, Kramann R.
Cell stem cell Volume 20 (2017) p.785-800.e8
DOI: 10.1016/j.stem.2017.03.008

Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.
Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J.
Cancer research Volume 77 (2017) p.3364-3375
DOI: 10.1158/0008-5472.can-17-0078

caspo: a toolbox for automated reasoning on the response of logical signaling networks families.
Videla S, Saez-Rodriguez J, Guziolowski C, Siegel A.
Bioinformatics Volume 33 (2017) p.947-950
DOI: 10.1093/bioinformatics/btw738

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA.
Cell systems Volume 5 (2017) p.485-497.e3
DOI: 10.1016/j.cels.2017.09.004

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin S, Alder C, Patel N, Gamble S, O'Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg Å, Stunnenberg H, van de Vijver M, Tan BK, Caldas C, Tutt A, Ueno NT, van 't Veer LJ, Martens JW, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjörd JE, Børresen-Dale AL, Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR.
Nature Volume 543 (2017) p.714-718
DOI: 10.1038/nature21703

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.
Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR.
PloS one Volume 12 (2017) p.e0182186
DOI: 10.1371/journal.pone.0182186

The ChEMBL database in 2017.
Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR.
Nucleic acids research Volume 45 (2017) p.D945-D954
DOI: 10.1093/nar/gkw1074

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.
Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A.
Expert opinion on drug discovery Volume 12 (2017) p.757-767
DOI: 10.1080/17460441.2017.1339032

GDSCTools for Mining Pharmacogenomic Interactions in Cancer.
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.
Bioinformatics (Oxford, England) Volume (2017) p.
DOI: 10.1093/bioinformatics/btx744

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R.
Cell systems Volume 5 (2017) p.604-619.e7
DOI: 10.1016/j.cels.2017.11.002

Building bridges between cellular and molecular structural biology.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ.
eLife Volume 6 (2017) p.
DOI: 10.7554/elife.25835

Logic Modeling in Quantitative Systems Pharmacology.
Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J.
CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.499-511
DOI: 10.1002/psp4.12225

Genomic Evolution of Breast Cancer Metastasis and Relapse.
Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG, Jones D, Raine K, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE, Campbell PJ.
Cancer cell Volume 32 (2017) p.169-184.e7
DOI: 10.1016/j.ccell.2017.07.005

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM.
Genome research Volume 27 (2017) p.849-864
DOI: 10.1101/gr.213611.116

A GWAS meta-analysis suggests roles for xenobiotic metabolism and ion channel activity in the biology of stool frequency.
Jankipersadsing SA, Hadizadeh F, Bonder MJ, Tigchelaar EF, Deelen P, Fu J, Andreasson A, Agreus L, Walter S, Wijmenga C, Hysi P, D'Amato M, Zhernakova A.
Gut Volume 66 (2017) p.756-758
DOI: 10.1136/gutjnl-2016-312398

Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M.
Nature communications Volume 8 (2017) p.16058
DOI: 10.1038/ncomms16058

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS.
Genome biology Volume 18 (2017) p.18
DOI: 10.1186/s13059-017-1156-8

The application of project-based learning in bioinformatics training.
Emery LR, Morgan SL.
PLoS Computational Biology Volume 13 (2017) p.e1005620
DOI: 10.1371/journal.pcbi.1005620

Report of the International Stem Cell Banking Initiative Workshop Activity: Current Hurdles and Progress in Seed-Stock Banking of Human Pluripotent Stem Cells.
Kim JH, Kurtz A, Yuan BZ, Zeng F, Lomax G, Loring JF, Crook J, Ju JH, Clarke L, Inamdar MS, Pera M, Firpo MT, Sheldon M, Rahman N, O'Shea O, Pranke P, Zhou Q, Isasi R, Rungsiwiwut R, Kawamata S, Oh S, Ludwig T, Masui T, Novak TJ, Takahashi T, Fujibuchi W, Koo SK, Stacey GN.
Stem cells translational medicine Volume 6 (2017) p.1956-1962
DOI: 10.1002/sctm.17-0144

Expansion of the Gene Ontology knowledgebase and resources.
The Gene Ontology Consortium.
Nucleic acids research Volume 45 (2017) p.D331-D338
DOI: 10.1093/nar/gkw1108

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR.
PLoS computational biology Volume 13 (2017) p.e1005379
DOI: 10.1371/journal.pcbi.1005379

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.
Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P.
Cell systems Volume 5 (2017) p.386-398.e4
DOI: 10.1016/j.cels.2017.08.013

Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M.
Seminars in cancer biology Volume (2017) p.
DOI: 10.1016/j.semcancer.2017.12.001

Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD.
BMC genomics Volume 18 (2017) p.101
DOI: 10.1186/s12864-016-3432-5

WormBase ParaSite - a comprehensive resource for helminth genomics.
Howe KL, Bolt BJ, Shafie M, Kersey P, Berriman M.
Molecular and biochemical parasitology Volume 215 (2017) p.2-10
DOI: 10.1016/j.molbiopara.2016.11.005

Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance.
Marquez-Ortiz RA, Haggerty L, Olarte N, Duarte C, Garza-Ramos U, Silva-Sanchez J, Castro BE, Sim EM, Beltran M, Moncada MV, Valderrama A, Castellanos JE, Charles IG, Vanegas N, Escobar-Perez J, Petty NK.
Genome biology and evolution Volume 9 (2017) p.1725-1741
DOI: 10.1093/gbe/evx115

Identification of context-dependent expression quantitative trait loci in whole blood.
Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MM, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JB, Jansen R, Heijmans BT, 't Hoen PA, Franke L.
Nature genetics Volume 49 (2017) p.139-145
DOI: 10.1038/ng.3737

Extracellular vesicles are independent metabolic units with asparaginase activity.
Iraci N, Gaude E, Leonardi T, Costa ASH, Cossetti C, Peruzzotti-Jametti L, Bernstock JD, Saini HK, Gelati M, Vescovi AL, Bastos C, Faria N, Occhipinti LG, Enright AJ, Frezza C, Pluchino S.
Nature chemical biology Volume 13 (2017) p.951-955
DOI: 10.1038/nchembio.2422

Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.
Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ.
EMBO reports Volume 18 (2017) p.1231-1247
DOI: 10.15252/embr.201744059

A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming.
Vasiliauskaitė L, Vitsios D, Berrens RV, Carrieri C, Reik W, Enright AJ, O'Carroll D.
Nature structural & molecular biology Volume 24 (2017) p.604-606
DOI: 10.1038/nsmb.3413

In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA.
Nature communications Volume 8 (2017) p.2109
DOI: 10.1038/s41467-017-00686-2

Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.
Kılınç GM, Koptekin D, Atakuman Ç, Sümer AP, Dönertaş HM, Yaka R, Bilgin CC, Büyükkarakaya AM, Baird D, Altınışık E, Flegontov P, Götherström A, Togan İ, Somel M.
Proceedings. Biological sciences Volume 284 (2017) p.
DOI: 10.1098/rspb.2017.2064

3' Uridylation controls mature microRNA turnover during CD4 T-cell activation.
Gutiérrez-Vázquez C, Enright AJ, Rodríguez-Galán A, Pérez-García A, Collier P, Jones MR, Benes V, Mizgerd JP, Mittelbrunn M, Ramiro AR, Sánchez-Madrid F.
RNA (New York, N.Y.) Volume 23 (2017) p.882-891
DOI: 10.1261/rna.060095.116

ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.
Pineda SS, Chaumeil PA, Kunert A, Kaas Q, Thang MWC, Li L, Nuhn M, Herzig V, Saez NJ, Cristofori-Armstrong B, Anangi R, Senff S, Gorse D, King GF.
Bioinformatics Volume (2017) p.
DOI: 10.1093/bioinformatics/btx661

BRIE: transcriptome-wide splicing quantification in single cells.
Huang Y, Sanguinetti G.
Genome biology Volume 18 (2017) p.123
DOI: 10.1186/s13059-017-1248-5

Reactome pathway analysis: a high-performance in-memory approach.
Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H.
BMC bioinformatics Volume 18 (2017) p.142
DOI: 10.1186/s12859-017-1559-2

Affinity purification of human m-calpain through an intrinsically disordered inhibitor, calpastatin.
Nguyen HH, Varadi M, Tompa P, Pauwels K.
PloS one Volume 12 (2017) p.e0174125
DOI: 10.1371/journal.pone.0174125

Reactome enhanced pathway visualization.
Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A.
Bioinformatics (Oxford, England) Volume 33 (2017) p.3461-3467
DOI: 10.1093/bioinformatics/btx441

Reactome diagram viewer: Data structures and strategies to boost performance.
Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H.
Bioinformatics (Oxford, England) Volume (2017) p.
DOI: 10.1093/bioinformatics/btx752

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H.
Nucleic acids research Volume 45 (2017) p.D896-D901
DOI: 10.1093/nar/gkw1133

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.
Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ, Berriman M.
PLoS neglected tropical diseases Volume 11 (2017) p.e0005559
DOI: 10.1371/journal.pntd.0005559

mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.
Morgan M, Much C, DiGiacomo M, Azzi C, Ivanova I, Vitsios DM, Pistolic J, Collier P, Moreira PN, Benes V, Enright AJ, O'Carroll D.
Nature Volume 548 (2017) p.347-351
DOI: 10.1038/nature23318

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG.
Nucleic acids research Volume 45 (2017) p.D566-D573
DOI: 10.1093/nar/gkw1004

Variation and Functional Impact of Neanderthal Ancestry in Western Asia.
Taskent RO, Alioglu ND, Fer E, Melike Donertas H, Somel M, Gokcumen O.
Genome biology and evolution Volume 9 (2017) p.3516-3524
DOI: 10.1093/gbe/evx216

Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity.
Paschalis V, Le Chatelier E, Green M, Képès F, Soultanas P, Janniere L.
Open biology Volume 7 (2017) p.
DOI: 10.1098/rsob.170146

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL.
Nucleic acids research Volume 45 (2017) p.W30-W35
DOI: 10.1093/nar/gkx343

Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S.
Bioinformatics (Oxford, England) Volume (2017) p.
DOI: 10.1093/bioinformatics/btx542

Epimetheus - a multi-profile normalizer for epigenomic sequencing data.
Saleem MM, Mendoza-Parra MA, Cholley PE, Blum M, Gronemeyer H.
BMC bioinformatics Volume 18 (2017) p.259
DOI: 10.1186/s12859-017-1655-3

Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.
Saidi R, Boudellioua I, Martin MJ, Solovyev V.
Methods in molecular biology (Clifton, N.J.) Volume 1613 (2017) p.311-331
DOI: 10.1007/978-1-4939-7027-8_12

Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.
Rifaioglu AS, Doğan T, Saraç ÖS, Ersahin T, Saidi R, Atalay MV, Martin MJ, Cetin-Atalay R.
Proteins Volume (2017) p.
DOI: 10.1002/prot.25416

The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence.
Ivanova I, Much C, Di Giacomo M, Azzi C, Morgan M, Moreira PN, Monahan J, Carrieri C, Enright AJ, O'Carroll D.
Molecular cell Volume 67 (2017) p.1059-1067.e4
DOI: 10.1016/j.molcel.2017.08.003

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
Vitsios DM, Davis MP, van Dongen S, Enright AJ.
Nucleic acids research Volume 45 (2017) p.1079-1090
DOI: 10.1093/nar/gkw1031

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.
Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ.
Nucleic acids research Volume 45 (2017) p.e177
DOI: 10.1093/nar/gkx836

Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M.
Scientific reports Volume 7 (2017) p.5894
DOI: 10.1038/s41598-017-05927-4

Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M.
Nucleic acids research Volume 45 (2017) p.D170-D176
DOI: 10.1093/nar/gkw1081

Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.
Contreras-Martos S, Piai A, Kosol S, Varadi M, Bekesi A, Lebrun P, Volkov AN, Gevaert K, Pierattelli R, Felli IC, Tompa P.
Scientific reports Volume 7 (2017) p.4676
DOI: 10.1038/s41598-017-04611-x

Plant Reactome: a resource for plant pathways and comparative analysis.
Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P.
Nucleic acids research Volume 45 (2017) p.D1029-D1039
DOI: 10.1093/nar/gkw932

From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.
Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š, Edwards S, Jurriaans S, Bakker M, Ong SH, Gras L, van Sighem A, Bezemer D, de Wolf F, Reiss P, Kellam P, Berkhout B, Fraser C, van der Kuyl AC, BEEHIVE Consortium.
Virus research Volume 239 (2017) p.10-16
DOI: 10.1016/j.virusres.2016.08.004

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration.
PLoS biology Volume 15 (2017) p.e2001855
DOI: 10.1371/journal.pbio.2001855

Genome-wide evolutionary dynamics of influenza B viruses on a global scale.
Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ.
PLoS pathogens Volume 13 (2017) p.e1006749
DOI: 10.1371/journal.ppat.1006749

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.
Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C.
AIDS research and human retroviruses Volume (2017) p.
DOI: 10.1089/aid.2017.0061

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C, STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration.
Molecular biology and evolution Volume (2017) p.
DOI: 10.1093/molbev/msx304

Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration.
PLoS biology Volume 15 (2017) p.e1002608
DOI: 10.1371/journal.pbio.1002608

Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape.
Leitman EM, Thobakgale CF, Adland E, Ansari MA, Raghwani J, Prendergast AJ, Tudor-Williams G, Kiepiela P, Hemelaar J, Brener J, Tsai MH, Mori M, Riddell L, Luzzi G, Jooste P, Ndung'u T, Walker BD, Pybus OG, Kellam P, Naranbhai V, Matthews PC, Gall A, Goulder PJR.
The Journal of experimental medicine Volume 214 (2017) p.3239-3261
DOI: 10.1084/jem.20162123

Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting
Mulder N, Adebamowo CA, Adebamowo SN, Adebayo O, Adeleye O, Alibi M, Baichoo S, Benkahla A, Fadlelmola FM, Ghazal H, Ghedira K, Matimba A, Moussa A, Mungloo-Dilmohamud Z, Owolabi MO, Radouani F, Rotimi CN, Stein DJ, Souiai O.
Data Science Journal Volume 16 (2017) p.49
DOI: 10.5334/dsj-2017-049

Universal Patterns of Selection in Cancer and Somatic Tissues.
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ.
Cell Volume 171 (2017) p.1029-1041.e21
DOI: 10.1016/j.cell.2017.09.042

The emerging landscape of dynamic DNA methylation in early childhood.
Xu CJ, Bonder MJ, Söderhäll C, Bustamante M, Baïz N, Gehring U, Jankipersadsing SA, van der Vlies P, van Diemen CC, van Rijkom B, Just J, Kull I, Kere J, Antó JM, Bousquet J, Zhernakova A, Wijmenga C, Annesi-Maesano I, Sunyer J, Melén E, Li Y, Postma DS, Koppelman GH.
BMC genomics Volume 18 (2017) p.25
DOI: 10.1186/s12864-016-3452-1

Development of Bioinformatics Infrastructure for Genomics Research.
Mulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, Akanle B, Alibi M, Armstrong DL, Aron S, Ashano E, Baichoo S, Benkahla A, Brown DK, Chimusa ER, Fadlelmola FM, Falola D, Fatumo S, Ghedira K, Ghouila A, Hazelhurst S, Isewon I, Jung S, Kassim SK, Kayondo JK, Mbiyavanga M, Meintjes A, Mohammed S, Mosaku A, Moussa A, Muhammd M, Mungloo-Dilmohamud Z, Nashiru O, Odia T, Okafor A, Oladipo O, Osamor V, Oyelade J, Sadki K, Salifu SP, Soyemi J, Panji S, Radouani F, Souiai O, Tastan Bishop Ö, H3ABioNet Consortium, as members of the H3Africa Consortium.
Global heart Volume 12 (2017) p.91-98
DOI: 10.1016/j.gheart.2017.01.005

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y.
Nucleic acids research Volume 45 (2017) p.D347-D352
DOI: 10.1093/nar/gkw918

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C, PANGEA-HIV Consortium.
Molecular biology and evolution Volume 34 (2017) p.185-203
DOI: 10.1093/molbev/msw217

Multi-tissue DNA methylation age predictor in mouse.
Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W.
Genome biology Volume 18 (2017) p.68
DOI: 10.1186/s13059-017-1203-5

An epigenome-wide association study meta-analysis of educational attainment.
Karlsson Linnér R, Marioni RE, Rietveld CA, Simpkin AJ, Davies NM, Watanabe K, Armstrong NJ, Auro K, Baumbach C, Bonder MJ, Buchwald J, Fiorito G, Ismail K, Iurato S, Joensuu A, Karell P, Kasela S, Lahti J, McRae AF, Mandaviya PR, Seppälä I, Wang Y, Baglietto L, Binder EB, Harris SE, Hodge AM, Horvath S, Hurme M, Johannesson M, Latvala A, Mather KA, Medland SE, Metspalu A, Milani L, Milne RL, Pattie A, Pedersen NL, Peters A, Polidoro S, Räikkönen K, Severi G, Starr JM, Stolk L, Waldenberger M, Eriksson JG, Esko T, Franke L, Gieger C, Giles GG, Hägg S, Jousilahti P, Kaprio J, Kähönen M, Lehtimäki T, Martin NG, van Meurs JBC, Ollikainen M, Perola M, Posthuma D, Raitakari OT, Sachdev PS, Taskesen E, Uitterlinden AG, Vineis P, Wijmenga C, Wright MJ, Relton C, Davey Smith G, Deary IJ, Koellinger PD, Benjamin DJ.
Molecular psychiatry Volume 22 (2017) p.1680-1690
DOI: 10.1038/mp.2017.210

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.
Journal of cheminformatics Volume 9 (2017) p.33
DOI: 10.1186/s13321-017-0220-4

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM.
Nucleic acids research Volume 45 (2017) p.11559-11569
DOI: 10.1093/nar/gkx814

The druggable genome and support for target identification and validation in drug development.
Finan C, Gaulton A, Kruger FA, Lumbers RT, Shah T, Engmann J, Galver L, Kelley R, Karlsson A, Santos R, Overington JP, Hingorani AD, Casas JP.
Science translational medicine Volume 9 (2017) p.
DOI: 10.1126/scitranslmed.aag1166

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA.
Cell systems Volume 4 (2017) p.291-305.e7
DOI: 10.1016/j.cels.2016.12.013

Pharos: Collating protein information to shed light on the druggable genome.
Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R.
Nucleic acids research Volume 45 (2017) p.D995-D1002
DOI: 10.1093/nar/gkw1072

Phenotype inference in an Escherichia coli strain panel.
Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P.
eLife Volume 6 (2017) p.
DOI: 10.7554/elife.31035

Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs.
Barra PA, Ribeiro AJ, Ramos MJ, Jiménez VA, Alderete JB, Fernandes PA.
Chemical biology & drug design Volume 89 (2017) p.114-123
DOI: 10.1111/cbdd.12837

Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.
Hu Z, Sim Y, Kon OL, Ng WH, Ribeiro AJ, Ramos MJ, Fernandes PA, Ganguly R, Xing B, García F, Yeow EK.
Bioconjugate chemistry Volume 28 (2017) p.590-599
DOI: 10.1021/acs.bioconjchem.6b00682

Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M.
Journal of structural biology Volume 199 (2017) p.12-26
DOI: 10.1016/j.jsb.2017.05.007

New insights into the GINS complex explain the controversy between existing structural models.
Carroni M, De March M, Medagli B, Krastanova I, Taylor IA, Amenitsch H, Araki H, Pisani FM, Patwardhan A, Onesti S.
Scientific reports Volume 7 (2017) p.40188
DOI: 10.1038/srep40188

Trends in the Electron Microscopy Data Bank (EMDB).
Patwardhan A.
Acta crystallographica. Section D, Structural biology Volume 73 (2017) p.503-508
DOI: 10.1107/s2059798317004181

Developing data interoperability using standards: A wheat community use case.
Dzale Yeumo E, Alaux M, Arnaud E, Aubin S, Baumann U, Buche P, Cooper L, Ćwiek-Kupczyńska H, Davey RP, Fulss RA, Jonquet C, Laporte MA, Larmande P, Pommier C, Protonotarios V, Reverte C, Shrestha R, Subirats I, Venkatesan A, Whan A, Quesneville H.
F1000Research Volume 6 (2017) p.1843
DOI: 10.12688/f1000research.12234.2

A comprehensive map of molecular drug targets.
Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI, Overington JP.
Nature reviews. Drug discovery Volume 16 (2017) p.19-34
DOI: 10.1038/nrd.2016.230

Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.
Bolli N, Biancon G, Moarii M, Gimondi S, Li Y, de Philippis C, Maura F, Sathiaseelan V, Tai YT, Mudie L, O'Meara S, Raine K, Teague JW, Butler AP, Carniti C, Gerstung M, Bagratuni T, Kastritis E, Dimopoulos M, Corradini P, Anderson K, Moreau P, Minvielle S, Campbell PJ, Papaemmanuil E, Avet-Loiseau H, Munshi NC.
Leukemia Volume (2017) p.
DOI: 10.1038/leu.2017.344

Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach.
Guruceaga E, Garin-Muga A, Prieto G, Bejarano B, Marcilla M, Marín-Vicente C, Perez-Riverol Y, Casal JI, Vizcaíno JA, Corrales FJ, Segura V.
Journal of proteome research Volume 16 (2017) p.4374-4390
DOI: 10.1021/acs.jproteome.7b00388

Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration.
Arno G, Carss KJ, Hull S, Zihni C, Robson AG, Fiorentino A, UK Inherited Retinal Disease Consortium, Hardcastle AJ, Holder GE, Cheetham ME, Plagnol V, NIHR Bioresource - Rare Diseases Consortium, Moore AT, Raymond FL, Matter K, Balda MS, Webster AR.
American journal of human genetics Volume 100 (2017) p.334-342
DOI: 10.1016/j.ajhg.2016.12.014

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.
Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, Carmichael J, Chitre M, Henderson RHH, Hurst J, MacLaren RE, Murphy E, Paterson J, Rosser E, Thompson DA, Wakeling E, Ouwehand WH, Michaelides M, Moore AT, NIHR-BioResource Rare Diseases Consortium, Webster AR, Raymond FL.
American journal of human genetics Volume 100 (2017) p.75-90
DOI: 10.1016/j.ajhg.2016.12.003

Reports from CAGI: The Critical Assessment of Genome Interpretation.
Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner SE.
Human mutation Volume 38 (2017) p.1039-1041
DOI: 10.1002/humu.23290

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.
Hadinnapola C, Bleda M, Haimel M, Screaton N, Swift A, Dorfmüller P, Preston SD, Southwood M, Hernandez-Sanchez J, Martin J, Treacy C, Yates K, Bogaard H, Church C, Coghlan G, Condliffe R, Corris PA, Gibbs S, Girerd B, Holden S, Humbert M, Kiely DG, Lawrie A, Machado R, MacKenzie Ross R, Moledina S, Montani D, Newnham M, Peacock A, Pepke-Zaba J, Rayner-Matthews P, Shamardina O, Soubrier F, Southgate L, Suntharalingam J, Toshner M, Trembath R, Vonk Noordegraaf A, Wilkins MR, Wort SJ, Wharton J, NIHR BioResource–Rare Diseases Consortium; UK National Cohort Study of Idiopathic and Heritable PAH, Gräf S, Morrell NW.
Circulation Volume 136 (2017) p.2022-2033
DOI: 10.1161/circulationaha.117.028351

The BEACH-domain containing protein, Nbeal2, interacts with Dock7, Sec16a and Vac14.
Mayer L, Jasztal M, Pardo M, Aguera de Haro S, Collins J, Bariana TK, Smethurst PA, Grassi L, Petersen R, Nurden P, Favier R, Yu L, Meacham S, Astle WJ, Choudhary J, Yue WW, Ouwehand WH, Guerrero JA.
Blood Volume (2017) p.
DOI: 10.1182/blood-2017-08-800359

Proteomics and phosphoproteomics in precision medicine: applications and challenges.
Giudice G, Petsalaki E.
Briefings in bioinformatics Volume (2017) p.
DOI: 10.1093/bib/bbx141

Systematic identification of phosphorylation-mediated protein interaction switches.
Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB.
PLoS computational biology Volume 13 (2017) p.e1005462
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Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.
Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD.
Human mutation Volume 38 (2017) p.1266-1276
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Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA.
Human mutation Volume 38 (2017) p.1182-1192
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Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor.
Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B.
Molecular & cellular proteomics : MCP Volume 16 (2017) p.1433-1446
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Literature evidence in open targets - a target validation platform.
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In silico prediction of novel therapeutic targets using gene-disease association data.
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Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.
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PLoS genetics Volume 13 (2017) p.e1006673
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Validation of Structures in the Protein Data Bank.
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Structure (London, England : 1993) Volume 25 (2017) p.1916-1927
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Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.
Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE.
Human mutation Volume 38 (2017) p.1042-1050
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Dual direction CRISPR transcriptional regulation screening uncovers gene networks driving drug resistance.
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Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
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BMC bioinformatics Volume 18 (2017) p.560
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Fifty important research questions in microbial ecology.
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Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.
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Molecular genetics & genomic medicine Volume 5 (2017) p.495-507
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Anna Tramontano 1957-2017.
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Nature structural & molecular biology Volume 24 (2017) p.431-432
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Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.
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Drug repurposing for aging research using model organisms.
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BMJ open Volume 7 (2017) p.e018647
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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
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Understanding enzyme function evolution from a computational perspective.
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Current opinion in structural biology Volume 47 (2017) p.131-139
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Editorial overview: Catalysis and regulation.
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Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
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The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.
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Nucleic acids research Volume 45 (2017) p.D854-D859
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Usage of cell nomenclature in biomedical literature.
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Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.
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Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041
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Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.
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PLoS genetics Volume 13 (2017) p.e1006593
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Uncovering novel repositioning opportunities using the Open Targets platform.
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Drug discovery today Volume 22 (2017) p.1800-1807
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Condensed tannins affect bacterial and fungal microbiomes and mycotoxin production during ensiling and upon aerobic exposure.
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Applied and environmental microbiology Volume (2017) p.
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eLife Volume 6 (2017) p.
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Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.
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Genome research Volume 27 (2017) p.1300-1311
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A novel community driven software for functional enrichment analysis of extracellular vesicles data.
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UniEuk: Time to Speak a Common Language in Protistology!
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The Journal of eukaryotic microbiology Volume 64 (2017) p.407-411
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Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.
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Journal of proteome research Volume 16 (2017) p.1825-1830
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.
Nature biotechnology Volume 35 (2017) p.725-731
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Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.
Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A, Muddyman D, McCarthy S, Hinney A, Hebebrand J, Scott RA, Langenberg C, Wareham NJ, Surendran P, Howson JM, Butterworth AS, Danesh J, Nordestgaard BG, Nielsen SF, Afzal S, Papadia S, Ashford S, Garg S, Millhauser GL, Palomino RI, Kwasniewska A, Tachmazidou I, O'Rahilly S, Zeggini E, Barroso I, Farooqi IS, Understanding Society Scientific Group, EPIC-CVD Consortium, UK10K Consortium.
Scientific reports Volume 7 (2017) p.4394
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A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.
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Yearbook of medical informatics Volume 26 (2017) p.178-187
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MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, MinION Analysis and Reference Consortium.
F1000Research Volume 6 (2017) p.760

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S.
Nature medicine Volume 23 (2017) p.517-525
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Genetic variants regulating expression levels and isoform diversity during embryogenesis.
Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE.
Nature Volume 541 (2017) p.402-406
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A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S.
Nature genetics Volume 49 (2017) p.341-348
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Biochemical Principles and Functional Aspects of Pipecolic Acid Biosynthesis in Plant Immunity.
Hartmann M, Kim D, Bernsdorff F, Ajami-Rashidi Z, Scholten N, Schreiber S, Zeier T, Schuck S, Reichel-Deland V, Zeier J.
Plant physiology Volume 174 (2017) p.124-153
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Promoter shape varies across populations and affects promoter evolution and expression noise.
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Nature genetics Volume 49 (2017) p.550-558
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PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.
Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE.
Nucleic acids research Volume 45 (2017) p.D604-D610
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Prevalence of sexual dimorphism in mammalian phenotypic traits.
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Nature communications Volume 8 (2017) p.15475
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AAgAtlas 1.0: a human autoantigen database.
Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D, Yu X.
Nucleic acids research Volume 45 (2017) p.D769-D776
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Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome.
Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P.
Handbook of experimental pharmacology Volume 240 (2017) p.377-401
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Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
Dolle DD, Liu Z, Cotten M, Simpson JT, Iqbal Z, Durbin R, McCarthy SA, Keane TM.
Genome research Volume 27 (2017) p.300-309
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The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.
Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V.
CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.73-86
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In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.
Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.
Journal of proteomics Volume 150 (2017) p.170-182
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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.
Nucleic acids research Volume 45 (2017) p.D1100-D1106
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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.
Journal of proteome research Volume 16 (2017) p.4288-4298
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Structural Variation Shapes the Landscape of Recombination in Mouse.
Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP.
Genetics Volume 206 (2017) p.603-619
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Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells.
Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM, Jackson SP.
Nature chemical biology Volume 13 (2017) p.12-14
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Corrigendum: High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA.
Nature Volume 551 (2017) p.398
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Comparison, alignment, and synchronization of cell line information between CLO and EFO.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y.
BMC bioinformatics Volume 18 (2017) p.557
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PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ.
Cancer research Volume 77 (2017) p.e62-e66
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A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.
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Nature communications Volume 8 (2017) p.886
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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
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PLoS biology Volume 15 (2017) p.e2001414
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Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.
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Nature genetics Volume 49 (2017) p.1231-1238
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Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.
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The Lancet. Infectious diseases Volume 17 (2017) p.164-173
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Nature Volume 552 (2017) p.96-100
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UniProt Protein Knowledgebase.
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An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.
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Protein engineering, design & selection : PEDS Volume 30 (2017) p.245-251
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From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB.
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The Biochemical journal Volume 474 (2017) p.493-515
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PLoS pathogens Volume 13 (2017) p.e1006755
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A Golden Age for Working with Public Proteomics Data.
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Trends in biochemical sciences Volume 42 (2017) p.333-341
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Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.
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Current protocols in bioinformatics Volume 59 (2017) p.13.31.1-13.31.12
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An "on-matrix" digestion procedure for AP-MS experiments dissects the interplay between complex-conserved and serotype-specific reactivities in Dengue virus-human plasma interactome.
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Nature methods Volume 14 (2017) p.565-571
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BMC genomics Volume 18 (2017) p.904
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Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
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Stem cell reports Volume 9 (2017) p.1898-1915
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Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
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Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
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Cell reports Volume 20 (2017) p.1215-1228
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Accurate and fast feature selection workflow for high-dimensional omics data.
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PloS one Volume 12 (2017) p.e0189875
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Synthetic human proteomes for accelerating protein research.
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Nature methods Volume 14 (2017) p.240-242
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Global open data management in metabolomics.
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Current opinion in chemical biology Volume 36 (2017) p.58-63
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Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
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System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.
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Navigating freely-available software tools for metabolomics analysis.
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mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
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The future of metabolomics in ELIXIR.
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Automated assembly of species metabolomes through data submission into a public repository.
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Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.
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OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
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Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
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A community proposal to integrate proteomics activities in ELIXIR.
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The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
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Molecular & cellular proteomics : MCP Volume 16 (2017) p.1275-1285
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Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
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Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.
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Oncogene Volume 36 (2017) p.2737-2749
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An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
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Genome research Volume 27 (2017) p.885-896
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Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
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Nature Volume 552 (2017) p.239-243
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Alignment of 1000 Genomes Project reads to reference assembly GRCh38.
Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium.
GigaScience Volume 6 (2017) p.1-8
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Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.
Pawlik A, van Gelder CWG, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Goble C.
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ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G.
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BioCIDER: a Contextualisation InDEx for biological Resources discovery.
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Bioinformatics (Oxford, England) Volume 33 (2017) p.2607-2608
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Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data.
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Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
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PLoS computational biology Volume 13 (2017) p.e1005297
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Dead simple OWL design patterns.
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Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
McCarthy DJ, Campbell KR, Lun AT, Wills QF.
Bioinformatics (Oxford, England) Volume 33 (2017) p.1179-1186
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NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.
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Genetic regulatory signatures underlying islet gene expression and type 2 diabetes.
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Proceedings of the National Academy of Sciences of the United States of America Volume 114 (2017) p.2301-2306
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A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data.
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Bioinformatics Volume 33 (2017) p.650-653
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AIM2-Like Receptors Positively and Negatively Regulate the Interferon Response Induced by Cytosolic DNA.
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mBio Volume 8 (2017) p.
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Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated.
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eLife Volume 6 (2017) p.
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f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
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Genome biology Volume 18 (2017) p.212
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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
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Scientific data Volume 4 (2017) p.170179
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Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P.
Bioinformatics (Oxford, England) Volume 33 (2017) p.1845-1851
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New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.
Cern A, Marcus D, Tropsha A, Barenholz Y, Goldblum A.
Journal of controlled release : official journal of the Controlled Release Society Volume 252 (2017) p.18-27
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Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.
Lun ATL, Calero-Nieto FJ, Haim-Vilmovsky L, Göttgens B, Marioni JC.
Genome research Volume 27 (2017) p.1795-1806
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ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD.
Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330
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Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.
Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS.
Genome research Volume 27 (2017) p.1859-1871
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How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
Marioni JC, Arendt D.
Annual review of cell and developmental biology Volume 33 (2017) p.537-553
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Testing for differential abundance in mass cytometry data.
Lun ATL, Richard AC, Marioni JC.
Nature methods Volume 14 (2017) p.707-709
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Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.
Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT.
Nature communications Volume 8 (2017) p.2128
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Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.
Lun ATL, Marioni JC.
Biostatistics (Oxford, England) Volume 18 (2017) p.451-464
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Dynamic landscape and regulation of RNA editing in mammals.
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Nature Volume 550 (2017) p.249-254
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Co-expression networks reveal the tissue-specific regulation of transcription and splicing.
Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium, Engelhardt BE, Battle A.
Genome research Volume 27 (2017) p.1843-1858
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Amino Acid Interaction (INTAA) web server.
Galgonek J, Vymetal J, Jakubec D, Vondrášek J.
Nucleic acids research Volume 45 (2017) p.W388-W392
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Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes.
Stasyuk OA, Jakubec D, Vondrášek J, Hobza P.
Journal of chemical theory and computation Volume 13 (2017) p.877-885
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Aging increases cell-to-cell transcriptional variability upon immune stimulation.
Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT.
Science (New York, N.Y.) Volume 355 (2017) p.1433-1436
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The impact of rare variation on gene expression across tissues.
Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB.
Nature Volume 550 (2017) p.239-243
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Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG.
Nature Volume 550 (2017) p.244-248
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Genetic effects on gene expression across human tissues.
GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB.
Nature Volume 550 (2017) p.204-213
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Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.
Nature biotechnology Volume 35 (2017) p.406-409
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LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.
Sehnal D, Deshpande M, Vařeková RS, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koča J.
Nature methods Volume 14 (2017) p.1121-1122
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DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, Sinha A, Rosenstiel P, Heuschkel R, Stegle O, Zilbauer M.
Gastroenterology Volume (2017) p.
DOI: 10.1053/j.gastro.2017.10.007

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M.
Gut Volume (2017) p.
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Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
Casale FP, Horta D, Rakitsch B, Stegle O.
PLoS genetics Volume 13 (2017) p.e1006693
DOI: 10.1371/journal.pgen.1006693

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.
Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, Moebus S, Pütz B, Hillmer A, Fricker N, Vatter H, Müller-Myhsok B, Nöthen MM, Becker AJ, Hoffmann P, Sander T, Cichon S.
Nature communications Volume 8 (2017) p.1511
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Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ, SpiroMeta Consortium, GoT2D Consortium, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG, arcOGEN Consortium, Understanding Society Scientific Group, UK10K Consortium, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E.
American journal of human genetics Volume 100 (2017) p.865-884
DOI: 10.1016/j.ajhg.2017.04.014

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA.
Science immunology Volume 2 (2017) p.
DOI: 10.1126/sciimmunol.aal2192

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R.
Genetics Volume 205 (2017) p.1425-1441
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Single-cell epigenomics: Recording the past and predicting the future.
Kelsey G, Stegle O, Reik W.
Science (New York, N.Y.) Volume 358 (2017) p.69-75
DOI: 10.1126/science.aan6826

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O, Stegle O.
Genome biology Volume 18 (2017) p.67
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Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.
Martín-Gálvez D, Dunoyer de Segonzac D, Ma MCJ, Kwitek AE, Thybert D, Flicek P.
BMC genomics Volume 18 (2017) p.986
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Applications of the 1000 Genomes Project resources.
Zheng-Bradley X, Flicek P.
Briefings in functional genomics Volume 16 (2017) p.163-170
DOI: 10.1093/bfgp/elw027

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.
Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C.
Nucleic acids research Volume 45 (2017) p.D517-D528
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The Gene Ontology of eukaryotic cilia and flagella.
Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J.
Cilia Volume 6 (2017) p.10
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PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J.
Structure (London, England : 1993) Volume 25 (2017) p.1317-1318
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Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ.
Proteins Volume 85 (2017) p.359-377
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The challenge of modeling protein assemblies: The CASP12-CAPRI experiment.
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ.
Proteins Volume (2017) p.
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easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.
Grimm DG, Roqueiro D, Salomé PA, Kleeberger S, Greshake B, Zhu W, Liu C, Lippert C, Stegle O, Schölkopf B, Weigel D, Borgwardt KM.
The Plant cell Volume 29 (2017) p.5-19
DOI: 10.1105/tpc.16.00551

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A.
Cell Volume 169 (2017) p.807-823.e19
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The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A.
Bioinformatics (Oxford, England) Volume 33 (2017) p.2218-2220
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Orchestrating differential data access for translational research: a pilot implementation.
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U.
BMC medical informatics and decision making Volume 17 (2017) p.30
DOI: 10.1186/s12911-017-0424-6

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.
Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y.
Scientific reports Volume 7 (2017) p.44876
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Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.
Cell reports Volume 20 (2017) p.2201-2214
DOI: 10.1016/j.celrep.2017.08.010

Short template switch events explain mutation clusters in the human genome.
Löytynoja A, Goldman N.
Genome research Volume 27 (2017) p.1039-1049
DOI: 10.1101/gr.214973.116

Genetic Variation in the Social Environment Contributes to Health and Disease.
Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O.
PLoS genetics Volume 13 (2017) p.e1006498
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Identifying genes for neurobehavioural traits in rodents: progress and pitfalls.
Baud A, Flint J.
Disease models & mechanisms Volume 10 (2017) p.373-383
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Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO.
Cell reports Volume 20 (2017) p.1229-1241
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clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A.
Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003
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Bridging the translational innovation gap through good biomarker practice.
van Gool AJ, Bietrix F, Caldenhoven E, Zatloukal K, Scherer A, Litton JE, Meijer G, Blomberg N, Smith A, Mons B, Heringa J, Koot WJ, Smit MJ, Hajduch M, Rijnders T, Ussi A.
Nature reviews. Drug discovery Volume 16 (2017) p.587-588
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General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J.
F1000Research Volume 6 (2017) p.273
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Two independent modes of chromatin organization revealed by cohesin removal.
Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, H Haering C, Mirny L, Spitz F.
Nature Volume 551 (2017) p.51-56
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Prediction of Protein Kinase-Ligand Interactions through 2.5D Kinochemometrics.
Bosc N, Wroblowski B, Meyer C, Bonnet P.
Journal of chemical information and modeling Volume 57 (2017) p.93-101
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The use of novel selectivity metrics in kinase research.
Bosc N, Meyer C, Bonnet P.
BMC bioinformatics Volume 18 (2017) p.17
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The EBI search engine: EBI search as a service-making biological data accessible for all.
Park YM, Squizzato S, Buso N, Gur T, Lopez R.
Nucleic acids research Volume 45 (2017) p.W545-W549
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Privileged Substructures to Modulate Protein-Protein Interactions.
Bosc N, Kuenemann MA, Bécot J, Vavrusa M, Cerdan AH, Sperandio O.
Journal of chemical information and modeling Volume 57 (2017) p.2448-2462
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Application of a Dot Blot Hybridization Platform to Assess Streptococcus uberis Population Structure in Dairy Herds.
Albuquerque P, Ribeiro N, Almeida A, Panschin I, Porfirio A, Vales M, Diniz F, Madeira H, Tavares F.
Frontiers in microbiology Volume 8 (2017) p.54
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Parallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations.
Almeida A, Rosinski-Chupin I, Plainvert C, Douarre PE, Borrego MJ, Poyart C, Glaser P.
mSystems Volume 2 (2017) p.
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Assessment of protein assembly prediction in CASP12.
Lafita A, Bliven S, Kryshtafovych A, Bertoni M, Monastyrskyy B, Duarte JM, Schwede T, Capitani G.
Proteins Volume (2017) p.
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Biological and functional relevance of CASP predictions.
Liu T, Ish-Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB.
Proteins Volume (2017) p.
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Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.
Pearson WR, Li W, Lopez R.
Nucleic acids research Volume 45 (2017) p.e46
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The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR.
Nature methods Volume 14 (2017) p.775-781
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Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features.
Carapito R, Konantz M, Paillard C, Miao Z, Pichot A, Leduc MS, Yang Y, Bergstrom KL, Mahoney DH, Shardy DL, Alsaleh G, Naegely L, Kolmer A, Paul N, Hanauer A, Rolli V, Müller JS, Alghisi E, Sauteur L, Macquin C, Morlon A, Sancho CS, Amati-Bonneau P, Procaccio V, Mosca-Boidron AL, Marle N, Osmani N, Lefebvre O, Goetz JG, Unal S, Akarsu NA, Radosavljevic M, Chenard MP, Rialland F, Grain A, Béné MC, Eveillard M, Vincent M, Guy J, Faivre L, Thauvin-Robinet C, Thevenon J, Myers K, Fleming MD, Shimamura A, Bottollier-Lemallaz E, Westhof E, Lengerke C, Isidor B, Bahram S.
The Journal of clinical investigation Volume 127 (2017) p.4090-4103
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Assessing Public Metabolomics Metadata, Towards Improving Quality.
Ferreira JD, Inácio B, Salek RM, Couto FM.
Journal of integrative bioinformatics Volume 14 (2017) p.
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The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.
Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL.
Analytical chemistry Volume 89 (2017) p.4474-4479
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UniProt: the universal protein knowledgebase.
The UniProt Consortium.
Nucleic acids research Volume 45 (2017) p.D158-D169
DOI: 10.1093/nar/gkw1099

Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells.
Penaud-Budloo M, Lecomte E, Guy-Duché A, Saleun S, Roulet A, Lopez-Roques C, Tournaire B, Cogné B, Léger A, Blouin V, Lindenbaum P, Moullier P, Ayuso E.
Human gene therapy methods Volume 28 (2017) p.148-162
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RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
Miao Z, Adamiak RW, Antczak M, Batey RT, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E.
RNA (New York, N.Y.) Volume 23 (2017) p.655-672
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The ProFunc Function Prediction Server.
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Methods in molecular biology (Clifton, N.J.) Volume 1611 (2017) p.75-95
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OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.
Structure (London, England : 1993) Volume 25 (2017) p.536-545
DOI: 10.1016/j.str.2017.01.004

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ.
Nature Volume 546 (2017) p.686
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The human-induced pluripotent stem cell initiative-data resources for cellular genetics.
Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium, Flicek P, Parkinson H, Clarke L.
Nucleic acids research Volume 45 (2017) p.D691-D697
DOI: 10.1093/nar/gkw928

Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.
De Sousa PA, Steeg R, Wachter E, Bruce K, King J, Hoeve M, Khadun S, McConnachie G, Holder J, Kurtz A, Seltmann S, Dewender J, Reimann S, Stacey G, O'Shea O, Chapman C, Healy L, Zimmermann H, Bolton B, Rawat T, Atkin I, Veiga A, Kuebler B, Serano BM, Saric T, Hescheler J, Brüstle O, Peitz M, Thiele C, Geijsen N, Holst B, Clausen C, Lako M, Armstrong L, Gupta SK, Kvist AJ, Hicks R, Jonebring A, Brolén G, Ebneth A, Cabrera-Socorro A, Foerch P, Geraerts M, Stummann TC, Harmon S, George C, Streeter I, Clarke L, Parkinson H, Harrison PW, Faulconbridge A, Cherubin L, Burdett T, Trigueros C, Patel MJ, Lucas C, Hardy B, Predan R, Dokler J, Brajnik M, Keminer O, Pless O, Gribbon P, Claussen C, Ringwald A, Kreisel B, Courtney A, Allsopp TE.
Stem cell research Volume 20 (2017) p.105-114
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Common genetic variation drives molecular heterogeneity in human iPSCs.
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Nature Volume 546 (2017) p.370-375
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Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P.
Database : the journal of biological databases and curation Volume 2017 (2017) p.
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Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.
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Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples.
Votintseva AA, Bradley P, Pankhurst L, Del Ojo Elias C, Loose M, Nilgiriwala K, Chatterjee A, Smith EG, Sanderson N, Walker TM, Morgan MR, Wyllie DH, Walker AS, Peto TEA, Crook DW, Iqbal Z.
Journal of clinical microbiology Volume 55 (2017) p.1285-1298
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RNA Structure: Advances and Assessment of 3D Structure Prediction.
Miao Z, Westhof E.
Annual review of biophysics Volume 46 (2017) p.483-503
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RNAcentral: a comprehensive database of non-coding RNA sequences.
The RNAcentral Consortium.
Nucleic acids research Volume 45 (2017) p.D128-D134
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The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G.
GigaScience Volume 6 (2017) p.1-11
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ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services.
Robertsen EM, Denise H, Mitchell A, Finn RD, Bongo LA, Willassen NP.
F1000Research Volume 6 (2017) p.
DOI: 10.12688/f1000research.10443.1

Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP.
Journal of the American Medical Informatics Association : JAMIA Volume 24 (2017) p.799-805
DOI: 10.1093/jamia/ocw167

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.
Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E.
Genome biology Volume 18 (2017) p.50
DOI: 10.1186/s13059-017-1173-7

Data management: A global coalition to sustain core data.
Anderson WP, Global Life Science Data Resources Working Group.
Nature Volume 543 (2017) p.179
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The yeast noncoding RNA interaction network.
Panni S, Prakash A, Bateman A, Orchard S.
RNA (New York, N.Y.) Volume 23 (2017) p.1479-1492
DOI: 10.1261/rna.060996.117

Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG.
The Journal of experimental medicine Volume 214 (2017) p.1111-1128
DOI: 10.1084/jem.20161382

InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL.
Nucleic acids research Volume 45 (2017) p.D190-D199
DOI: 10.1093/nar/gkw1107

Ensembl 2017.
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P.
Nucleic acids research Volume 45 (2017) p.D635-D642
DOI: 10.1093/nar/gkw1104

Structure and dynamics of the insulin receptor: implications for receptor activation and drug discovery.
Ye L, Maji S, Sanghera N, Gopalasingam P, Gorbunov E, Tarasov S, Epstein O, Klein-Seetharaman J.
Drug discovery today Volume 22 (2017) p.1092-1102
DOI: 10.1016/j.drudis.2017.04.011

The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD.
Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23
DOI: 10.1002/cpbi.40

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, UniProt Consortium T.
Bioinformatics (Oxford, England) Volume 33 (2017) p.3454-3460
DOI: 10.1093/bioinformatics/btx439

Structure of the Escherichia coli ProQ RNA-binding protein.
Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW.
RNA (New York, N.Y.) Volume 23 (2017) p.696-711
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More on the Best Evolutionary Rate for Phylogenetic Analysis.
Klopfstein S, Massingham T, Goldman N.
Systematic biology Volume 66 (2017) p.769-785
DOI: 10.1093/sysbio/syx051

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.
Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, de Groot NG, Flicek P, Bontrop RE, Hammond JA, Marsh SG.
Nucleic acids research Volume 45 (2017) p.D860-D864
DOI: 10.1093/nar/gkw1050

Reevaluation of SNP heritability in complex human traits.
Speed D, Cai N, UCLEB Consortium, Johnson MR, Nejentsev S, Balding DJ.
Nature genetics Volume 49 (2017) p.986-992
DOI: 10.1038/ng.3865

Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development.
Gialitakis M, Tolaini M, Li Y, Pardo M, Yu L, Toribio A, Choudhary JS, Niakan K, Papayannopoulos V, Stockinger B.
Stem cell reports Volume 9 (2017) p.1377-1386
DOI: 10.1016/j.stemcr.2017.09.025

11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project.
Cai N, Bigdeli TB, Kretzschmar WW, Li Y, Liang J, Hu J, Peterson RE, Bacanu S, Webb BT, Riley B, Li Q, Marchini J, Mott R, Kendler KS, Flint J.
Scientific data Volume 4 (2017) p.170011
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High-Throughput Mapping and Clonal Quantification of Retroviral Integration Sites.
Gillet NA, Melamed A, Bangham CR.
Methods in molecular biology (Clifton, N.J.) Volume 1582 (2017) p.127-141
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PGBD5 promotes site-specific oncogenic mutations in human tumors.
Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A.
Nature genetics Volume 49 (2017) p.1005-1014
DOI: 10.1038/ng.3866

European Nucleotide Archive in 2016.
Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 45 (2017) p.D32-D36
DOI: 10.1093/nar/gkw1106

Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation.
Zhyvoloup A, Melamed A, Anderson I, Planas D, Lee CH, Kriston-Vizi J, Ketteler R, Merritt A, Routy JP, Ancuta P, Bangham CRM, Fassati A.
PLoS pathogens Volume 13 (2017) p.e1006460
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The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.
Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS.
JAMA psychiatry Volume 74 (2017) p.162-168
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The impact of HTLV-1 on the cellular genome.
Cook L, Melamed A, Yaguchi H, Bangham CR.
Current opinion in virology Volume 26 (2017) p.125-131
DOI: 10.1016/j.coviro.2017.07.013

2016

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.
Miao Z, Westhof E.
Nucleic acids research Volume 44 (2016) p.W562-7
DOI: 10.1093/nar/gkw251

Quantifying side-chain conformational variations in protein structure.
Miao Z, Cao Y.
Scientific Reports Volume 6 (2016) p.37024
DOI: 10.1038/srep37024

HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S.
Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195
DOI: 10.1093/bioinformatics/btw224

First Draft Genome Sequence of a UK Strain (UK99) of Fusarium culmorum.
Urban M, King R, Andongabo A, Maheswari U, Pedro H, Kersey P, Hammond-Kosack K.
Genome announcements Volume 4 (2016) p.
DOI: 10.1128/genomea.00771-16

Towards an open grapevine information system.
Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H.
Horticulture research Volume 3 (2016) p.16056

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Lun AT, Bach K, Marioni JC.
Genome biology Volume 17 (2016) p.75
DOI: 10.1186/s13059-016-0947-7

PhytoPath: an integrative resource for plant pathogen genomics.
Pedro H, Maheswari U, Urban M, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ.
Nucleic acids research Volume 44 (2016) p.D688-93
DOI: 10.1093/nar/gkv1052

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT.
PLoS genetics Volume 12 (2016) p.e1006024
DOI: 10.1371/journal.pgen.1006024

Tools and data services registry: a community effort to document bioinformatics resources.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.
Nucleic acids research Volume 44 (2016) p.D38-47
DOI: 10.1093/nar/gkv1116

Biocuration of functional annotation at the European nucleotide archive.
Gibson R, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Pallreddy S, Pakseresht N, Rajan J, Rosselló M, Silvester N, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 44 (2016) p.D58-66
DOI: 10.1093/nar/gkv1311

A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies.
Turro E, Greene D, Wijgaerts A, Thys C, Lentaigne C, Bariana TK, Westbury SK, Kelly AM, Selleslag D, Stephens JC, Papadia S, Simeoni I, Penkett CJ, Ashford S, Attwood A, Austin S, Bakchoul T, Collins P, Deevi SV, Favier R, Kostadima M, Lambert MP, Mathias M, Millar CM, Peerlinck K, Perry DJ, Schulman S, Whitehorn D, Wittevrongel C, BRIDGE-BPD Consortium, De Maeyer M, Rendon A, Gomez K, Erber WN, Mumford AD, Nurden P, Stirrups K, Bradley JR, Raymond FL, Laffan MA, Van Geet C, Richardson S, Freson K, Ouwehand WH.
Science translational medicine Volume 8 (2016) p.328ra30
DOI: 10.1126/scitranslmed.aad7666

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.
Bolser D, Staines DM, Pritchard E, Kersey P.
Methods in molecular biology (Clifton, N.J.) Volume 1374 (2016) p.115-140
DOI: 10.1007/978-1-4939-3167-5_6

GENOMICS. A federated ecosystem for sharing genomic, clinical data.
Global Alliance for Genomics and Health.
Science (New York, N.Y.) Volume 352 (2016) p.1278-1280
DOI: 10.1126/science.aaf6162

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.
Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD.
Nucleic acids research Volume 44 (2016) p.D604-9
DOI: 10.1093/nar/gkv1216

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.
Sangrador-Vegas A, Mitchell AL, Chang HY, Yong SY, Finn RD.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
DOI: 10.1093/database/baw027

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.
Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Hide W, Ibrahimi A, Jaufeerally Fakim Y, Jongeneel CV, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Mansour Alzohairy A, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N, H3ABioNet Consortium.
Genome research Volume 26 (2016) p.271-277
DOI: 10.1101/gr.196295.115

Genetic and Environmental Risk for Chronic Pain and the Contribution of Risk Variants for Major Depressive Disorder: A Family-Based Mixed-Model Analysis.
McIntosh AM, Hall LS, Zeng Y, Adams MJ, Gibson J, Wigmore E, Hagenaars SP, Davies G, Fernandez-Pujals AM, Campbell AI, Clarke TK, Hayward C, Haley CS, Porteous DJ, Deary IJ, Smith DJ, Nicholl BI, Hinds DA, Jones AV, Scollen S, Meng W, Smith BH, Hocking LJ.
PLoS medicine Volume 13 (2016) p.e1002090
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Value, but high costs in post-deposition data curation.
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Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Measures for interoperability of phenotypic data: minimum information requirements and formatting.
Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone SA, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P.
Plant methods Volume 12 (2016) p.44
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EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data.
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Nucleic acids research Volume 44 (2016) p.D595-603
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Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.
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BMC bioinformatics Volume 17 (2016) p.400
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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
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Journal of biomedical semantics Volume 7 (2016) p.44
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A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.
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Blood Volume 127 (2016) p.2791-2803
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PhenoImageShare: an image annotation and query infrastructure.
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Resolving early mesoderm diversification through single-cell expression profiling.
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Nature Volume 535 (2016) p.289-293
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Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
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Cell reports Volume 14 (2016) p.1246-1257
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Guidelines for the functional annotation of microRNAs using the Gene Ontology.
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RNA (New York, N.Y.) Volume 22 (2016) p.667-676
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The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1.
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Development (Cambridge, England) Volume 143 (2016) p.851-863
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The Evolutionary Fates of a Large Segmental Duplication in Mouse.
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Structure of bacterial respiratory complex I.
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Biochimica et biophysica acta Volume 1857 (2016) p.892-901
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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
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Cell Volume 167 (2016) p.1398-1414.e24
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The BLUEPRINT Data Analysis Portal.
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Cell systems Volume 3 (2016) p.491-495.e5
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An atlas of human kinase regulation.
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Molecular systems biology Volume 12 (2016) p.888
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Evolution of protein phosphorylation across 18 fungal species.
Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J.
Science (New York, N.Y.) Volume 354 (2016) p.229-232
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M.
Open biology Volume 6 (2016) p.160009
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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.
Cell Volume 167 (2016) p.1369-1384.e19
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The Ensembl Variant Effect Predictor.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.
Genome biology Volume 17 (2016) p.122
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CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M.
Genome biology Volume 17 (2016) p.127
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UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.
Doğan T, MacDougall A, Saidi R, Poggioli D, Bateman A, O'Donovan C, Martin MJ.
Bioinformatics (Oxford, England) Volume 32 (2016) p.2264-2271
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Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C.
Nature genetics Volume 48 (2016) p.593-599
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Ensembl regulation resources.
Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, Brent S, Amode R, Parker A, Trevanion S, Birney E, Dunham I, Flicek P.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.
Wagih O, Sugiyama N, Ishihama Y, Beltrao P.
Molecular & cellular proteomics : MCP Volume 15 (2016) p.236-245
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Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803.
Hollingshead S, Kopečná J, Armstrong DR, Bučinská L, Jackson PJ, Chen GE, Dickman MJ, Williamson MP, Sobotka R, Hunter CN.
Frontiers in plant science Volume 7 (2016) p.292
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Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.
Jupp S, Burdett T, Welter D, Sarntivijai S, Parkinson H, Malone J.
Journal of biomedical semantics Volume 7 (2016) p.17
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The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
Stunnenberg HG, International Human Epigenome Consortium, Hirst M.
Cell Volume 167 (2016) p.1145-1149
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Corrigendum: 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 7 (2016) p.10415
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
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Genome biology Volume 17 (2016) p.70
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Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.
Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C.
Nature Volume 537 (2016) p.544-547
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Extending gene ontology in the context of extracellular RNA and vesicle communication.
Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC.
Journal of biomedical semantics Volume 7 (2016) p.19
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Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.
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Oncotarget Volume 7 (2016) p.6693-6710
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Data standards can boost metabolomics research, and if there is a will, there is a way.
Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S.
Metabolomics : Official journal of the Metabolomic Society Volume 12 (2016) p.14
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The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.
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Progress in lipid research Volume 61 (2016) p.30-39
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Logical Modeling and Dynamical Analysis of Cellular Networks.
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.
Frontiers in genetics Volume 7 (2016) p.94
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Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR.
Oncotarget Volume 7 (2016) p.15648-15661
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LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.
Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC, Lagomorph Genomics Consortium.
The Journal of heredity Volume 107 (2016) p.295-308
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ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
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Journal of cheminformatics Volume 8 (2016) p.61

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.
Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS.
Journal of proteome research Volume 15 (2016) p.360-373
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Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.
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Drug discovery today Volume 21 (2016) p.1063-1075
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Effects of Pin1 Loss in Hdh(Q111) Knock-in Mice.
Agostoni E, Michelazzi S, Maurutto M, Carnemolla A, Ciani Y, Vatta P, Roncaglia P, Zucchelli S, Leanza G, Mantovani F, Gustincich S, Santoro C, Piazza S, Del Sal G, Persichetti F.
Frontiers in cellular neuroscience Volume 10 (2016) p.110
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Crowdsourcing biomedical research: leveraging communities as innovation engines.
Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G.
Nature reviews. Genetics Volume 17 (2016) p.470-486
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CHRONICITY OF DEPRESSION AND MOLECULAR MARKERS IN A LARGE SAMPLE OF HAN CHINESE WOMEN.
Edwards AC, Aggen SH, Cai N, Bigdeli TB, Peterson RE, Docherty AR, Webb BT, Bacanu SA, Flint J, Kendler KS.
Depression and anxiety Volume (2016) p.
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Looking beyond the cancer cell for effective drug combinations.
Dry JR, Yang M, Saez-Rodriguez J.
Genome medicine Volume 8 (2016) p.125
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OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
Türei D, Korcsmáros T, Saez-Rodriguez J.
Nature methods Volume 13 (2016) p.966-967
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Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A.
Science advances Volume 2 (2016) p.e1601017
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A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.
Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J, Overington JP.
Journal of biomedical semantics Volume 7 (2016) p.59

Efficient randomization of biological networks while preserving functional characterization of individual nodes.
Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J.
BMC bioinformatics Volume 17 (2016) p.542
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Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
Meng D, Dubin M, Zhang P, Osborne EJ, Stegle O, Clark RM, Nordborg M.
PLoS genetics Volume 12 (2016) p.e1006141
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Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA.
Science (New York, N.Y.) Volume 354 (2016) p.751-757
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A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C.
BMC bioinformatics Volume 17 (2016) p.155
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Circular RNA enrichment in platelets is a signature of transcriptome degradation.
Alhasan AA, Izuogu OG, Al-Balool HH, Steyn JS, Evans A, Colzani M, Ghevaert C, Mountford JC, Marenah L, Elliott DJ, Santibanez-Koref M, Jackson MS.
Blood Volume 127 (2016) p.e1-e11
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PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.
Izuogu OG, Alhasan AA, Alafghani HM, Santibanez-Koref M, Elliott DJ, Jackson MS.
BMC bioinformatics Volume 17 (2016) p.31
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A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.
Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K.
Cell reports Volume 17 (2016) p.1193-1205
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The Time Is Right to Focus on Model Organism Metabolomes.
Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR.
Metabolites Volume 6 (2016) p.
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An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.
Genome biology Volume 17 (2016) p.184
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Making sense of big data in health research: Towards an EU action plan.
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Genome medicine Volume 8 (2016) p.71
DOI: 10.1186/s13073-016-0323-y

Genome-wide association analysis of pain severity in dysmenorrhea identifies association at chromosome 1p13.2, near the nerve growth factor locus.
Jones AV, Hockley JR, Hyde C, Gorman D, Sredic-Rhodes A, Bilsland J, McMurray G, Furlotte NA, Hu Y, Hinds DA, Cox PJ, Scollen S.
Pain Volume 157 (2016) p.2571-2581
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A gain-of-function variant in DIAPH1 causes dominant macrothrombocytopenia and hearing loss.
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Blood Volume 127 (2016) p.2903-2914
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Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.
Neely BA, Wilkins CE, Marlow LA, Malyarenko D, Kim Y, Ignatchenko A, Sasinowska H, Sasinowski M, Nyalwidhe JO, Kislinger T, Copland JA, Drake RR.
PloS one Volume 11 (2016) p.e0154074
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Erratum to: Making sense of big data in health research: towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.
Genome medicine Volume 8 (2016) p.118
DOI: 10.1186/s13073-016-0376-y

Ten Simple Rules for Taking Advantage of Git and GitHub.
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.
PLoS computational biology Volume 12 (2016) p.e1004947
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Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.
Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI.
Cancer cell Volume 30 (2016) p.806-821
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Overview of the interactive task in BioCreative V.
Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M.
Cell Volume 165 (2016) p.61-74
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Integration of EGA secure data access into Galaxy.
Hoogstrate Y, Zhang C, Senf A, Bijlard J, Hiltemann S, van Enckevort D, Repo S, Heringa J, Jenster G, J A Fijneman R, Boiten JW, A Meijer G, Stubbs A, Rambla J, Spalding D, Abeln S.
F1000Research Volume 5 (2016) p.
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Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.
Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V.
Journal of proteome research Volume 15 (2016) p.4101-4115
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Exploring the potential of public proteomics data.
Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H.
Proteomics Volume 16 (2016) p.214-225
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SPLASH, a hashed identifier for mass spectra.
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O.
Nature biotechnology Volume 34 (2016) p.1099-1101
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MetaboLights: An Open-Access Database Repository for Metabolomics Data.
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C.
Current protocols in bioinformatics Volume 53 (2016) p.14.13.1-18
DOI: 10.1002/0471250953.bi1413s53

Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM.
Bioinformatics (Oxford, England) Volume 32 (2016) p.2065-2066
DOI: 10.1093/bioinformatics/btw096

A Landscape of Pharmacogenomic Interactions in Cancer.
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ.
Cell Volume 166 (2016) p.740-754
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Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.
Nature methods Volume 13 (2016) p.310-318
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Old knowledge and new technologies allow rapid development of model organisms.
Cook CE, Chenevert J, Larsson TA, Arendt D, Houliston E, Lénárt P.
Molecular biology of the cell Volume 27 (2016) p.882-887
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A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice.
McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G, Mott R, Flint J, Adams DJ.
G3 (Bethesda, Md.) Volume 6 (2016) p.2343-2354
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Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.
Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E.
MedChemComm Volume 7 (2016) p.1237-1244
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Identifying ELIXIR Core Data Resources.
Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A.
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The European Bioinformatics Institute in 2016: Data growth and integration.
Cook CE, Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R.
Nucleic acids research Volume 44 (2016) p.D20-6
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Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.
Rensch T, Villar D, Horvath J, Odom DT, Flicek P.
Genome biology Volume 17 (2016) p.139
DOI: 10.1186/s13059-016-0996-y

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
Lun AT, McCarthy DJ, Marioni JC.
F1000Research Volume 5 (2016) p.2122

The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.
PloS one Volume 11 (2016) p.e0154556
DOI: 10.1371/journal.pone.0154556

High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KC, McKerlie C, Beaudet AL, Bućan M, Murray SA.
Nature Volume 537 (2016) p.508-514
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Focus on Extracellular Vesicles: Physiological Role and Signalling Properties of Extracellular Membrane Vesicles.
Iraci N, Leonardi T, Gessler F, Vega B, Pluchino S.
International journal of molecular sciences Volume 17 (2016) p.171
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.
Nature Volume 534 (2016) p.47-54
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Computational clustering for viral reference proteomes.
Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH, UniProt Consortium.
Bioinformatics Volume 32 (2016) p.2041-2043
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T Cell Receptor Vβ Staining Identifies the Malignant Clone in Adult T cell Leukemia and Reveals Killing of Leukemia Cells by Autologous CD8+ T cells.
Rowan AG, Witkover A, Melamed A, Tanaka Y, Cook LB, Fields P, Taylor GP, Bangham CR.
PLoS pathogens Volume 12 (2016) p.e1006030
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Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells.
Rattay K, Meyer HV, Herrmann C, Brors B, Kyewski B.
Journal of autoimmunity Volume 67 (2016) p.65-75
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Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
Jakubec D, Laskowski RA, Vondrasek J.
PloS one Volume 11 (2016) p.e0158704
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FFPred 3: feature-based function prediction for all Gene Ontology domains.
Cozzetto D, Minneci F, Currant H, Jones DT.
Scientific reports Volume 6 (2016) p.31865
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Rising levels of atmospheric oxygen and evolution of Nrf2.
Gacesa R, Dunlap WC, Barlow DJ, Laskowski RA, Long PF.
Scientific reports Volume 6 (2016) p.27740
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General control non-derepressible 2 (GCN2) in T cells controls disease progression of autoimmune neuroinflammation.
Keil M, Sonner JK, Lanz TV, Oezen I, Bunse T, Bittner S, Meyer HV, Meuth SG, Wick W, Platten M.
Journal of neuroimmunology Volume 297 (2016) p.117-126
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Reporting phenotypes in mouse models when considering body size as a potential confounder.
Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK, Karp NA.
Journal of biomedical semantics Volume 7 (2016) p.2
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UniProt Tools.
Pundir S, Martin MJ, O'Donovan C, UniProt Consortium.
Current protocols in bioinformatics Volume 53 (2016) p.1.29.1-15
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ISMB 2016 Proceedings.
Baldi P, Przytycka T.
Bioinformatics (Oxford, England) Volume 32 (2016) p.i1-i2
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The UniProtKB guide to the human proteome.
Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.
Nature methods Volume 13 (2016) p.425-430
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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.
Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS.
Journal of proteome research Volume 15 (2016) p.3961-3970
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Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA.
Nature methods Volume 13 (2016) p.651-656
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2016 update of the PRIDE database and its related tools.
Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.
Nucleic acids research Volume 44 (2016) p.D447-56
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Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.
Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM, de Villena FP.
G3 (Bethesda, Md.) Volume 6 (2016) p.4211-4216
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Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations.
Doran AG, Wong K, Flint J, Adams DJ, Hunter KW, Keane TM.
Genome biology Volume 17 (2016) p.167
DOI: 10.1186/s13059-016-1024-y

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.
Molecular & cellular proteomics : MCP Volume 15 (2016) p.305-317
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Consolidating and Exploring Antibiotic Resistance Gene Data Resources.
Xavier BB, Das AJ, Cochrane G, De Ganck S, Kumar-Singh S, Aarestrup FM, Goossens H, Malhotra-Kumar S.
Journal of clinical microbiology Volume 54 (2016) p.851-859
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Plant specimen contextual data consensus.
Hoopen PT, Walls RL, Cannon EK, Cochrane G, Cole J, Johnston A, Karsch-Mizrachi I, Yilmaz P.
GigaScience Volume 5 (2016) p.1-4
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Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability.
Schiffthaler B, Kostadima M, NGS Trainer Consortium, Delhomme N, Rustici G.
PLoS computational biology Volume 12 (2016) p.e1004937
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BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.
Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS.
Nucleic acids research Volume 44 (2016) p.W416-23
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Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements.
Kohl A, Pondeville E, Schnettler E, Crisanti A, Supparo C, Christophides GK, Kersey PJ, Maslen GL, Takken W, Koenraadt CJ, Oliva CF, Busquets N, Abad FX, Failloux AB, Levashina EA, Wilson AJ, Veronesi E, Pichard M, Arnaud Marsh S, Simard F, Vernick KD.
Pathogens and global health Volume 110 (2016) p.164-172
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The Mighty Fruit Fly Moves into Outbred Genetics.
Birney E.
PLoS genetics Volume 12 (2016) p.e1006388
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The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome.
Satou Y, Miyazato P, Ishihara K, Yaguchi H, Melamed A, Miura M, Fukuda A, Nosaka K, Watanabe T, Rowan AG, Nakao M, Bangham CR.
Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.3054-3059
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Genome wide association analysis of the heart using high-resolution 3D cardiac MRI identifies new genetic loci underlying cardiac structure and function.
Marvao Ad, Meyer HV, Dawes TJ, Shi W, Bai W, Rueckert D, Birney E, O'Regan DP, Cook S.
Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance Volume 18 (2016) p.

The EMBL-EBI channel.
McEntyre J, Birney E.
F1000Research Volume 5 (2016) p.52
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The topography of mutational processes in breast cancer genomes.
Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S.
Nature communications Volume 7 (2016) p.11383
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eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.
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Cell reports Volume 17 (2016) p.2137-2150
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Epigenome-wide Association Studies and the Interpretation of Disease -Omics.
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PLoS genetics Volume 12 (2016) p.e1006105
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PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
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WormBase 2016: expanding to enable helminth genomic research.
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Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
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The archiving and dissemination of biological structure data.
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Current opinion in structural biology Volume 40 (2016) p.17-22
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libChEBI: an API for accessing the ChEBI database.
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Journal of cheminformatics Volume 8 (2016) p.11
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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
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Structure (London, England : 1993) Volume 24 (2016) p.502-508
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ChEBI in 2016: Improved services and an expanding collection of metabolites.
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Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, Martin S, Davies HR, Debets R, Gelder ME, van Deurzen CH, MacGrogan G, Van den Eynden GG, Purdie C, Thompson AM, Caldas C, Span PN, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Ringnér M, Tommasi S, Eyford J, Broeks A, Vincent-Salomon A, Futreal PA, Knappskog S, King T, Thomas G, Viari A, Langerød A, Børresen-Dale AL, Birney E, Stunnenberg HG, Stratton M, Foekens JA, Martens JW.
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Resolution of ab initio shapes determined from small-angle scattering.
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EMPIAR: a public archive for raw electron microscopy image data.
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Nature methods Volume 13 (2016) p.387-388
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Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles.
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Cell chemical biology Volume 23 (2016) p.1103-1112
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Testing and Validation of Computational Methods for Mass Spectrometry.
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Journal of proteome research Volume 15 (2016) p.809-814
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Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.
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Human molecular genetics Volume 25 (2016) p.927-935
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Metadata management for high content screening in OMERO.
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The cellular microscopy phenotype ontology.
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Journal of biomedical semantics Volume 7 (2016) p.28
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Consent Codes: Upholding Standard Data Use Conditions.
Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, Fiume M, Sherry ST.
PLoS genetics Volume 12 (2016) p.e1005772
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Genomic epidemiology of artemisinin resistant malaria.
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Characterising Complex Enzyme Reaction Data.
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Exploring the chemistry and evolution of the isomerases.
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Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.1796-1801
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ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C.
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Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.
Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA.
Journal of molecular biology Volume 428 (2016) p.3131-3146
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CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.
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Bioinformatics Volume 32 (2016) p.2511-2513
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Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.
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Journal of molecular biology Volume 428 (2016) p.253-267
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Admixture into and within sub-Saharan Africa.
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Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.
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Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
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Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains.
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The genetic architecture of type 2 diabetes.
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Nature Volume 536 (2016) p.41-47
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Classification of low quality cells from single-cell RNA-seq data.
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Genome biology Volume 17 (2016) p.29
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A high-content platform to characterise human induced pluripotent stem cell lines.
Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A, Stegle O, Kielty CM, HipSci Consortium, Durbin R, Watt FM, Danovi D.
Methods (San Diego, Calif.) Volume 96 (2016) p.85-96
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CPEB and miR-15/16 Co-Regulate Translation of Cyclin E1 mRNA during Xenopus Oocyte Maturation.
Wilczynska A, Git A, Argasinska J, Belloc E, Standart N.
PloS one Volume 11 (2016) p.e0146792
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The pig X and Y Chromosomes: structure, sequence, and evolution.
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Genome research Volume 26 (2016) p.130-139
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De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma.
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Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.
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Genome biology and evolution Volume 8 (2016) p.1233-1242
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Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
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The genetic regulatory signature of type 2 diabetes in human skeletal muscle.
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Letter to the editor for "Update of the human and mouse Fanconi anemia genes".
Nebert DW, Dong H, Bruford EA, Thompson DC, Joenje H, Vasiliou V.
Human genomics Volume 10 (2016) p.25
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Organization, evolution and functions of the human and mouse Ly6/uPAR family genes.
Loughner CL, Bruford EA, McAndrews MS, Delp EE, Swamynathan S, Swamynathan SK.
Human genomics Volume 10 (2016) p.10
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Infection Susceptibility in Gastric Intrinsic Factor (Vitamin B12)-Defective Mice Is Subject to Maternal Influences.
Mottram L, Speak AO, Selek RM, Cambridge EL, McIntyre Z, Kane L, Mukhopadhyay S, Grove C, Colin A, Brandt C, Duque-Correa MA, Forbester J, Nguyen TA, Hale C, Vasilliou GS, Arends MJ, Wren BW, Dougan G, Clare S.
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The ORFeome Collaboration: a genome-scale human ORF-clone resource.
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Genomic Classification and Prognosis in Acute Myeloid Leukemia.
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The New England journal of medicine Volume 374 (2016) p.2209-2221
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Editorial: Metabolome Informatics and Statistics: Current State and Emerging Trends.
Carroll AJ, Salek RM, Arita M, Kopka J, Walther D.
Frontiers in bioengineering and biotechnology Volume 4 (2016) p.63
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FlyBase portals to human disease research using Drosophila models.
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Disease models & mechanisms Volume 9 (2016) p.245-252
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The Dfam database of repetitive DNA families.
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Nucleic acids research Volume 44 (2016) p.D81-9
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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.
Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB.
PLoS computational biology Volume 12 (2016) p.e1004862
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Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.
Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y.
Bioinformatics (Oxford, England) Volume 32 (2016) p.821-827
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BiologicalWeb services: Integration, optimization, and reasoning
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CEUR workshop proceedings Volume (2016) p.21-27
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2016 update of the PRIDE database and its related tools.
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Nucleic acids research Volume 44 (2016) p.11033
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Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Finn R.
Nucleic acids research Volume 44 (2016) p.D343-50
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Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics.
Harper AL, McKinney LV, Nielsen LR, Havlickova L, Li Y, Trick M, Fraser F, Wang L, Fellgett A, Sollars ES, Janacek SH, Downie JA, Buggs RJ, Kjær ED, Bancroft I.
Scientific reports Volume 6 (2016) p.19335
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Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R.
Genome biology Volume 17 (2016) p.32
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The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A.
Nucleic acids research Volume 44 (2016) p.D279-85
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Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting.
Kalman LV, Agúndez J, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Caudle K, Coulthard SA, Daly AK, Del Tredici A, den Dunnen JT, Drozda K, Everts RE, Flockhart D, Freimuth RR, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale RF, van Schaik R, Whirl-Carrillo M, Yeo K, Zanger UM.
Clinical pharmacology and therapeutics Volume 99 (2016) p.172-185
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A review of the new HGNC gene family resource.
Gray KA, Seal RL, Tweedie S, Wright MW, Bruford EA.
Human genomics Volume 10 (2016) p.6
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The genome of Onchocerca volvulus, agent of river blindness.
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S.
Nature microbiology Volume 2 (2016) p.16216
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Selenoprotein Gene Nomenclature.
Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y.
The Journal of biological chemistry Volume 291 (2016) p.24036-24040
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RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H.
Leukemia Volume 30 (2016) p.2282
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Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.
Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR.
Drug safety Volume 39 (2016) p.697-707
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Rapid dissemination of human T-lymphotropic virus type 1 during primary infection in transplant recipients.
Cook LB, Melamed A, Demontis MA, Laydon DJ, Fox JM, Tosswill JH, de Freitas D, Price AD, Medcalf JF, Martin F, Neuberger JM, Bangham CR, Taylor GP.
Retrovirology Volume 13 (2016) p.3
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Retroviruses integrate into a shared, non-palindromic DNA motif.
Kirk PD, Huvet M, Melamed A, Maertens GN, Bangham CR.
Nature microbiology Volume 2 (2016) p.16212
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Ensembl 2016.
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P.
Nucleic acids research Volume 44 (2016) p.D710-6
DOI: 10.1093/nar/gkv1157

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.
Venkatesan A, Kim JH, Talo F, Ide-Smith M, Gobeill J, Carter J, Batista-Navarro R, Ananiadou S, Ruch P, McEntyre J.
Wellcome open research Volume 1 (2016) p.25
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Top 10 metrics for life science software good practices.
Artaza H, Chue Hong N, Corpas M, Corpuz A, Hooft R, Jimenez RC, Leskošek B, Olivier BG, Stourac J, Svobodová Vařeková R, Van Parys T, Vaughan D.
F1000Research Volume 5 (2016) p.
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JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
Nucleic acids research Volume 44 (2016) p.W320-7
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Sirtuin 1 stimulates the proliferation and the expression of glycolysis genes in pancreatic neoplastic lesions.
Pinho AV, Mawson A, Gill A, Arshi M, Warmerdam M, Giry-Laterriere M, Eling N, Lie T, Kuster E, Camargo S, Biankin AV, Wu J, Rooman I.
Oncotarget Volume 7 (2016) p.74768-74778
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Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.
Truszkowski J, Goldman N.
Systematic biology Volume 65 (2016) p.328-333
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Impaired removal of H3K4 methylation affects cell fate determination and gene transcription.
Lussi YC, Mariani L, Friis C, Peltonen J, Myers TR, Krag C, Wong G, Salcini AE.
Development (Cambridge, England) Volume 143 (2016) p.3751-3762
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The FAIR Guiding Principles for scientific data management and stewardship.
Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.
Scientific data Volume 3 (2016) p.160018
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The Ensembl gene annotation system.
Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SM.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.
Pancsa R, Varadi M, Tompa P, Vranken WF.
Nucleic acids research Volume 44 (2016) p.D429-34
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An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway.
Robertson KA, Hsieh WY, Forster T, Blanc M, Lu H, Crick PJ, Yutuc E, Watterson S, Martin K, Griffiths SJ, Enright AJ, Yamamoto M, Pradeepa MM, Lennox KA, Behlke MA, Talbot S, Haas J, Dölken L, Griffiths WJ, Wang Y, Angulo A, Ghazal P.
PLoS biology Volume 14 (2016) p.e1002364
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HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.
Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ.
Journal of proteome research Volume 15 (2016) p.2072-2079
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Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.
Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ.
F1000Research Volume 5 (2016) p.1745

Divergence in gene expression within and between two closely related flycatcher species.
Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H.
Molecular ecology Volume 25 (2016) p.2015-2028
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ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N.
Nucleic acids research Volume 44 (2016) p.e77
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Mixed Nodule Infection in Sinorhizobium meliloti-Medicago sativa Symbiosis Suggest the Presence of Cheating Behavior.
Checcucci A, Azzarello E, Bazzicalupo M, Galardini M, Lagomarsino A, Mancuso S, Marti L, Marzano MC, Mocali S, Squartini A, Zanardo M, Mengoni A.
Frontiers in plant science Volume 7 (2016) p.835
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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH.
Nature genetics Volume 48 (2016) p.427-437
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COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.
Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K.
Nucleic acids research Volume 44 (2016) p.D620-3
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Population-level analysis of gut microbiome variation.
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.
Science (New York, N.Y.) Volume 352 (2016) p.560-564
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Gramene Database: Navigating Plant Comparative Genomics Resources.
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P.
Current plant biology Volume 7-8 (2016) p.10-15
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GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.
Greenfield DL, Stegle O, Rrustemi A.
Bioinformatics (Oxford, England) Volume 32 (2016) p.3124-3132
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ProbOnto: ontology and knowledge base of probability distributions.
Swat MJ, Grenon P, Wimalaratne S.
Bioinformatics (Oxford, England) Volume 32 (2016) p.2719-2721
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Deep learning for computational biology.
Angermueller C, Pärnamaa T, Parts L, Stegle O.
Molecular systems biology Volume 12 (2016) p.878
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Blood lipids influence DNA methylation in circulating cells.
Dekkers KF, van Iterson M, Slieker RC, Moed MH, Bonder MJ, van Galen M, Mei H, Zhernakova DV, van den Berg LH, Deelen J, van Dongen J, van Heemst D, Hofman A, Hottenga JJ, van der Kallen CJ, Schalkwijk CG, Stehouwer CD, Tigchelaar EF, Uitterlinden AG, Willemsen G, Zhernakova A, Franke L, 't Hoen PA, Jansen R, van Meurs J, Boomsma DI, van Duijn CM, van Greevenbroek MM, Veldink JH, Wijmenga C, BIOS Consortium, van Zwet EW, Slagboom PE, Jukema JW, Heijmans BT.
Genome biology Volume 17 (2016) p.138
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Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.
Nicod J, Davies RW, Cai N, Hassett C, Goodstadt L, Cosgrove C, Yee BK, Lionikaite V, McIntyre RE, Remme CA, Lodder EM, Gregory JS, Hough T, Joynson R, Phelps H, Nell B, Rowe C, Wood J, Walling A, Bopp N, Bhomra A, Hernandez-Pliego P, Callebert J, Aspden RM, Talbot NP, Robbins PA, Harrison M, Fray M, Launay JM, Pinto YM, Blizard DA, Bezzina CR, Adams DJ, Franken P, Weaver T, Wells S, Brown SD, Potter PK, Klenerman P, Lionikas A, Mott R, Flint J.
Nature genetics Volume 48 (2016) p.912-918
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Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W.
Nature methods Volume 13 (2016) p.229-232
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Association between DNA Methylation in Whole Blood and Measures of Glucose Metabolism: KORA F4 Study.
Kriebel J, Herder C, Rathmann W, Wahl S, Kunze S, Molnos S, Volkova N, Schramm K, Carstensen-Kirberg M, Waldenberger M, Gieger C, Peters A, Illig T, Prokisch H, Roden M, Grallert H.
PloS one Volume 11 (2016) p.e0152314
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The effect of host genetics on the gut microbiome.
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A.
Nature genetics Volume 48 (2016) p.1407-1412
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SureChEMBL: a large-scale, chemically annotated patent document database.
Papadatos G, Davies M, Dedman N, Chambers J, Gaulton A, Siddle J, Koks R, Irvine SA, Pettersson J, Goncharoff N, Hersey A, Overington JP.
Nucleic acids research Volume 44 (2016) p.D1220-8
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Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia.
Vallée F, Luciani A, Cox MP.
Genetics Volume 204 (2016) p.1495-1506
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Subtype-specific micro-RNA expression signatures in breast cancer progression.
Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å.
International journal of cancer Volume 139 (2016) p.1117-1128
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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.
Proteins Volume 84 Suppl 1 (2016) p.323-348
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Proton pump inhibitors affect the gut microbiome.
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A.
Gut Volume 65 (2016) p.740-748
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Evidence for mitochondrial genetic control of autosomal gene expression.
Kassam I, Qi T, Lloyd-Jones L, Holloway A, Jan Bonder M, Henders AK, Martin NG, Powell JE, Franke L, Montgomery GW, Visscher PM, McRae AF.
Human molecular genetics Volume 25 (2016) p.5332-5338
DOI: 10.1093/hmg/ddw347

GWAS for executive function and processing speed suggests involvement of the CADM2 gene.
Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann R, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia S, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp R, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Generation Scotland, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen A, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH.
Molecular psychiatry Volume 21 (2016) p.189-197
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From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
DOI: 10.1093/database/baw055

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.
Nucleic acids research Volume 44 (2016) p.D746-52
DOI: 10.1093/nar/gkv1045

The influence of a short-term gluten-free diet on the human gut microbiome.
Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y, Zhernakova A.
Genome medicine Volume 8 (2016) p.45
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Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.
Kenyan Bacteraemia Study Group, Wellcome Trust Case Control Consortium 2 (WTCCC2), Rautanen A, Pirinen M, Mills TC, Rockett KA, Strange A, Ndungu AW, Naranbhai V, Gilchrist JJ, Bellenguez C, Freeman C, Band G, Bumpstead SJ, Edkins S, Giannoulatou E, Gray E, Dronov S, Hunt SE, Langford C, Pearson RD, Su Z, Vukcevic D, Macharia AW, Uyoga S, Ndila C, Mturi N, Njuguna P, Mohammed S, Berkley JA, Mwangi I, Mwarumba S, Kitsao BS, Lowe BS, Morpeth SC, Khandwalla I, Kilifi Bacteraemia Surveillance Group, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CNA, Plomin R, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Deloukas P, Peltonen L, Williams TN, Scott JAG, Chapman SJ, Donnelly P, Hill AVS, Spencer CCA.
American journal of human genetics Volume 98 (2016) p.1092-1100
DOI: 10.1016/j.ajhg.2016.03.025

Exploring regulatory networks of miR-96 in the developing inner ear.
Lewis MA, Buniello A, Hilton JM, Zhu F, Zhang WI, Evans S, van Dongen S, Enright AJ, Steel KP.
Scientific reports Volume 6 (2016) p.23363
DOI: 10.1038/srep23363

Activation of the TGFβ pathway impairs endothelial to haematopoietic transition.
Vargel Ö, Zhang Y, Kosim K, Ganter K, Foehr S, Mardenborough Y, Shvartsman M, Enright AJ, Krijgsveld J, Lancrin C.
Scientific reports Volume 6 (2016) p.21518
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Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
Slieker RC, van Iterson M, Luijk R, Beekman M, Zhernakova DV, Moed MH, Mei H, van Galen M, Deelen P, Bonder MJ, Zhernakova A, Uitterlinden AG, Tigchelaar EF, Stehouwer CD, Schalkwijk CG, van der Kallen CJ, Hofman A, van Heemst D, de Geus EJ, van Dongen J, Deelen J, van den Berg LH, van Meurs J, Jansen R, 't Hoen PA, Franke L, Wijmenga C, Veldink JH, Swertz MA, van Greevenbroek MM, van Duijn CM, Boomsma DI, BIOS consortium, Slagboom PE, Heijmans BT.
Genome biology Volume 17 (2016) p.191

Single-cell technologies to study the immune system.
Proserpio V, Mahata B.
Immunology Volume 147 (2016) p.133-140
DOI: 10.1111/imm.12553

Minimizing proteome redundancy in the UniProt Knowledgebase.
Bursteinas B, Britto R, Bely B, Auchincloss A, Rivoire C, Redaschi N, O'Donovan C, Martin MJ.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
DOI: 10.1093/database/baw139

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.
Cell Volume 167 (2016) p.1125-1136.e8
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Genome-wide analysis identifies 12 loci influencing human reproductive behavior.
Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A, BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC, LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC.
Nature genetics Volume 48 (2016) p.1462-1472
DOI: 10.1038/ng.3698

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M.
Scientific reports Volume 6 (2016) p.32406
DOI: 10.1038/srep32406

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.
Nature communications Volume 7 (2016) p.11778
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transPLANT Resources for Triticeae Genomic Data.
Spannagl M, Alaux M, Lange M, Bolser DM, Bader KC, Letellier T, Kimmel E, Flores R, Pommier C, Kerhornou A, Walts B, Nussbaumer T, Grabmuller C, Chen J, Colmsee C, Beier S, Mascher M, Schmutzer T, Arend D, Thanki A, Ramirez-Gonzalez R, Ayling M, Ayling S, Caccamo M, Mayer KF, Scholz U, Steinbach D, Quesneville H, Kersey PJ.
The plant genome Volume 9 (2016) p.
DOI: 10.3835/plantgenome2015.06.0038

Ensembl Genomes 2016: more genomes, more complexity.
Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM.
Nucleic acids research Volume 44 (2016) p.D574-80
DOI: 10.1093/nar/gkv1209

Gut microbiota composition associated with stool consistency.
Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A.
Gut Volume 65 (2016) p.540-542
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Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.
Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT.
eLife Volume 5 (2016) p.
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HMGB1 binds to the rs7903146 locus in TCF7L2 in human pancreatic islets.
Zhou Y, Oskolkov N, Shcherbina L, Ratti J, Kock KH, Su J, Martin B, Oskolkova MZ, Göransson O, Bacon J, Li W, Bucciarelli S, Cilio C, Brazma A, Thatcher B, Rung J, Wierup N, Renström E, Groop L, Hansson O.
Molecular and cellular endocrinology Volume 430 (2016) p.138-145
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Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution.
Fernández-Sampedro MA, Invergo BM, Ramon E, Bertranpetit J, Garriga P.
Scientific reports Volume 6 (2016) p.21570
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Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.
Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, Otto TD, Keane JA.
Microbial Genomics Volume 2 (2016) p.e000083
DOI: 10.1099/mgen.0.000083

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.
Nucleic acids research Volume 44 (2016) p.W176-80
DOI: 10.1093/nar/gkw443

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.
Cell Volume 167 (2016) p.1897
DOI: 10.1016/j.cell.2016.11.046

MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.
Bioinformatics Volume 32 (2016) p.1905-1906
DOI: 10.1093/bioinformatics/btw056

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.
diCenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, Finan TM, Galardini M, Fondi M.
Nature communications Volume 7 (2016) p.12219
DOI: 10.1038/ncomms12219

NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.
Mendoza-Parra MA, Saleem MA, Blum M, Cholley PE, Gronemeyer H.
Methods in molecular biology (Clifton, N.J.) Volume 1418 (2016) p.243-265
DOI: 10.1007/978-1-4939-3578-9_13

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.
Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD.
Nature communications Volume 7 (2016) p.13555
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Clustering Genes of Common Evolutionary History.
Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C.
Molecular biology and evolution Volume 33 (2016) p.1590-1605
DOI: 10.1093/molbev/msw038

Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
Ricaño-Ponce I, Zhernakova DV, Deelen P, Luo O, Li X, Isaacs A, Karjalainen J, Di Tommaso J, Borek ZA, Zorro MM, Gutierrez-Achury J, Uitterlinden AG, Hofman A, van Meurs J, BIOS Consortium, Lifelines Cohort Study, Netea MG, Jonkers IH, Withoff S, van Duijn CM, Li Y, Ruan Y, Franke L, Wijmenga C, Kumar V.
Journal of autoimmunity Volume 68 (2016) p.62-74
DOI: 10.1016/j.jaut.2016.01.002

The Degradation Pathway of the Mitophagy Receptor Atg32 Is Re-Routed by a Posttranslational Modification.
Levchenko M, Lorenzi I, Dudek J.
PloS one Volume 11 (2016) p.e0168518
DOI: 10.1371/journal.pone.0168518

Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Rakitsch B, Stegle O.
Genome biology Volume 17 (2016) p.33
DOI: 10.1186/s13059-016-0895-2

GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes.
Tuggle CK, Giuffra E, White SN, Clarke L, Zhou H, Ross PJ, Acloque H, Reecy JM, Archibald A, Bellone RR, Boichard M, Chamberlain A, Cheng H, Crooijmans RP, Delany ME, Finno CJ, Groenen MA, Hayes B, Lunney JK, Petersen JL, Plastow GS, Schmidt CJ, Song J, Watson M.
Animal genetics Volume 47 (2016) p.528-533
DOI: 10.1111/age.12466

Sudden Cardiac Arrest and Rare Genetic Variants in the Community.
Milano A, Blom MT, Lodder EM, van Hoeijen DA, Barc J, Koopmann TT, Bardai A, Beekman L, Lichtner P, van den Berg MP, Wilde AA, Bezzina CR, Tan HL.
Circulation. Cardiovascular genetics Volume 9 (2016) p.147-153
DOI: 10.1161/circgenetics.115.001263

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T.
PLoS computational biology Volume 12 (2016) p.e1004943
DOI: 10.1371/journal.pcbi.1004943

Modelling-based experiment retrieval: a case study with gene expression clustering.
Blomstedt P, Dutta R, Seth S, Brazma A, Kaski S.
Bioinformatics (Oxford, England) Volume 32 (2016) p.1388-1394
DOI: 10.1093/bioinformatics/btv762

A multiple-phenotype imputation method for genetic studies.
Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J.
Nature genetics Volume 48 (2016) p.466-472
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Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.
Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R.
Biophysical journal Volume 110 (2016) p.372-381
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PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.
Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FS.
Nucleic acids research Volume 44 (2016) p.D663-8
DOI: 10.1093/nar/gkv1271

Gramene 2016: comparative plant genomics and pathway resources.
Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.
Nucleic acids research Volume 44 (2016) p.D1133-40
DOI: 10.1093/nar/gkv1179

ncRNA orthologies in the vertebrate lineage.
Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J.
Database : the journal of biological databases and curation Volume 2016 (2016) p.
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Genetic and environmental influences interact with age and sex in shaping the human methylome.
van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S, BIOS Consortium, Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI.
Nature communications Volume 7 (2016) p.11115
DOI: 10.1038/ncomms11115

Tobacco smoking is associated with DNA methylation of diabetes susceptibility genes.
Ligthart S, Steenaard RV, Peters MJ, van Meurs JB, Sijbrands EJ, Uitterlinden AG, Bonder MJ, BIOS consortium, Hofman A, Franco OH, Dehghan A.
Diabetologia Volume 59 (2016) p.998-1006
DOI: 10.1007/s00125-016-3872-0

A multicenter study benchmarks software tools for label-free proteome quantification.
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.
Nature biotechnology Volume 34 (2016) p.1130-1136
DOI: 10.1038/nbt.3685

Ten Simple Rules for Selecting a Bio-ontology.
Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C.
PLoS computational biology Volume 12 (2016) p.e1004743
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Databases and Archiving for CryoEM.
Patwardhan A, Lawson CL.
Methods in enzymology Volume 579 (2016) p.393-412
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Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins.
Huerta V, Ramos Y, Yero A, Pupo D, Martín D, Toledo P, Fleitas N, Gallien S, Martín AM, Márquez GJ, Pérez-Riverol Y, Sarría M, Guirola O, González LJ, Domon B, Chinea G.
Journal of proteomics Volume 131 (2016) p.205-213
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Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.
Rouhani FJ, Nik-Zainal S, Wuster A, Li Y, Conte N, Koike-Yusa H, Kumasaka N, Vallier L, Yusa K, Bradley A.
PLoS genetics Volume 12 (2016) p.e1005932
DOI: 10.1371/journal.pgen.1005932

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD).
Sousa SF, Sousa JF, Barbosa AC, Ferreira CE, Neves RP, Ribeiro AJ, Fernandes PA, Ramos MJ.
The journal of physical chemistry. A Volume 120 (2016) p.5300-5306
DOI: 10.1021/acs.jpca.6b01536

EMDataBank unified data resource for 3DEM.
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W.
Nucleic acids research Volume 44 (2016) p.D396-403
DOI: 10.1093/nar/gkv1126

Improved definition of the mouse transcriptome via targeted RNA sequencing.
Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ.
Genome research Volume 26 (2016) p.705-716
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The MIntAct Project and Molecular Interaction Databases.
Licata L, Orchard S.
Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.55-69
DOI: 10.1007/978-1-4939-3572-7_3

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.
Science (New York, N.Y.) Volume 352 (2016) p.565-569
DOI: 10.1126/science.aad3369

The Reactome pathway Knowledgebase.
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.
Nucleic acids research Volume 44 (2016) p.D481-7
DOI: 10.1093/nar/gkv1351

Antibody performance in ChIP-sequencing assays: From quality scores of public data sets to quantitative certification.
Mendoza-Parra MA, Saravaki V, Cholley PE, Blum M, Billoré B, Gronemeyer H.
F1000Research Volume 5 (2016) p.54
DOI: 10.12688/f1000research.7637.2

The health care and life sciences community profile for dataset descriptions.
Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A.
PeerJ Volume 4 (2016) p.e2331
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Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A.
PloS one Volume 11 (2016) p.e0157484
DOI: 10.1371/journal.pone.0157484

Cox26 is a novel stoichiometric subunit of the yeast cytochrome c oxidase.
Levchenko M, Wuttke JM, Römpler K, Schmidt B, Neifer K, Juris L, Wissel M, Rehling P, Deckers M.
Biochimica et biophysica acta Volume 1863 (2016) p.1624-1632
DOI: 10.1016/j.bbamcr.2016.04.007

Promiscuous or discriminating: Has the favored mRNA target of Fragile X Mental Retardation Protein been overlooked?
McMahon AC, Rosbash M.
Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.7009-7011
DOI: 10.1073/pnas.1607665113

HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015).
Oliveira EF, Santos-Martins D, Ribeiro AM, Brás NF, Cerqueira NS, Sousa SF, Ramos MJ, Fernandes PA.
Expert opinion on therapeutic patents Volume 26 (2016) p.1257-1272
DOI: 10.1080/13543776.2016.1216977

LOGIQA: a database dedicated to long-range genome interactions quality assessment.
Mendoza-Parra MA, Blum M, Malysheva V, Cholley PE, Gronemeyer H.
BMC genomics Volume 17 (2016) p.355
DOI: 10.1186/s12864-016-2642-1

Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.
Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S.
Cell reports Volume 17 (2016) p.2101-2111
DOI: 10.1016/j.celrep.2016.10.054

The Electron Microscopy eXchange (EMX) initiative.
Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM.
Journal of structural biology Volume 194 (2016) p.156-163
DOI: 10.1016/j.jsb.2016.02.008

Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining.
Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V.
PloS one Volume 11 (2016) p.e0158896
DOI: 10.1371/journal.pone.0158896

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins.
McMahon AC, Rahman R, Jin H, Shen JL, Fieldsend A, Luo W, Rosbash M.
Cell Volume 165 (2016) p.742-753
DOI: 10.1016/j.cell.2016.03.007

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.
Foulger RE, Denny P, Hardy J, Martin MJ, Sawford T, Lovering RC.
Neuroinformatics Volume 14 (2016) p.297-304
DOI: 10.1007/s12021-015-9293-2

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance.
Novakovic B, Habibi E, Wang SY, Arts RJW, Davar R, Megchelenbrink W, Kim B, Kuznetsova T, Kox M, Zwaag J, Matarese F, van Heeringen SJ, Janssen-Megens EM, Sharifi N, Wang C, Keramati F, Schoonenberg V, Flicek P, Clarke L, Pickkers P, Heath S, Gut I, Netea MG, Martens JHA, Logie C, Stunnenberg HG.
Cell Volume 167 (2016) p.1354-1368.e14
DOI: 10.1016/j.cell.2016.09.034

2015

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
DOI: 10.1016/j.jprot.2015.05.024

Preface. Bacterial pangenomics.
Mengoni A, Fondi M, Galardini M.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.v-vi
DOI: 10.1007/978-1-4939-1720-4

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
DOI: 10.1007/978-1-4939-1720-4_7

Proteins: interaction at a distance.
Laskowski RA, Thornton JM.
IUCrJ Volume 2 (2015) p.609-610
DOI: 10.1107/s2052252515020217

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.
DOI: 10.1128/mbio.00352-15

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
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Subclonal diversification of primary breast cancer revealed by multiregion sequencing.
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diXa: a data infrastructure for chemical safety assessment.
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Bioinformatics (Oxford, England) Volume 31 (2015) p.1505-1507
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The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.
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Briefings in bioinformatics Volume 16 (2015) p.865-872
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ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.
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Systematic biology Volume 64 (2015) p.42-55
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Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.
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Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E99-100
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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.
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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
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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
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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
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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
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Data integration in biological research: an overview.
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Journal of biological research (Thessalonike, Greece) Volume 22 (2015) p.9
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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
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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
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UniProt: a hub for protein information.
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Nucleic acids research Volume 43 (2015) p.D204-12
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Longevity GWAS Using the Drosophila Genetic Reference Panel.
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The journals of gerontology. Series A, Biological sciences and medical sciences Volume 70 (2015) p.1470-1478
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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.
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The Classification and Evolution of Enzyme Function.
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Biophysical journal Volume 109 (2015) p.1082-1086
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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
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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
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Gene Ontology Consortium: going forward.
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Nucleic acids research Volume 43 (2015) p.D1049-56
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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
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Devising a Consensus Framework for Validation of Novel Human Coding Loci.
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Journal of proteome research Volume 14 (2015) p.4945-4948
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The new science of ageing.
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Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 370 (2015) p.
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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
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The BioStudies database.
McEntyre J, Sarkans U, Brazma A.
Molecular systems biology Volume 11 (2015) p.847
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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
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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
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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
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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
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Mapping contigs using CONTIGuator.
Galardini M, Mengoni A, Bazzicalupo M.
Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.163-176
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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
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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
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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
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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
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Cancer evolution: mathematical models and computational inference.
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.
Systematic biology Volume 64 (2015) p.e1-25
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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
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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
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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
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What you need to know to make the most of big data in biology.
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Lancet (London, England) Volume 385 Suppl 1 (2015) p.S5-6
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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
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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
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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
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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
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VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D.
Nucleic acids research Volume 43 (2015) p.D707-13
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Expression data analysis with Reactome.
Jupe S, Fabregat A, Hermjakob H.
Current protocols in bioinformatics Volume 49 (2015) p.8.20.1-9
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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
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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
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ISMB/ECCB 2015.
Moreau Y, Beerenwinkel N.
Bioinformatics Volume 31 (2015) p.i1-2
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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
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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
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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
DOI: 10.2390/biecoll-jib-2015-266

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
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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
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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 Volume 31 (2015) p.1337-1339
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
DOI: 10.1128/mcb.00773-14

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
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INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.
INFRAFRONTIER Consortium.
Nucleic acids research Volume 43 (2015) p.D1171-5
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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
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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
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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
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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
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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
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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
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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
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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
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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
DOI: 10.1186/s13326-015-0003-7

Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease.
Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JA, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJ, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJ, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA.
Science translational medicine Volume 7 (2015) p.270ra6
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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
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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
DOI: 10.1038/ng.3202

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
DOI: 10.1371/journal.pgen.1005177

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
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Using human genetics to make new medicines.
Barrett JC, Dunham I, Birney E.
Nature reviews. Genetics Volume 16 (2015) p.561-562
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Human genomics: The end of the start for population sequencing.
Birney E, Soranzo N.
Nature Volume 526 (2015) p.52-53
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Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.
Louis A, Nguyen NT, Muffato M, Roest Crollius H.
Nucleic acids research Volume 43 (2015) p.D682-9
DOI: 10.1093/nar/gku1112

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
DOI: 10.1016/s2352-3026(15)00152-0

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
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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
DOI: 10.1093/bioinformatics/btv376

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
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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
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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
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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
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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
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Europe PMC: a full-text literature database for the life sciences and platform for innovation.
Europe PMC Consortium.
Nucleic acids research Volume 43 (2015) p.D1042-8
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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
DOI: 10.12688/f1000research.7201.1

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
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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
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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
DOI: 10.1038/ncomms6681

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
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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
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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
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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
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ISMB/ECCB 2015 Proceedings Papers Committee.

Bioinformatics Volume 31 (2015) p.i3-i8

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
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Proteomics data visualisation.
Vizcaíno JA, Barsnes H, Hermjakob H.
Proteomics Volume 15 (2015) p.1339-1340
DOI: 10.1002/pmic.201570063

Shared resources, shared costs--leveraging biocuration resources.
Orchard S, Hermjakob H.
Database : the journal of biological databases and curation Volume 2015 (2015) p.
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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
DOI: 10.1093/nar/gkv382

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
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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
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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
DOI: 10.1038/ng.3437

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
DOI: 10.1371/journal.pone.0144176

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
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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
DOI: 10.1038/nature14962

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
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Chimira: analysis of small RNA sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3365-3367
DOI: 10.1093/bioinformatics/btv380

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
DOI: 10.1371/journal.pone.0117581

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
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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
DOI: 10.1093/nar/gku944

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
DOI: 10.1186/1471-2164-16-s8-s2

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
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Nomenclature of Toso, Fas apoptosis inhibitory molecule 3, and IgM FcR.
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Journal of immunology (Baltimore, Md. : 1950) Volume 194 (2015) p.4055-4057
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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
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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
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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
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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.
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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
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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
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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
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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
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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
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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
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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.
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The cardiovascular gene annotation initiative: Impact on data analysis
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Atherosclerosis Volume 241 (2015) p.e37
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High-density P300 enhancers control cell state transitions.
Witte S, Bradley A, Enright AJ, Muljo SA.
BMC genomics Volume 16 (2015) p.903
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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
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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
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Open source libraries and frameworks for biological data visualisation: a guide for developers.
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Proteomics Volume 15 (2015) p.1356-1374
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Identifying novel biomarkers through data mining-a realistic scenario?
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Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.
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CPT: pharmacometrics & systems pharmacology Volume 4 (2015) p.316-319
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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
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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
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Getting the right answers: understanding metabolomics challenges.
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Expert review of molecular diagnostics Volume 15 (2015) p.97-109
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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
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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
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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
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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
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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
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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
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Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P.
Plant & cell physiology Volume 56 (2015) p.e3
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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
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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
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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
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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
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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
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The IPD and IMGT/HLA database: allele variant databases.
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Nucleic acids research Volume 43 (2015) p.D423-31
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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
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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
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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
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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
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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
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Diverse phenotypic consequences of mutations affecting the C-terminus of FLNA.
van Kogelenberg M, Clark AR, Jenkins Z, Morgan T, Anandan A, Sawyer GM, Edwards M, Dudding T, Homfray T, Castle B, Tolmie J, Stewart F, Kivuva E, Pilz DT, Gabbett M, Sutherland-Smith AJ, Robertson SP.
Journal of molecular medicine (Berlin, Germany) Volume 93 (2015) p.773-782
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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
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The Protein Ensemble Database.
Varadi M, Tompa P.
Advances in experimental medicine and biology Volume 870 (2015) p.335-349
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC.
Nature reviews. Genetics Volume 16 (2015) p.133-145
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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
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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
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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
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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
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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
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Palmitoylation and palmitoyl-transferases in Plasmodium parasites.
Hodson N, Invergo B, Rayner JC, Choudhary JS.
Biochemical Society transactions Volume 43 (2015) p.240-245
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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
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Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
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PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.
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Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
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An atlas of mouse CD4(+) T cell transcriptomes.
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Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
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Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
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Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.
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Computational proteomics: Integrating mass spectral data into a biological context.
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Journal of proteomics Volume 129 (2015) p.1-2
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Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism.
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PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.
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Nature Volume 528 (2015) p.84-87
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A single-cell model of PIP3 dynamics using chemical dimerization.
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Bioorganic & medicinal chemistry Volume 23 (2015) p.2868-2876
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Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
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ChEMBL web services: streamlining access to drug discovery data and utilities.
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Nucleic acids research Volume 43 (2015) p.W612-20
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Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
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Bioinformatics (Oxford, England) Volume 31 (2015) p.2999-3007
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GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.
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PLoS computational biology Volume 11 (2015) p.e1004143
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Activity, assay and target data curation and quality in the ChEMBL database.
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Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.
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An integrated map of structural variation in 2,504 human genomes.
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Nature Volume 526 (2015) p.75-81
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Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
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Genome biology Volume 16 (2015) p.57
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The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
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Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
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Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2015) p.342-346

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
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Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
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PloS one Volume 10 (2015) p.e0137206
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Computational approaches for inferring the functions of intrinsically disordered proteins.
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Frontiers in molecular biosciences Volume 2 (2015) p.45
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COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
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Metabolomics : Official journal of the Metabolomic Society Volume 11 (2015) p.1587-1597
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Europe: Lifelong learning for all in biomedicine.
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Nature Volume 524 (2015) p.415
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Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
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Frontiers in genetics Volume 6 (2015) p.107
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Chemical databases: curation or integration by user-defined equivalence?
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Drug discovery today. Technologies Volume 14 (2015) p.17-24
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Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
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BMC genomics Volume 16 (2015) p.982
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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, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B.
Genome research Volume 25 (2015) p.41-56
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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
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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.
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BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
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SpeckTackle: JavaScript charts for spectroscopy.
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Third Report on Chicken Genes and Chromosomes 2015.
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Roary: rapid large-scale prokaryote pan genome analysis.
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Bioinformatics (Oxford, England) Volume 31 (2015) p.3691-3693
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Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.
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Multiple sclerosis (Houndmills, Basingstoke, England) Volume 21 (2015) p.138-146
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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
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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, 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.
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Operon and non-operon gene clusters in the C. elegans genome.
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WormBook : the online review of C. elegans biology Volume (2015) p.1-20
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Updates in Rhea--a manually curated resource of biochemical reactions.
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Nucleic acids research Volume 43 (2015) p.D459-64
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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
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Empirical inference of circuitry and plasticity in a kinase signaling network.
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Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.7719-7724
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eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
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Modeling Signaling Networks to Advance New Cancer Therapies.
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Annual review of biomedical engineering Volume 17 (2015) p.143-163
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Integrative approaches for signalling and metabolic networks.
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Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.844-845
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A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
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PloS one Volume 10 (2015) p.e0139446
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Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
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Designing Experiments to Discriminate Families of Logic Models.
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Frontiers in bioengineering and biotechnology Volume 3 (2015) p.131
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The ensembl regulatory build.
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Genome biology Volume 16 (2015) p.56
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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.
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The Importance of Biological Databases in Biological Discovery.
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Current protocols in bioinformatics Volume 50 (2015) p.1.1.1-8
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Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.
Twigg SR, Forecki J, Goos JA, Richardson IC, Hoogeboom AJ, van den Ouweland AM, Swagemakers SM, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA, WGS500 Consortium, van der Spek PJ, Mathijssen IM, Pauws E, Merzdorf CS, Wilkie AO.
American journal of human genetics Volume 97 (2015) p.378-388
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Kinase-two-hybrid: towards the conditional interactome.
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Molecular systems biology Volume 11 (2015) p.798
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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
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Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.
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Molecular biology and evolution Volume 32 (2015) p.2646-2656
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Collaborative computational project for electron cryo-microscopy.
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Acta crystallographica. Section D, Biological crystallography Volume 71 (2015) p.123-126
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Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation.
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Genetics Volume 201 (2015) p.587-598
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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.
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Domain atrophy creates rare cases of functional partial protein domains.
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Identification of artesunate as a specific activator of ferroptosis in pancreatic cancer cells.
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Oncoscience Volume 2 (2015) p.517-532

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.
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HMMER web server: 2015 update.
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Nucleic acids research Volume 43 (2015) p.W30-8
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RNAcentral: an international database of ncRNA sequences.
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Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
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Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314
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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
DOI: 10.2174/1568009615666150512102957

Towards the computational design of protein post-translational regulation.
Strumillo M, Beltrao P.
Bioorganic & medicinal chemistry Volume 23 (2015) p.2877-2882
DOI: 10.1016/j.bmc.2015.04.056

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
DOI: 10.1371/journal.pcbi.1003972

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
DOI: 10.1016/j.stemcr.2015.09.013

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
DOI: 10.1101/gr.180240.114

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
DOI: 10.15252/msb.20145606

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
DOI: 10.1038/ng.3291

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
DOI: 10.1007/s00335-015-9586-7

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
DOI: 10.3389/fimmu.2015.00026

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
DOI: 10.1371/journal.pbio.1002033

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
DOI: 10.1093/nar/gku975

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
DOI: 10.1038/ng.3360

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
DOI: 10.1016/j.ymeth.2015.06.021

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.
Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P.
Genome research Volume 25 (2015) p.167-178
DOI: 10.1101/gr.177840.114

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
DOI: 10.1186/2041-1480-6-1

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
DOI: 10.1186/s12866-015-0481-x

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
DOI: 10.1177/1087057114557232

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
DOI: 10.1371/journal.pcbi.1004362

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
DOI: 10.1038/nbt.3102

The ELIXIR channel in F1000Research.
Blomberg N, Oliveira A, Mons B, Persson B, Jonassen I.
F1000Research Volume 4 (2015) p.
DOI: 10.12688/f1000research.7587.2

Testing the mean matrix in high-dimensional transposable data.
Touloumis A, Tavaré S, Marioni JC.
Biometrics Volume 71 (2015) p.157-166
DOI: 10.1111/biom.12257

Detection of significant protein coevolution.
Ochoa D, Juan D, Valencia A, Pazos F.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2166-2173
DOI: 10.1093/bioinformatics/btv102

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
DOI: 10.1080/02640414.2014.953982

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
DOI: 10.3390/nu7042589

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S.
PLoS computational biology Volume 11 (2015) p.e1004333
DOI: 10.1371/journal.pcbi.1004333

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
DOI: 10.1073/pnas.1501339112

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
DOI: 10.1002/prot.24803

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
DOI: 10.1111/mec.13113

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
DOI: 10.1016/j.molcel.2015.04.005

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
DOI: 10.1371/journal.pone.0131274

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
DOI: 10.1371/journal.pone.0139731

Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK, Geeleher P, Seoighe C.
BMC bioinformatics Volume 16 (2015) p.286
DOI: 10.1186/s12859-015-0712-z

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
DOI: 10.1371/journal.pone.0137367

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.
Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C.
Cancer research Volume 75 (2015) p.194-202
DOI: 10.1158/0008-5472.can-13-3131

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
DOI: 10.1016/j.yjmcc.2015.03.008

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
DOI: 10.1371/journal.pone.0144391

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
DOI: 10.1038/ncomms9687

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
DOI: 10.1038/nbt.3209

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
DOI: 10.1038/srep11487

The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD.
Nucleic acids research Volume 43 (2015) p.D213-21
DOI: 10.1093/nar/gku1243

2014

BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
Kim JK, Cho Y, Laskowski RA, Ryu SE, Sugihara K, Kim DS.
Proteins Volume 82 (2014) p.1829-1849
DOI: 10.1002/prot.24537

A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium.
Nature Volume 515 (2014) p.355-364
DOI: 10.1038/nature13992

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y, Mashima J, Nakamura Y, Cochrane G, Karsch-Mizrachi I.
Standards in genomic sciences Volume 9 (2014) p.1275-1277
DOI: 10.4056/sigs.4851102

Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.
Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD.
Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1170-1182
DOI: 10.1039/c4ib00086b

A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Tamuri AU, Goldman N, dos Reis M.
Genetics Volume 197 (2014) p.257-271
DOI: 10.1534/genetics.114.162263

Genomic standards consortium projects.
Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.
Standards in genomic sciences Volume 9 (2014) p.599-601
DOI: 10.4056/sigs.5559680

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ.
BMC bioinformatics Volume 15 (2014) p.155
DOI: 10.1186/1471-2105-15-155

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Kultys M, Nicholas L, Schwarz R, Goldman N, King J.
BMC Proceedings Volume 8 (2014) p.S8
DOI: 10.1186/1753-6561-8-s2-s8

Smoothing 3D protein structure motifs through graph mining and amino acid similarities.
Dhifli W, Saidi R, Nguifo EM.
Journal of computational biology : a journal of computational molecular cell biology Volume 21 (2014) p.162-172
DOI: 10.1089/cmb.2013.0092

A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium 2, Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Arranz MJ, Bakker S, Bender S, Bruggeman R, Cahn W, Chandler D, Collier DA, Crespo-Facorro B, Dazzan P, de Haan L, Di Forti M, Dragović M, Giegling I, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Kravariti E, Lawrie S, Linszen DH, Mata I, McDonald C, McIntosh A, Myin-Germeys I, Ophoff RA, Pariante CM, Paunio T, Picchioni M, Psychiatric Genomics Consortium, Ripke S, Rujescu D, Sauer H, Shaikh M, Sussmann J, Suvisaari J, Tosato S, Toulopoulou T, Van Os J, Walshe M, Weisbrod M, Whalley H, Wiersma D, Blackwell JM, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Wood NW, Barroso I, Peltonen L, Lewis CM, Murray RM, Donnelly P, Powell J, Spencer CC.
Biological psychiatry Volume 75 (2014) p.386-397
DOI: 10.1016/j.biopsych.2013.03.033

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z.
Genome biology Volume 15 (2014) p.459
DOI: 10.1186/preaccept-1262842421127991

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers.
Villaveces JM, Jimenez RC, Habermann BH.
F1000Research Volume 3 (2014) p.44
DOI: 10.12688/f1000research.3-44.v1

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R.
Molecular systems biology Volume 10 (2014) p.767
DOI: 10.15252/msb.20145112

DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.
Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S.
Genomics Volume 103 (2014) p.1-10
DOI: 10.1016/j.ygeno.2013.11.005

Sequence, a BioJS component for visualising sequences.
Gomez J, Jimenez R.
F1000Research Volume 3 (2014) p.52
DOI: 10.12688/f1000research.3-52.v1

PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA.
Nucleic acids research Volume 42 (2014) p.D292-6
DOI: 10.1093/nar/gkt940

Large-scale identification of phosphorylation sites for profiling protein kinase selectivity.
Imamura H, Sugiyama N, Wakabayashi M, Ishihama Y.
Journal of proteome research Volume 13 (2014) p.3410-3419
DOI: 10.1021/pr500319y

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw.
Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS.
Biotechnology for biofuels Volume 7 (2014) p.495
DOI: 10.1186/s13068-014-0180-0

IMG 4 version of the integrated microbial genomes comparative analysis system.
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC.
Nucleic acids research Volume 42 (2014) p.D560-7
DOI: 10.1093/nar/gkt963

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.
Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest AR, Hayashizaki Y, Carloni P, Ferrer I, Lodovichi C, Plessy C, FANTOM Consortium, Carninci P, Gustincich S.
BMC genomics Volume 15 (2014) p.729
DOI: 10.1186/1471-2164-15-729

Ten simple rules for running interactive workshops.
Pavelin K, Pundir S, Cham JA.
PLoS computational biology Volume 10 (2014) p.e1003485
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Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange.
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IMG/M 4 version of the integrated metagenome comparative analysis system.
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Characterizing genetic variants for clinical action.
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American journal of medical genetics. Part C, Seminars in medical genetics Volume 166C (2014) p.93-104
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Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
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Biomarkers in autism spectrum disorder: the old and the new.
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Psychopharmacology Volume 231 (2014) p.1201-1216
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Phylogenetic quantification of intra-tumour heterogeneity.
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PLoS computational biology Volume 10 (2014) p.e1003535
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Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation.
Billis K, Billini M, Tripp HJ, Kyrpides NC, Mavromatis K.
PloS one Volume 9 (2014) p.e109738
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Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.
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Journal of the American Society of Nephrology : JASN Volume 25 (2014) p.1509-1522
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Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
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Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
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Bioinformatics Volume 30 (2014) p.2999-3003
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Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.
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Human molecular genetics Volume 23 (2014) p.4420-4432
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EC-BLAST: a tool to automatically search and compare enzyme reactions.
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Nature methods Volume 11 (2014) p.171-174
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WormBase 2014: new views of curated biology.
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Comparative analysis of the transcriptome across distant species.
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Nature Volume 512 (2014) p.445-448
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Innate immunity. A Spaetzle-like role for nerve growth factor β in vertebrate immunity to Staphylococcus aureus.
Hepburn L, Prajsnar TK, Klapholz C, Moreno P, Loynes CA, Ogryzko NV, Ogryzko NV, Brown K, Schiebler M, Hegyi K, Antrobus R, Hammond KL, Connolly J, Ochoa B, Bryant C, Otto M, Surewaard B, Seneviratne SL, Grogono DM, Cachat J, Ny T, Kaser A, Török ME, Peacock SJ, Holden M, Blundell T, Wang L, Ligoxygakis P, Minichiello L, Woods CG, Foster SJ, Renshaw SA, Floto RA.
Science (New York, N.Y.) Volume 346 (2014) p.641-646
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Overview of gene structure in C. elegans.
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Relationship between genome and epigenome--challenges and requirements for future research.
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BMC genomics Volume 15 (2014) p.487
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Genome sequencing of normal cells reveals developmental lineages and mutational processes.
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Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.
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Dissecting the transcriptional phenotype of ribosomal protein deficiency: implications for Diamond-Blackfan Anemia.
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Gene Volume 545 (2014) p.282-289
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Response to On prompt update of literature references in the Protein Data Bank.
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Acta crystallographica. Section D, Biological crystallography Volume 70 (2014) p.2780
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The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.
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PloS one Volume 9 (2014) p.e92632
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
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The Protein Data Bank archive as an open data resource.
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Journal of computer-aided molecular design Volume 28 (2014) p.1009-1014
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Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
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Trends in biotechnology Volume 32 (2014) p.396-399
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PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.
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Anatomy of enzyme channels.
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Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress.
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Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.13427-13432
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FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences.
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Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
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The Plant cell Volume 26 (2014) p.4298-4310
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Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
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Genome biology Volume 15 (2014) p.R88
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OAE: The Ontology of Adverse Events.
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Use of internet search logs to evaluate potential drug adverse events.
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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
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Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
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Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.
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Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
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Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.
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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
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DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.
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PLoS genetics Volume 10 (2014) p.e1004109
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Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.
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PLoS computational biology Volume 10 (2014) p.e1003733
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Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
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Journal of proteome research Volume 13 (2014) p.433-446
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Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.
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A standardized framing for reporting protein identifications in mzIdentML 1.2.
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Proteomics Volume 14 (2014) p.2389-2399
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The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
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Computational approaches to interpreting genomic sequence variation.
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Genome medicine Volume 6 (2014) p.87
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Proceedings of the 13th European Conference on Computational Biology (ECCB’14), September 7-10, 2014, Strasbourg, France.

Bioinformatics Volume 30 (2014) p.i341-645

Evaluation of prompted annotation of activity data recorded from a smart phone.
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Sensors (Basel, Switzerland) Volume 14 (2014) p.15861-15879
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A predictive model for assistive technology adoption for people with dementia.
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IEEE journal of biomedical and health informatics Volume 18 (2014) p.375-383
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Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene.
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Genome biology and evolution Volume 6 (2014) p.3025-3038
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A promoter-level mammalian expression atlas.
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Nature Volume 507 (2014) p.462-470
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Protection against colitis by CD100-dependent modulation of intraepithelial γδ T lymphocyte function.
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The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age.
MacArthur JA, Spector TD, Lindsay SJ, Mangino M, Gill R, Small KS, Hurles ME.
PLoS genetics Volume 10 (2014) p.e1004195
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Assessing the state of substitution models describing noncoding RNA evolution.
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Genome biology and evolution Volume 6 (2014) p.65-75
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Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.
Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S, FANTOM Consortium.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.5289-5294
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An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A.
Nature Volume 507 (2014) p.455-461
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Single Cell Genomics meeting in Stockholm: from single cells to cell types.
Scialdone A, Achim K, Marioni JC.
Genome biology Volume 15 (2014) p.496
DOI: 10.1186/s13059-014-0496-x

Data standardization and sharing-the work of the HUPO-PSI.
Orchard S.
Biochimica et biophysica acta Volume 1844 (2014) p.82-87
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Functional annotation of noncoding sequence variants.
Ritchie GR, Dunham I, Zeggini E, Flicek P.
Nature methods Volume 11 (2014) p.294-296
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Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler TJ, Clements J, Finn RD.
BMC bioinformatics Volume 15 (2014) p.7
DOI: 10.1186/1471-2105-15-7

BC4GO: a full-text corpus for the BioCreative IV GO task.
Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z.
Database : the journal of biological databases and curation Volume 2014 (2014) p.
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Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.
Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F.
Nature genetics Volume 46 (2014) p.753-758
DOI: 10.1038/ng.2971

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Cejuela JM, McQuilton P, Ponting L, Marygold SJ, Stefancsik R, Millburn GH, Rost B, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau033
DOI: 10.1093/database/bau033

Overview of the gene ontology task at BioCreative IV.
Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z.
Database : the journal of biological databases and curation Volume 2014 (2014) p.
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Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D (1)H-NMR data.
Gómez J, Brezmes J, Mallol R, Rodríguez MA, Vinaixa M, Salek RM, Correig X, Cañellas N.
Analytical and bioanalytical chemistry Volume 406 (2014) p.7967-7976
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Identifying cell types from spatially referenced single-cell expression datasets.
Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J.
PLoS computational biology Volume 10 (2014) p.e1003824
DOI: 10.1371/journal.pcbi.1003824

A survey of molecular descriptors used in mass spectrometry based proteomics.
Audain E, Sanchez A, Vizcaíno JA, Perez-Riverol Y.
Current topics in medicinal chemistry Volume 14 (2014) p.388-397
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jmzTab: a java interface to the mzTab data standard.
Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.
Proteomics Volume 14 (2014) p.1328-1332
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Evolution of transcription factor binding in metazoans - mechanisms and functional implications.
Villar D, Flicek P, Odom DT.
Nature reviews. Genetics Volume 15 (2014) p.221-233
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High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.
Genome research Volume 24 (2014) p.1797-1807
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KEGGViewer, a BioJS component to visualize KEGG Pathways.
Villaveces JM, Jimenez RC, Habermann BH.
F1000Research Volume 3 (2014) p.43
DOI: 10.12688/f1000research.3-43.v1

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.
Journal of biomedical semantics Volume 5 (2014) p.25
DOI: 10.1186/2041-1480-5-25

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.
Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Rydén M, Arner P, FANTOM Consortium.
PloS one Volume 9 (2014) p.e80274
DOI: 10.1371/journal.pone.0080274

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C.
Angewandte Chemie (International ed. in English) Volume 53 (2014) p.6720-6723
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MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.
BMC bioinformatics Volume 15 (2014) p.136
DOI: 10.1186/1471-2105-15-136

PIP₃ induces the recycling of receptor tyrosine kinases.
Laketa V, Zarbakhsh S, Traynor-Kaplan A, Macnamara A, Subramanian D, Putyrski M, Mueller R, Nadler A, Mentel M, Saez-Rodriguez J, Pepperkok R, Schultz C.
Science signaling Volume 7 (2014) p.ra5
DOI: 10.1126/scisignal.2004532

A community computational challenge to predict the activity of pairs of compounds.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community.
Nature biotechnology Volume 32 (2014) p.1213-1222
DOI: 10.1038/nbt.3052

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.
Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W.
Cell reports Volume 9 (2014) p.1990-2000
DOI: 10.1016/j.celrep.2014.11.034

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D802-9
DOI: 10.1093/nar/gkt977

CLO: The cell line ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.
Journal of biomedical semantics Volume 5 (2014) p.37
DOI: 10.1186/2041-1480-5-37

Enly: Improving Draft Genomes through Reads Recycling.
Fondi M, Orlandini V, Corti G, Severgnini M, Galardini M, Pietrelli A, Fuligni F, Iacono M, Rizzi E, De Bellis G, Fani R.
Journal of genomics Volume 2 (2014) p.89-93
DOI: 10.7150/jgen.7298

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J.
BMC systems biology Volume 8 (2014) p.13
DOI: 10.1186/1752-0509-8-13

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression.
Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AE, Wardle FC.
BMC biology Volume 12 (2014) p.81
DOI: 10.1186/s12915-014-0081-5

The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.
Current opinion in structural biology Volume 26 (2014) p.121-130
DOI: 10.1016/j.sbi.2014.06.002

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.
Bio Systems Volume 124 (2014) p.26-38
DOI: 10.1016/j.biosystems.2014.07.002

Fast randomization of large genomic datasets while preserving alteration counts.
Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J.
Bioinformatics Volume 30 (2014) p.i617-23
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Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM.
Nature methods Volume 11 (2014) p.171-174

Mining Molecular Pharmacological Effects from Biomedical Text: a Case Study for Eliciting Anti-Obesity/Diabetes Effects of Chemical Compounds.
Dura E, Muresan S, Engkvist O, Blomberg N, Chen H.
Molecular informatics Volume 33 (2014) p.332-342
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Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.
eLife Volume 3 (2014) p.e02626
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Controlled vocabularies and ontologies in proteomics: overview, principles and practice.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.
Biochimica et biophysica acta Volume 1844 (2014) p.98-107
DOI: 10.1016/j.bbapap.2013.02.017

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.
Biochimica et biophysica acta Volume 1844 (2014) p.63-76
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Maximum likelihood inference of small trees in the presence of long branches.
Parks SL, Goldman N.
Systematic biology Volume 63 (2014) p.798-811
DOI: 10.1093/sysbio/syu044

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

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
Nucleic acids research Volume 42 (2014) p.D485-9
DOI: 10.1093/nar/gkt1243

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA.
Proteomics Volume 14 (2014) p.2233-2241
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The common marmoset genome provides insight into primate biology and evolution.
Marmoset Genome Sequencing and Analysis Consortium.
Nature genetics Volume 46 (2014) p.850-857
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BioJS: an open source standard for biological visualisation - its status in 2014.
Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H.
F1000Research Volume 3 (2014) p.55
DOI: 10.12688/f1000research.3-55.v1

ISMB 2014 Proceedings Papers Committee.

Bioinformatics Volume 30 (2014) p.i3-i8

A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.
Nature biotechnology Volume 32 (2014) p.1202-1212
DOI: 10.1038/nbt.2877

ECCB 2014: The 13th European Conference on Computational Biology.
Devignes MD, Moreau Y.
Bioinformatics Volume 30 (2014) p.i345-8
DOI: 10.1093/bioinformatics/btu512

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.
Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR, FANTOM Consortium, Suzuki H.
Scientific reports Volume 4 (2014) p.5228
DOI: 10.1038/srep05228

qcML: an exchange format for quality control metrics from mass spectrometry experiments.
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.
Molecular & cellular proteomics : MCP Volume 13 (2014) p.1905-1913
DOI: 10.1074/mcp.m113.035907

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.
Nature biotechnology Volume 32 (2014) p.223-226
DOI: 10.1038/nbt.2839

Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi N, Lippert C, Lawrence ND, Stegle O.
Nature communications Volume 5 (2014) p.4890
DOI: 10.1038/ncomms5890

Exploring the biological and chemical complexity of the ligases.
Holliday GL, Rahman SA, Furnham N, Thornton JM.
Journal of molecular biology Volume 426 (2014) p.2098-2111
DOI: 10.1016/j.jmb.2014.03.008

BioModels linked dataset.
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C.
BMC systems biology Volume 8 (2014) p.91
DOI: 10.1186/s12918-014-0091-5

Practical aspects of protein co-evolution.
Ochoa D, Pazos F.
Frontiers in cell and developmental biology Volume 2 (2014) p.14
DOI: 10.3389/fcell.2014.00014

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA.
Journal of biomedical semantics Volume 5 (2014) p.34
DOI: 10.1186/2041-1480-5-34

Meeting report: advancing practical applications of biodiversity ontologies.
Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N, Denslow MW, Gallery RE, Parnell JJ, Osumi-Sutherland D, Robbins RJ, Rocca-Serra P, Wieczorek J, Zheng J.
Standards in genomic sciences Volume 9 (2014) p.17-17
DOI: 10.1186/1944-3277-9-17

TermGenie - a web-application for pattern-based ontology class generation.
Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ.
Journal of biomedical semantics Volume 5 (2014) p.48
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On best practices in the development of bioinformatics software.
Leprevost Fda V, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC.
Frontiers in genetics Volume 5 (2014) p.199
DOI: 10.3389/fgene.2014.00199

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D1001-6
DOI: 10.1093/nar/gkt1229

Assembly information services in the European Nucleotide Archive.
Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G.
Nucleic acids research Volume 42 (2014) p.D38-43
DOI: 10.1093/nar/gkt1082

A unifying model of genome evolution under parsimony.
Paten B, Zerbino DR, Hickey G, Haussler D.
BMC bioinformatics Volume 15 (2014) p.206
DOI: 10.1186/1471-2105-15-206

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P.
Bioinformatics Volume 30 (2014) p.1008-1009
DOI: 10.1093/bioinformatics/btt737

Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL.
Developmental cell Volume 28 (2014) p.351-365
DOI: 10.1016/j.devcel.2014.01.017

A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region.
Kraaijenbrink T, van der Gaag KJ, Zuniga SB, Xue Y, Carvalho-Silva DR, Tyler-Smith C, Jobling MA, Parkin EJ, Su B, Shi H, Xiao CJ, Tang WR, Kashyap VK, Trivedi R, Sitalaximi T, Banerjee J, Karma Tshering of Gaselô, Tuladhar NM, Opgenort JR, van Driem GL, Barbujani G, de Knijff P.
PloS one Volume 9 (2014) p.e91534
DOI: 10.1371/journal.pone.0091534

Bioinformatics curriculum guidelines: toward a definition of core competencies.
Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV.
PLoS computational biology Volume 10 (2014) p.e1003496
DOI: 10.1371/journal.pcbi.1003496

A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.
Rebholz-Schuhmann D, Grabmüller C, Kavaliauskas S, Croset S, Woollard P, Backofen R, Filsell W, Clark D.
Drug discovery today Volume 19 (2014) p.882-889
DOI: 10.1016/j.drudis.2013.10.024

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.
Pinnick KE, Nicholson G, Manolopoulos KN, McQuaid SE, Valet P, Frayn KN, Denton N, Min JL, Zondervan KT, Fleckner J, MolPAGE Consortium, McCarthy MI, Holmes CC, Karpe F.
Diabetes Volume 63 (2014) p.3785-3797
DOI: 10.2337/db14-0385

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F.
Nucleic acids research Volume 42 (2014) p.D873-8
DOI: 10.1093/nar/gkt1198

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N, UK1OK Consortium Members, UK1OK Consortium Members.
Nature communications Volume 5 (2014) p.4871
DOI: 10.1038/ncomms5871

The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.
Nucleic acids research Volume 42 (2014) p.D18-25
DOI: 10.1093/nar/gkt1206

Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats.
Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C, Jobling MA.
Human mutation Volume 35 (2014) p.609-617
DOI: 10.1002/humu.22542

Antibody informatics for drug discovery.
Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K.
Biochimica et biophysica acta Volume 1844 (2014) p.2002-2015
DOI: 10.1016/j.bbapap.2014.07.006

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic acids research Volume 42 (2014) p.D926-32
DOI: 10.1093/nar/gkt1270

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA.
Nucleic acids research Volume 42 (2014) p.D600-6
DOI: 10.1093/nar/gkt961

InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1236-1240
DOI: 10.1093/bioinformatics/btu031

Big data and other challenges in the quest for orthologs.
Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs consortium.
Bioinformatics Volume 30 (2014) p.2993-2998
DOI: 10.1093/bioinformatics/btu492

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
Huntley RP, Sawford T, Martin MJ, O'Donovan C.
GigaScience Volume 3 (2014) p.4
DOI: 10.1186/2047-217x-3-4

Representing kidney development using the gene ontology.
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP.
PloS one Volume 9 (2014) p.e99864
DOI: 10.1371/journal.pone.0099864

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau016
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Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.
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Human mutation Volume 35 (2014) p.927-935
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Nucleic acids research Volume 42 (2014) p.7486-7486

Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.6131-6138
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Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.E3366
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Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z.
PLoS genetics Volume 10 (2014) p.e1004132
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Activities at the Universal Protein Resource (UniProt).
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Nucleic acids research Volume 42 (2014) p.D191-8
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Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.
Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH.
Structure (London, England : 1993) Volume 22 (2014) p.1862-1874
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Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.
Rawlings ND, Barrett AJ, Bateman A.
Current protocols in bioinformatics Volume 48 (2014) p.1.25.1-33
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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Waller M, Barrett AJ, Bateman A.
Nucleic acids research Volume 42 (2014) p.D503-9
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TreeFam v9: a new website, more species and orthology-on-the-fly.
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Nucleic acids research Volume 42 (2014) p.D922-5
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iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A.
Nucleic acids research Volume 42 (2014) p.D364-73
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Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M.
Nucleic acids research Volume 42 (2014) p.D222-30
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Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.
Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L.
BMC bioinformatics Volume 15 (2014) p.75
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De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P.
PloS one Volume 9 (2014) p.e96855
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An overview of tools for the validation of protein NMR structures.
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Journal of biomolecular NMR Volume 58 (2014) p.259-285
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Ensembl 2014.
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Nucleic acids research Volume 42 (2014) p.D749-55
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Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM.
Nature communications Volume 5 (2014) p.5135
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Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
Greger L, Su J, Rung J, Ferreira PG, Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.
PloS one Volume 9 (2014) p.e104567
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Chemical, target, and bioactive properties of allosteric modulation.
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PLoS computational biology Volume 10 (2014) p.e1003559
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Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM.
Nucleic acids research Volume 42 (2014) p.D546-52
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The ChEMBL bioactivity database: an update.
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Nucleic acids research Volume 42 (2014) p.D1083-90
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Gramene 2013: comparative plant genomics resources.
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Transporter assays and assay ontologies: useful tools for drug discovery.
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Transporter taxonomy - a comparison of different transport protein classification schemes.
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Turtle ghrelin.
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Nature genetics Volume 46 (2014) p.526
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The cavefish genome reveals candidate genes for eye loss.
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UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers.
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Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes.
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Evolution; international journal of organic evolution Volume 68 (2014) p.605-613
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A comprehensive model of the phototransduction cascade in mouse rod cells.
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Molecular bioSystems Volume 10 (2014) p.1481-1489
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The Nucleic Acid Database: new features and capabilities.
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Visualisation of BioPAX Networks using BioLayout Express (3D).
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F1000Research Volume 3 (2014) p.246
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Serum levels of mature microRNAs in DICER1-mutated pleuropulmonary blastoma.
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Oncogenesis Volume 3 (2014) p.e87
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Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.
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The Reactome pathway knowledgebase.
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Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.
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Molecular cell Volume 56 (2014) p.193-204
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The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
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Nucleic acids research Volume 42 (2014) p.D358-63
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Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.
Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, Hebenstreit D, Dingler FA, Moignard V, Göttgens B, Arlt W, McKenzie AN, Teichmann SA.
Cell reports Volume 7 (2014) p.1130-1142
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A 3D cellular context for the macromolecular world.
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Nature structural & molecular biology Volume 21 (2014) p.841-845
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The EBI RDF platform: linked open data for the life sciences.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.
Bioinformatics (Oxford, England) Volume 30 (2014) p.1338-1339
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Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.
Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC.
Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.17230-17235
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The architecture of parent-of-origin effects in mice.
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Cell Volume 156 (2014) p.332-342
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High-resolution genome screen for bone mineral density in heterogeneous stock rat.
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Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Volume 29 (2014) p.1619-1626
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Genomes and phenomes of a population of outbred rats and its progenitors.
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Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat.
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PLoS genetics Volume 10 (2014) p.e1004151
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Bioinformatics tools for the functional interpretation of quantitative proteomics results.
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Current topics in medicinal chemistry Volume 14 (2014) p.435-449
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Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat.
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Physiological genomics Volume 46 (2014) p.418-428
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Editorial: Genomics and proteomics behind drug design.
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Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.
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RNA biology Volume 11 (2014) p.702-714
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RNA-Seq gene profiling--a systematic empirical comparison.
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Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b.
Toribio AL, Pickard D, Cerdeño-Tárraga AM, Petty NK, Thomson N, Salmond G, Dougan G.
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Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription.
García P, Paulo E, Gao J, Wahls WP, Ayté J, Lowy E, Hidalgo E.
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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG.
Nature biotechnology Volume 32 (2014) p.1250-1255
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Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.
Maina AN, Mwaura FB, Oyugi J, Goulding D, Toribio AL, Kariuki S.
Current microbiology Volume 68 (2014) p.64-70
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Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
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Current protocols in bioinformatics Volume 48 (2014) p.3.12.1-50
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L.
Science (New York, N.Y.) Volume 345 (2014) p.1074-1079
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Current status and new features of the Consensus Coding Sequence database.
Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD.
Nucleic acids research Volume 42 (2014) p.D865-72
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Gibbon genome and the fast karyotype evolution of small apes.
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Nature Volume 513 (2014) p.195-201
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The sheep genome illuminates biology of the rumen and lipid metabolism.
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP.
Science (New York, N.Y.) Volume 344 (2014) p.1168-1173
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The genomic substrate for adaptive radiation in African cichlid fish.
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F.
Nature Volume 513 (2014) p.375-381
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The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.
Molecular & cellular proteomics : MCP Volume 13 (2014) p.2765-2775
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Transcriptional diversity during lineage commitment of human blood progenitors.
Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium B, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HHD, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A.
Science (New York, N.Y.) Volume 345 (2014) p.1251033
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Reliable protocols for whole-mount fluorescent in situ hybridization (FISH) in the pea aphid Acyrthosiphon pisum: a comprehensive survey and analysis.
Chung CY, Cook CE, Lin GW, Huang TY, Chang CC.
Insect science Volume 21 (2014) p.265-277
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Posterior localization of ApVas1 positions the preformed germ plasm in the sexual oviparous pea aphid Acyrthosiphon pisum.
Lin GW, Cook CE, Miura T, Chang CC.
EvoDevo Volume 5 (2014) p.18
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Integrative knowledge management to enhance pharmaceutical R&D.
Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F.
Nature reviews. Drug discovery Volume 13 (2014) p.239-240
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Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array.
Wong YC, Kwong QB, Lee HL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H.
Microarrays (Basel, Switzerland) Volume 3 (2014) p.263-281
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PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Nucleic acids research Volume 42 (2014) p.D285-91
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Archaic humans: Four makes a party.
Birney E, Pritchard JK.
Nature Volume 505 (2014) p.32-34
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Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.
PLoS genetics Volume 10 (2014) p.e1004798
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Updates to BioSamples database at European Bioinformatics Institute.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research Volume 42 (2014) p.D50-2
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Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J.
G3 (Bethesda, Md.) Volume 4 (2014) p.433-445
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Small molecule annotation for the Protein Data Bank.
Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau116
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MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.
Beisken S, Earll M, Portwood D, Seymour M, Steinbeck C.
Molecular informatics Volume 33 (2014) p.307-310

A molecular fragment cheminformatics roadmap for mesoscopic simulation.
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Journal of Cheminformatics Volume 6 (2014) p.45
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The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.
Venkata C, Forster MJ, Howe PW, Steinbeck C.
PloS one Volume 9 (2014) p.e111576
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Efficient ring perception for the Chemistry Development Kit.
May JW, Steinbeck C.
Journal of Cheminformatics Volume 6 (2014) p.3
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Ten recommendations for software engineering in research.
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GigaScience Volume 3 (2014) p.31
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A formal re-description of the cockroach Hebardina concinna anchored on DNA Barcodes confirms wing polymorphism and identifies morphological characters for field identification.
Yue Q, Wu K, Qiu D, Hu J, Liu D, Wei X, Chen J, Cook CE.
PloS one Volume 9 (2014) p.e106789
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Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.
Jayaseelan KV, Steinbeck C.
BMC bioinformatics Volume 15 (2014) p.234
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Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.
Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C.
Scientific data Volume 1 (2014) p.140029
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Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.
Proteins Volume 81 (2013) p.1980-1987
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.
GigaScience Volume 2 (2013) p.10
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Visualization and analysis of biological networks.
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Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.63-88
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High-resolution analysis of cis-acting regulatory networks at the α-globin locus.
Hughes JR, Lower KM, Dunham I, Taylor S, De Gobbi M, Sloane-Stanley JA, McGowan S, Ragoussis J, Vernimmen D, Gibbons RJ, Higgs DR.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 368 (2013) p.20120361
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DbVar and DGVa: public archives for genomic structural variation.
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM.
Nucleic acids research Volume 41 (2013) p.D936-41
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ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.
Nucleic acids research Volume 41 (2013) p.D987-90
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Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.
Wallach T, Schellenberg K, Maier B, Kalathur RK, Porras P, Wanker EE, Futschik ME, Kramer A.
PLoS genetics Volume 9 (2013) p.e1003398
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Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.
Nature Volume 501 (2013) p.506-511
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Optimal placement of accelerometers for the detection of everyday activities.
Cleland I, Kikhia B, Nugent C, Boytsov A, Hallberg J, Synnes K, McClean S, Finlay D.
Sensors (Basel, Switzerland) Volume 13 (2013) p.9183-9200
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Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM.
PLoS computational biology Volume 9 (2013) p.e1003382
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Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Raspé O, Vieira CP.
Journal of experimental botany Volume 64 (2013) p.2423-2434
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Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.
Fonseca NA, Morales-Hojas R, Reis M, Rocha H, Vieira CP, Nolte V, Schlötterer C, Vieira J.
Genome biology and evolution Volume 5 (2013) p.661-679
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The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.
Araújo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, Macedo-Ribeiro S, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Vieira J.
PloS one Volume 8 (2013) p.e63747
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Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.
Nature biotechnology Volume 31 (2013) p.1015-1022
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Improving the performance of Transposable Elements detection tools.
Loureiro T, Camacho R, Vieira J, Fonseca NA.
Journal of integrative bioinformatics Volume 10 (2013) p.40-50
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Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.
Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR.
Genome biology Volume 14 (2013) p.R37
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LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2395-2402
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Development and application of a DNA microarray-based yeast two-hybrid system.
Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE.
Nucleic acids research Volume 41 (2013) p.1496-1507
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Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM.
PLoS genetics Volume 9 (2013) p.e1003803
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Vive la différence: naming structural variants in the human reference genome.
Seal RL, Wright MW, Gray KA, Bruford EA.
Human genomics Volume 7 (2013) p.12
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Ontology based molecular signatures for immune cell types via gene expression analysis.
Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD.
BMC bioinformatics Volume 14 (2013) p.263
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Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.
Cell Volume 154 (2013) p.530-540
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Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project.
Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M, Groza T, Hamilton CM, Hamosh A, Kerner B, MacArthur JA, Maglott DR, Mons B, Rehm HL, Schofield PN, Searle BA, Smedley D, Smith CL, Bernstein IT, Zankl A, Zhao EY.
Human mutation Volume 34 (2013) p.661-666
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The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume (2013) p.456-458

Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G.
Nucleic acids research Volume 41 (2013) p.5189-5198
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Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O.
Bioinformatics Volume 29 (2013) p.1382-1389
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LifeTrain: towards a European framework for continuing professional development in biomedical sciences
Brooksbank C.
Nature reviews. Drug discovery Volume (2013) p.
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Genenames.org: the HGNC resources in 2013.
Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA.
Nucleic acids research Volume 41 (2013) p.D545-52
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Skirting the pitfalls: a clear-cut nomenclature for H3K4 methyltransferases.
Bögershausen N, Bruford E, Wollnik B.
Clinical genetics Volume 83 (2013) p.212-214
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An estimated 5% of new protein structures solved today represent a new Pfam family.
Mistry J, Kloppmann E, Rost B, Punta M.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2186-2193
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A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
Ryberg M, Sandberg S, Mellberg C, Stegle O, Lindahl B, Larsson C, Hauksson J, Olsson T.
Journal of internal medicine Volume 274 (2013) p.67-76
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Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.
Science (New York, N.Y.) Volume 342 (2013) p.1235587
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Improving the performance of Transposable Elements detection tools.
Loureiro T, Camacho R, Vieira J, Fonseca NA.
Journal of integrative bioinformatics Volume 10 (2013) p.231
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The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.
Moulos P, Klein J, Jupp S, Stevens R, Bascands JL, Schanstra JP.
BMC bioinformatics Volume 14 (2013) p.235
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Update on the Kelch-like (KLHL) gene family.
Dhanoa BS, Cogliati T, Satish AG, Bruford EA, Friedman JS.
Human genomics Volume 7 (2013) p.13
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Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.
Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J.
PloS one Volume 8 (2013) p.e61318
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Response to Diaz.
Bögershausen N, Bruford E, Wollnik B.
Clinical genetics Volume 83 (2013) p.296
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The ABCs of membrane transporters in health and disease (SLC series): introduction.
Hediger MA, Clémençon B, Burrier RE, Bruford EA.
Molecular aspects of medicine Volume 34 (2013) p.95-107
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A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.
Bioinformatics Volume 29 (2013) p.206-214
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The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J.
Journal of biomedical semantics Volume 4 (2013) p.20
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PRIDE Cluster: building a consensus of proteomics data.
Griss J, Foster JM, Hermjakob H, Vizcaíno JA.
Nature methods Volume 10 (2013) p.95-96
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The Drosophila phenotype ontology.
Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.
Journal of biomedical semantics Volume 4 (2013) p.30
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A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden.
Funnell AP, Wilson MD, Ballester B, Mak KS, Burdach J, Magan N, Pearson RC, Lemaigre FP, Stowell KM, Odom DT, Flicek P, Crossley M.
American journal of human genetics Volume 92 (2013) p.460-467
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Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.
Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S.
Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.4009-4014
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Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.
Nature methods Volume 10 (2013) p.723-729
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The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N.
Nature genetics Volume 45 (2013) p.701-706
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Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR, Apweiler R, Ge J, Hermjakob H, Ping P.
Circulation research Volume 113 (2013) p.1043-1053
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Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.
White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Sanger Institute Mouse Genetics Project, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP.
Cell Volume 154 (2013) p.452-464
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Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.
Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.
Proteomics Volume 13 (2013) p.2931-2937
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FlyBase: improvements to the bibliography.
Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ, FlyBase consortium.
Nucleic acids research Volume 41 (2013) p.D751-7
DOI: 10.1093/nar/gks1024

Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.
Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE.
British journal of cancer Volume 109 (2013) p.983-993
DOI: 10.1038/bjc.2013.396

Systematic analysis of experimental phenotype data reveals gene functions.
Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.
PloS one Volume 8 (2013) p.e60847
DOI: 10.1371/journal.pone.0060847

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC.
Genome biology Volume 14 (2013) p.R7
DOI: 10.1186/gb-2013-14-1-r7

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.
Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F.
Molecular bioSystems Volume 9 (2013) p.70-76
DOI: 10.1039/c2mb25325a

Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
Ilsley GR, Fisher J, Apweiler R, De Pace AH, Luscombe NM.
eLife Volume 2 (2013) p.e00522
DOI: 10.7554/elife.00522

Comment on on the propagation of errors by Jaskolski (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2297
DOI: 10.1107/s090744491302917x

How community has shaped the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure (London, England : 1993) Volume 21 (2013) p.1485-1491
DOI: 10.1016/j.str.2013.07.010

The Drosophila anatomy ontology.
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D.
Journal of biomedical semantics Volume 4 (2013) p.32
DOI: 10.1186/2041-1480-4-32

Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2296
DOI: 10.1107/s0907444913029168

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.
Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, Guirola O, Bringas R, Cabrera G, Guillen G, Padron G, Gonzalez LJ, Besada V.
Journal of proteomics Volume 87 (2013) p.134-138
DOI: 10.1016/j.jprot.2013.01.019

Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG.
Nature methods Volume 10 (2013) p.1093-1095
DOI: 10.1038/nmeth.2645

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ.
Cell Volume 154 (2013) p.691-703
DOI: 10.1016/j.cell.2013.06.040

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V.
Analytical chemistry Volume 85 (2013) p.3515-3520
DOI: 10.1021/ac303239g

BioModels Database: a repository of mathematical models of biological processes.
Chelliah V, Laibe C, Le Novère N.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.189-199
DOI: 10.1007/978-1-62703-450-0_10

A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones.
Hirani N, Westenberg M, Gami MS, Davis P, Hope IA, Dolphin CT.
BMC biotechnology Volume 13 (2013) p.1
DOI: 10.1186/1472-6750-13-1

Latent regulatory potential of human-specific repetitive elements.
Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT.
Molecular cell Volume 49 (2013) p.262-272
DOI: 10.1016/j.molcel.2012.11.013

Towards the collaborative curation of the registry underlying Identifiers.org.
Juty N, Le Novère N, Hermjakob H, Laibe C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat017
DOI: 10.1093/database/bat017

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC.
Journal of proteomics Volume 89 (2013) p.179-182
DOI: 10.1016/j.jprot.2013.06.013

Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways.
Mancini C, Roncaglia P, Brussino A, Stevanin G, Lo Buono N, Krmac H, Maltecca F, Gazzano E, Bartoletti Stella A, Calvaruso MA, Iommarini L, Cagnoli C, Forlani S, Le Ber I, Durr A, Brice A, Ghigo D, Casari G, Porcelli AM, Funaro A, Gasparre G, Gustincich S, Brusco A.
BMC medical genomics Volume 6 (2013) p.22
DOI: 10.1186/1755-8794-6-22

Abstracting knowledge from the Protein Data Bank.
Furnham N, Laskowski RA, Thornton JM.
Biopolymers Volume 99 (2013) p.183-188
DOI: 10.1002/bip.22107

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.
Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J.
Molecular bioSystems Volume 9 (2013) p.1576-1583
DOI: 10.1039/c3mb25489e

DNA damage in mammalian neural stem cells leads to astrocytic differentiation mediated by BMP2 signaling through JAK-STAT.
Schneider L, Pellegatta S, Favaro R, Pisati F, Roncaglia P, Testa G, Nicolis SK, Finocchiaro G, d'Adda di Fagagna F.
Stem cell reports Volume 1 (2013) p.123-138
DOI: 10.1016/j.stemcr.2013.06.004

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J.
Bioinformatics Volume 29 (2013) p.2320-2326
DOI: 10.1093/bioinformatics/btt393

A new reference implementation of the PSICQUIC web service.
del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.
Nucleic acids research Volume 41 (2013) p.W601-6
DOI: 10.1093/nar/gkt392

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.
Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR.
Molecular & cellular proteomics : MCP Volume 12 (2013) p.3026-3035
DOI: 10.1074/mcp.o113.029777

Maximising proteomics data for the scientific community
Hermjakob H, Apweiler R.
European Pharmaceutical Review Volume 9 (2013) p.23-29

From Peptidome to PRIDE: public proteomics data migration at a large scale.
Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H.
Proteomics Volume 13 (2013) p.1692-1695
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Crystal structure of the entire respiratory complex I.
Baradaran R, Berrisford JM, Minhas GS, Sazanov LA.
Nature Volume 494 (2013) p.443-448
DOI: 10.1038/nature11871

A long road towards the structure of respiratory complex I, a giant molecular proton pump.
Sazanov LA, Baradaran R, Efremov RG, Berrisford JM, Minhas G.
Biochemical Society transactions Volume 41 (2013) p.1265-1271
DOI: 10.1042/bst20130193

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I.
BMC bioinformatics Volume 14 (2013) p.104
DOI: 10.1186/1471-2105-14-104

Database citation in full text biomedical articles.
Kafkas Ş, Kim JH, McEntyre JR.
PloS one Volume 8 (2013) p.e63184
DOI: 10.1371/journal.pone.0063184

KNIME-CDK: Workflow-driven cheminformatics.
Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C.
BMC bioinformatics Volume 14 (2013) p.257
DOI: 10.1186/1471-2105-14-257

Capturing cooperative interactions with the PSI-MI format.
Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat066
DOI: 10.1093/database/bat066

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.
Genome research Volume 23 (2013) p.749-761
DOI: 10.1101/gr.148718.112

Adhesion to carbon nanotube conductive scaffolds forces action-potential appearance in immature rat spinal neurons.
Fabbro A, Sucapane A, Toma FM, Calura E, Rizzetto L, Carrieri C, Roncaglia P, Martinelli V, Scaini D, Masten L, Turco A, Gustincich S, Prato M, Ballerini L.
PloS one Volume 8 (2013) p.e73621
DOI: 10.1371/journal.pone.0073621

Recommendations of the wwPDB NMR Validation Task Force.
Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL.
Structure (London, England : 1993) Volume 21 (2013) p.1563-1570
DOI: 10.1016/j.str.2013.07.021

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.
Science (New York, N.Y.) Volume 342 (2013) p.1516-1517
DOI: 10.1126/science.1241130

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.
Nucleic acids research Volume 41 (2013) p.D490-8
DOI: 10.1093/nar/gks1211

Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Magnusson PK, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Psychosis Endophenotypes International Consortium, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Wellcome Trust Case Control Consortium 2, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CC, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CC, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF.
Nature genetics Volume 45 (2013) p.1150-1159
DOI: 10.1038/ng.2742

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC), Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL.
Nature genetics Volume 45 (2013) p.1353-1360
DOI: 10.1038/ng.2770

A system-level, molecular evolutionary analysis of mammalian phototransduction.
Invergo BM, Montanucci L, Laayouni H, Bertranpetit J.
BMC evolutionary biology Volume 13 (2013) p.52
DOI: 10.1186/1471-2148-13-52

Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling.
Invergo BM, Montanucci L, Koch KW, Bertranpetit J, Dell'orco D.
Cell communication and signaling : CCS Volume 11 (2013) p.36
DOI: 10.1186/1478-811x-11-36

World Health Organization International Standard to harmonize assays for detection of hepatitis E virus RNA.
Baylis SA, Blümel J, Mizusawa S, Matsubayashi K, Sakata H, Okada Y, Nübling CM, Hanschmann KM, HEV Collaborative Study Group.
Emerging infectious diseases Volume 19 (2013) p.729-735
DOI: 10.3201/eid1905.121845

Hepatitis E virus infection in Ghanaian blood donors - the importance of immunoassay selection and confirmation.
Meldal BH, Sarkodie F, Owusu-Ofori S, Allain JP.
Vox sanguinis Volume 104 (2013) p.30-36
DOI: 10.1111/j.1423-0410.2012.01637.x

JBioWH: an open-source Java framework for bioinformatics data integration.
Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat051
DOI: 10.1093/database/bat051

Meta-analysis of gene-level associations for rare variants based on single-variant statistics.
Hu YJ, Berndt SI, Gustafsson S, Ganna A, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn J, North KE, Ingelsson E, Lin DY.
American journal of human genetics Volume 93 (2013) p.236-248
DOI: 10.1016/j.ajhg.2013.06.011

Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.
LeishGEN Consortium, Wellcome Trust Case Control Consortium 2, Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SM, Sundar S, Spencer CC, Blackwell JM, Donnelly P.
Nature genetics Volume 45 (2013) p.208-213
DOI: 10.1038/ng.2518

The Amborella genome and the evolution of flowering plants.
Amborella Genome Project.
Science (New York, N.Y.) Volume 342 (2013) p.1241089
DOI: 10.1126/science.1241089

Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus.
Blue Mountains Eye Study (BMES), Wellcome Trust Case Control Consortium 2 (WTCCC2).
Human molecular genetics Volume 22 (2013) p.4653-4660
DOI: 10.1093/hmg/ddt293

UniChem: a unified chemical structure cross-referencing and identifier tracking system.
Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP.
Journal of Cheminformatics Volume 5 (2013) p.3
DOI: 10.1186/1758-2946-5-3

Ensembl 2013.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Yates A, Zadissa A, Searle SM.
Nucleic acids research Volume 41 (2013) p.D48-55
DOI: 10.1093/nar/gks1236

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.
Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM, Duong S, Nguon C, Chuor CM, Saunders D, Se Y, Lon C, Fukuda MM, Amenga-Etego L, Hodgson AV, Asoala V, Imwong M, Takala-Harrison S, Nosten F, Su XZ, Ringwald P, Ariey F, Dolecek C, Hien TT, Boni MF, Thai CQ, Amambua-Ngwa A, Conway DJ, Djimdé AA, Doumbo OK, Zongo I, Ouedraogo JB, Alcock D, Drury E, Auburn S, Koch O, Sanders M, Hubbart C, Maslen G, Ruano-Rubio V, Jyothi D, Miles A, O'Brien J, Gamble C, Oyola SO, Rayner JC, Newbold CI, Berriman M, Spencer CC, McVean G, Day NP, White NJ, Bethell D, Dondorp AM, Plowe CV, Fairhurst RM, Kwiatkowski DP.
Nature genetics Volume 45 (2013) p.648-655
DOI: 10.1038/ng.2624

Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.
Auburn S, Marfurt J, Maslen G, Campino S, Ruano Rubio V, Manske M, Machunter B, Kenangalem E, Noviyanti R, Trianty L, Sebayang B, Wirjanata G, Sriprawat K, Alcock D, Macinnis B, Miotto O, Clark TG, Russell B, Anstey NM, Nosten F, Kwiatkowski DP, Price RN.
PloS one Volume 8 (2013) p.e53160
DOI: 10.1371/journal.pone.0053160

Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.
Hamilton-Williams EE, Rainbow DB, Cheung J, Christensen M, Lyons PA, Peterson LB, Steward CA, Sherman LA, Wicker LS.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 24 (2013) p.358-375
DOI: 10.1007/s00335-013-9466-y

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.
Sanseverino W, Hermoso A, D'Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR.
Nucleic acids research Volume 41 (2013) p.D1167-71
DOI: 10.1093/nar/gks1183

Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya.
Borrmann S, Straimer J, Mwai L, Abdi A, Rippert A, Okombo J, Muriithi S, Sasi P, Kortok MM, Lowe B, Campino S, Assefa S, Auburn S, Manske M, Maslen G, Peshu N, Kwiatkowski DP, Marsh K, Nzila A, Clark TG.
Scientific reports Volume 3 (2013) p.3318
DOI: 10.1038/srep03318

Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.
Nucleic acids research Volume 41 (2013) p.827-841
DOI: 10.1093/nar/gks1284

Diagnostic criteria and clinical guidelines standardization to automate case classification.
Courtot M, Zheng J, Stoeckert CJ, Brinkman RR, Ruttenberg A.
CEURS proceedings: International Conference on Biomedical Ontologies Volume 1060 (2013) p.101-104

Genomicus: five genome browsers for comparative genomics in eukaryota.
Louis A, Muffato M, Roest Crollius H.
Nucleic acids research Volume 41 (2013) p.D700-5
DOI: 10.1093/nar/gks1156

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA.
PloS one Volume 8 (2013) p.e61951
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miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs.
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LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.
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The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.
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Reconstructing Native American migrations from whole-genome and whole-exome data.
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Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
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Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
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Histone deacetylase 1 and 2 are essential for normal T-cell development and genomic stability in mice.
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Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture.
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The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.
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Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.
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A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus.
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Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
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Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
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A community-driven global reconstruction of human metabolism.
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A variant in LDLR is associated with abdominal aortic aneurysm.
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Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.
Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M, Naghra H, Cotton JA, Berriman M, Britton C, Gilleard JS.
International journal for parasitology Volume 43 (2013) p.465-475
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Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM.
Molecular bioSystems Volume 9 (2013) p.1756-1764
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Elucidating human phosphatase-substrate networks.
Li X, Wilmanns M, Thornton J, Köhn M.
Science signaling Volume 6 (2013) p.rs10
DOI: 10.1126/scisignal.2003203

Detection and imaging the expression of the trans-membrane protein CD44 in RT112 cells by use of enzyme-labeled antibodies and SECM.
Roberts WS, Davis F, Holmes JL, Collyer SD, Larcombe LD, Morgan SL, Higson SP.
Biosensors & bioelectronics Volume 41 (2013) p.282-288
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SMIM1 underlies the Vel blood group and influences red blood cell traits.
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, Karjalainen J, Kerstens HH, Kiddle G, Lloyd-Jones H, Needs M, Poole J, Soussan AA, Rendon A, Rieneck K, Sambrook JG, Schepers H, Silljé HHW, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA.
Nature genetics Volume 45 (2013) p.542-545
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The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.
Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA.
Genome biology Volume 14 (2013) p.R88
DOI: 10.1186/gb-2013-14-8-r88

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau MT, Heinig M, Lee YA, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FP, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, Jones EY, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hubner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J.
Nature genetics Volume 45 (2013) p.767-775
DOI: 10.1038/ng.2644

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson WO, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimäki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt MF, Mohlke KL, O'Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E.
Nature genetics Volume 45 (2013) p.501-512
DOI: 10.1038/ng.2606

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Ziehm M, Piper MD, Thornton JM.
Aging cell Volume 12 (2013) p.917-922
DOI: 10.1111/acel.12123

Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium.
Nature methods Volume 10 (2013) p.1185-1191
DOI: 10.1038/nmeth.2722

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.
Genome biology Volume 14 (2013) p.R70
DOI: 10.1186/gb-2013-14-7-r70

Genome-wide meta-analysis identifies new susceptibility loci for migraine.
Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G, Medland SE, Todt U, McArdle WL, Quaye L, Koiranen M, Ikram MA, Lehtimäki T, Stam AH, Ligthart L, Wedenoja J, Dunham I, Neale BM, Palta P, Hamalainen E, Schürks M, Rose LM, Buring JE, Ridker PM, Steinberg S, Stefansson H, Jakobsson F, Lawlor DA, Evans DM, Ring SM, Färkkilä M, Artto V, Kaunisto MA, Freilinger T, Schoenen J, Frants RR, Pelzer N, Weller CM, Zielman R, Heath AC, Madden PAF, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FMK, Hartikainen AL, Pouta A, van den Ende J, Uitterlinden AG, Hofman A, Amin N, Hottenga JJ, Vink JM, Heikkilä K, Alexander M, Muller-Myhsok B, Schreiber S, Meitinger T, Wichmann HE, Aromaa A, Eriksson JG, Traynor B, Trabzuni D, North American Brain Expression Consortium, UK Brain Expression Consortium, Rossin E, Lage K, Jacobs SBR, Gibbs JR, Birney E, Kaprio J, Penninx BW, Boomsma DI, van Duijn C, Raitakari O, Jarvelin MR, Zwart JA, Cherkas L, Strachan DP, Kubisch C, Ferrari MD, van den Maagdenberg AMJM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman D, Palotie A.
Nature genetics Volume 45 (2013) p.912-917
DOI: 10.1038/ng.2676

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M.
Nucleic acids research Volume 41 (2013) p.e121
DOI: 10.1093/nar/gkt263

HAMAP in 2013, new developments in the protein family classification and annotation system.
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium.
Nucleic acids research Volume 41 (2013) p.D584-9
DOI: 10.1093/nar/gks1157

Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1343-1344
DOI: 10.1093/bioinformatics/btt106

A decadal view of biodiversity informatics: challenges and priorities.
Hardisty A, Roberts D, Biodiversity Informatics Community, Addink W, Aelterman B, Agosti D, Amaral-Zettler L, Ariño AH, Arvanitidis C, Backeljau T, Bailly N, Belbin L, Berendsohn W, Bertrand N, Caithness N, Campbell D, Cochrane G, Conruyt N, Culham A, Damgaard C, Davies N, Fady B, Faulwetter S, Feest A, Field D, Garnier E, Geser G, Gilbert J, Grosche, Grosser D, Hardisty A, Herbinet B, Hobern D, Jones A, de Jong Y, King D, Knapp S, Koivula H, Los W, Meyer C, Morris RA, Morrison N, Morse D, Obst M, Pafilis E, Page LM, Page R, Pape T, Parr C, Paton A, Patterson D, Paymal E, Penev L, Pollet M, Pyle R, von Raab-Straube E, Robert V, Roberts D, Robertson T, Rovellotti O, Saarenmaa H, Schalk P, Schaminee J, Schofield P, Sier A, Sierra S, Smith V, van Spronsen E, Thornton-Wood S, van Tienderen P, van Tol J, Tuama ÉÓ, Uetz P, Vaas L, Vignes Lebbe R, Vision T, Vu D, De Wever A, White R, Willis K, Young F.
BMC ecology Volume 13 (2013) p.16
DOI: 10.1186/1472-6785-13-16

The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat023
DOI: 10.1093/database/bat023

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR.
Molecular & cellular proteomics : MCP Volume 12 (2013) p.2332-2340
DOI: 10.1074/mcp.o113.028506

The SHOCT domain: a widespread domain under-represented in model organisms.
Eberhardt RY, Bartholdson SJ, Punta M, Bateman A.
PloS one Volume 8 (2013) p.e57848
DOI: 10.1371/journal.pone.0057848

The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M.
Database: The Journal of Biological Databases and Curation Volume 2013 (2013) p.

The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat029
DOI: 10.1093/database/bat029

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M, HUPO-PSI Group.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat009
DOI: 10.1093/database/bat009

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.
Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L.
Journal of proteomics Volume 95 (2013) p.89-92
DOI: 10.1016/j.jprot.2013.04.011

Critical assessment of automated flow cytometry data analysis techniques.
Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.
Nature methods Volume 10 (2013) p.228-238
DOI: 10.1038/nmeth.2365

BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
Bioinformatics Volume 29 (2013) p.1103-1104
DOI: 10.1093/bioinformatics/btt100

Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium.
Nucleic acids research Volume 41 (2013) p.D43-7
DOI: 10.1093/nar/gks1068

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1325-1332
DOI: 10.1093/bioinformatics/btt113

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D781-6
DOI: 10.1093/nar/gks1004

Bioinformatics workflows and web services in systems biology made easy for experimentalists.
Jimenez RC, Corpas M.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.299-310
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The impact of mathematical modeling on the understanding of diabetes and related complications.
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V.
CPT: pharmacometrics & systems pharmacology Volume 2 (2013) p.e54
DOI: 10.1038/psp.2013.30

Expanding natural product chemistry resources at the EBI.
Hastings J, Conesa P, Dekker A, Ennis M, Haug K, Jayaseelan K, Kale N, Mahendraker T, Moreno P, Muthukrishnan V, Owen G, Salek R, Turner S, Steinbeck C.
Journal of Cheminformatics Volume 5 (2013) p.P43-P43

Modeling signaling networks with different formalisms: a preview.
MacNamara A, Henriques D, Saez-Rodriguez J.
Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.89-105
DOI: 10.1007/978-1-62703-450-0_5

Evolutionary biology: The handiwork of tinkering.
Flicek P.
Nature Volume 500 (2013) p.158-159
DOI: 10.1038/500158a

Noncanonical expression of caudal during early embryogenesis in the pea aphid Acyrthosiphon pisum: maternal cad-driven posterior development is not conserved.
Chang CC, Hsiao YM, Huang TY, Cook CE, Shigenobu S, Chang TH.
Insect molecular biology Volume 22 (2013) p.442-455
DOI: 10.1111/imb.12035

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.
Hill AF, Pegtel DM, Lambertz U, Leonardi T, O'Driscoll L, Pluchino S, Ter-Ovanesyan D, Nolte-'t Hoen EN.
Journal of extracellular vesicles Volume 2 (2013) p.
DOI: 10.3402/jev.v2i0.22859

Filling out the structural map of the NTF2-like superfamily.
Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L.
BMC bioinformatics Volume 14 (2013) p.327
DOI: 10.1186/1471-2105-14-327

ISMB/ECCB 2013 Proceedings Papers Committee.

Bioinformatics Volume 29 (2013) p.i3-i8

Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.
BMC systems biology Volume 7 (2013) p.116
DOI: 10.1186/1752-0509-7-116

A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2808-2809
DOI: 10.1093/bioinformatics/btt484

Construction of cell type-specific logic models of signaling networks using CellNOpt.
Morris MK, Melas I, Saez-Rodriguez J.
Methods in molecular biology (Clifton, N.J.) Volume 930 (2013) p.179-214
DOI: 10.1007/978-1-62703-059-5_8

Evolution and functional cross-talk of protein post-translational modifications.
Beltrao P, Bork P, Krogan NJ, van Noort V.
Molecular systems biology Volume 9 (2013) p.714
DOI: 10.1002/msb.201304521

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP.
Nucleic acids research Volume 41 (2013) p.4549-4564
DOI: 10.1093/nar/gkt148

Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.
Nucleic acids research Volume 41 (2013) p.D226-32
DOI: 10.1093/nar/gks1005

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D456-63
DOI: 10.1093/nar/gks1146

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.
Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ.
Genome biology Volume 14 (2013) p.R11
DOI: 10.1186/gb-2013-14-2-r11

OntoQuery: easy-to-use web-based OWL querying.
Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.
Bioinformatics Volume 29 (2013) p.2955-2957
DOI: 10.1093/bioinformatics/btt514

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
Nature methods Volume 10 (2013) p.676-682
DOI: 10.1038/nmeth.2519

The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.
PLoS biology Volume 11 (2013) p.e1001638
DOI: 10.1371/journal.pbio.1001638

The IMGT/HLA database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic acids research Volume 41 (2013) p.D1222-7
DOI: 10.1093/nar/gks949

LUD, a new protein domain associated with lactate utilization.
Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A.
BMC bioinformatics Volume 14 (2013) p.341
DOI: 10.1186/1471-2105-14-341

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat077
DOI: 10.1093/database/bat077

The annotation-enriched non-redundant patent sequence databases.
Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bat005
DOI: 10.1093/database/bat005

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM.
Current opinion in structural biology Volume 23 (2013) p.443-450
DOI: 10.1016/j.sbi.2013.03.006

IPD--the Immuno Polymorphism Database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG.
Nucleic acids research Volume 41 (2013) p.D1234-40
DOI: 10.1093/nar/gks1140

bioWeb3D: an online webGL 3D data visualisation tool.
Pettit JB, Marioni JC.
BMC bioinformatics Volume 14 (2013) p.185
DOI: 10.1186/1471-2105-14-185

ISCB computational biology Wikipedia competition.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B.
PLoS computational biology Volume 9 (2013) p.e1003242
DOI: 10.1371/journal.pcbi.1003242

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.
Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A.
BMC bioinformatics Volume 14 (2013) p.265
DOI: 10.1186/1471-2105-14-265

Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.
Nature biotechnology Volume 31 (2013) p.126-134
DOI: 10.1038/nbt.2486

Proteomics data exchange and storage: the need for common standards and public repositories.
Jiménez RC, Vizcaíno JA.
Methods in molecular biology (Clifton, N.J.) Volume 1007 (2013) p.317-333
DOI: 10.1007/978-1-62703-392-3_14

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.
Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G, Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire P, Birney E, Müller F, Stupka E.
Nucleic acids research Volume 41 (2013) p.3600-3618
DOI: 10.1093/nar/gkt030

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 29 (2013) p.132-134
DOI: 10.1093/bioinformatics/bts656

Biomarkers of food intake and metabolite differences between plasma and red blood cell matrices; a human metabolomic profile approach.
Catalán Ú, Rodríguez MÁ, Ras MR, Maciá A, Mallol R, Vinaixa M, Fernández-Castillejo S, Valls RM, Pedret A, Griffin JL, Salek R, Correig X, Motilva MJ, Solà R.
Molecular bioSystems Volume 9 (2013) p.1411-1422
DOI: 10.1039/c3mb25554a

Characterization of a versatile organometallic pro-drug (CORM) for experimental CO based therapeutics.
Seixas JD, Mukhopadhyay A, Santos-Silva T, Otterbein LE, Gallo DJ, Rodrigues SS, Guerreiro BH, Gonçalves AM, Penacho N, Marques AR, Coelho AC, Reis PM, Romão MJ, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 42 (2013) p.5985-5998
DOI: 10.1039/c2dt32174b

The role of structural bioinformatics resources in the era of integrative structural biology.
Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.710-721
DOI: 10.1107/s0907444913001157

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV.
Briefings in bioinformatics Volume 14 (2013) p.548-555
DOI: 10.1093/bib/bbt045

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P.
Genome biology Volume 14 (2013) p.R148
DOI: 10.1186/gb-2013-14-12-r148

Epimutation profiling in Beckwith-Wiedemann syndrome: relationship with assisted reproductive technology.
Tee L, Lim DH, Dias RP, Baudement MO, Slater AA, Kirby G, Hancocks T, Stewart H, Hardy C, Macdonald F, Maher ER.
Clinical epigenetics Volume 5 (2013) p.23
DOI: 10.1186/1868-7083-5-23

BioServices: a common Python package to access biological Web Services programmatically.
Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J.
Bioinformatics Volume 29 (2013) p.3241-3242
DOI: 10.1093/bioinformatics/btt547

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins Volume 81 (2013) p.583-591
DOI: 10.1002/prot.24213

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic acids research Volume 41 (2013) p.D773-80
DOI: 10.1093/nar/gks1112

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E.
Nature Volume 494 (2013) p.77-80
DOI: 10.1038/nature11875

Transcriptional data: a new gateway to drug repositioning?
Iorio F, Rittman T, Ge H, Menden M, Saez-Rodriguez J.
Drug discovery today Volume 18 (2013) p.350-357
DOI: 10.1016/j.drudis.2012.07.014

The International Nucleotide Sequence Database Collaboration.
Nakamura Y, Cochrane G, Karsch-Mizrachi I, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 41 (2013) p.D21-4
DOI: 10.1093/nar/gks1084

The future of the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Biopolymers Volume 99 (2013) p.218-222
DOI: 10.1002/bip.22132

Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J, Bertone P.
Nature methods Volume 10 (2013) p.1177-1184
DOI: 10.1038/nmeth.2714

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M.
Genome research Volume 23 (2013) p.2066-2077
DOI: 10.1101/gr.161620.113

ROCK: a resource for integrative breast cancer data analysis.
Ur-Rehman S, Gao Q, Mitsopoulos C, Zvelebil M.
Breast cancer research and treatment Volume 139 (2013) p.907-921
DOI: 10.1007/s10549-013-2593-z

Genetic susceptibility to non-necrotizing erysipelas/cellulitis.
Hannula-Jouppi K, Massinen S, Siljander T, Mäkelä S, Kivinen K, Leinonen R, Jiao H, Aitos P, Karppelin M, Vuopio J, Syrjänen J, Kere J.
PloS one Volume 8 (2013) p.e56225
DOI: 10.1371/journal.pone.0056225

HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Hickey G, Paten B, Earl D, Zerbino D, Haussler D.
Bioinformatics (Oxford, England) Volume 29 (2013) p.1341-1342
DOI: 10.1093/bioinformatics/btt128

Structural and functional annotation of the porcine immunome.
Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK.
BMC genomics Volume 14 (2013) p.332
DOI: 10.1186/1471-2164-14-332

Network based elucidation of drug response: from modulators to targets.
Iorio F, Saez-Rodriguez J, di Bernardo D.
BMC systems biology Volume 7 (2013) p.139
DOI: 10.1186/1752-0509-7-139

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.
Nucleic acids research Volume 41 (2013) p.D499-507
DOI: 10.1093/nar/gks1266

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.
BMC systems biology Volume 7 (2013) p.135
DOI: 10.1186/1752-0509-7-135

Facing growth in the European Nucleotide Archive.
Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V.
Nucleic acids research Volume 41 (2013) p.D30-5
DOI: 10.1093/nar/gks1175

Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ.
G3 (Bethesda, Md.) Volume 3 (2013) p.2031-2047
DOI: 10.1534/g3.113.007153

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic acids research Volume 41 (2013) p.D530-5
DOI: 10.1093/nar/gks1050

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ.
Nucleic acids research Volume 41 (2013) p.D483-9
DOI: 10.1093/nar/gks1258

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R.
Database : the journal of biological databases and curation Volume 2013 (2013) p.bas062
DOI: 10.1093/database/bas062

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.
BMC genomics Volume 14 (2013) p.513
DOI: 10.1186/1471-2164-14-513

Shorthand notation for lipid structures derived from mass spectrometry.
Liebisch G, Vizcaíno JA, Köfeler H, Trötzmüller M, Griffiths WJ, Schmitz G, Spener F, Wakelam MJ.
Journal of lipid research Volume 54 (2013) p.1523-1530
DOI: 10.1194/jlr.m033506

CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system.
Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG.
Cell reports Volume 5 (2013) p.271-282
DOI: 10.1016/j.celrep.2013.09.001

2012

CING: an integrated residue-based structure validation program suite.
Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW.
Journal of biomolecular NMR Volume 54 (2012) p.267-283
DOI: 10.1007/s10858-012-9669-7

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Genome research Volume 22 (2012) p.9-24
DOI: 10.1101/gr.127597.111

Molecular interaction databases.
Orchard S.
Proteomics Volume 12 (2012) p.1656-1662
DOI: 10.1002/pmic.201100484

Looking for Darwin in genomic sequences--validity and success of statistical methods.
Zhai W, Nielsen R, Goldman N, Yang Z.
Molecular biology and evolution Volume 29 (2012) p.2889-2893
DOI: 10.1093/molbev/mss104

The kinase Sgg modulates temporal development of macrochaetes in Drosophila by phosphorylation of Scute and Pannier.
Yang M, Hatton-Ellis E, Simpson P.
Development (Cambridge, England) Volume 139 (2012) p.325-334
DOI: 10.1242/dev.074260

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.
Wimalaratne SM, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B.
Bioinformatics Volume 28 (2012) p.448-450
DOI: 10.1093/bioinformatics/btr662

FlyBase 101--the basics of navigating FlyBase.
McQuilton P, St Pierre SE, Thurmond J, FlyBase Consortium.
Nucleic acids research Volume 40 (2012) p.D706-14
DOI: 10.1093/nar/gkr1030

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A.
Circulation Volume 125 (2012) p.2751-2761
DOI: 10.1161/circulationaha.111.044354

European initiative towards quality standards in education and training for discovery, development and use of medicines.
Klech H, Brooksbank C, Price S, Verpillat P, Bühler FR, Dubois D, Haider N, Johnson C, Lindén HH, Payton T, Renn O, See W.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences Volume 45 (2012) p.515-520
DOI: 10.1016/j.ejps.2011.12.005

Correction: Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival.
Sokolowski B, Orchard S, Harvey M, Sridhar S, Sakai Y.
PloS one Volume 7 (2012) p.

The HUPO initiative on Model Organism Proteomes, iMOP.
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.
Proteomics Volume 12 (2012) p.340-345
DOI: 10.1002/pmic.201290014

A transcription factor collective defines cardiac cell fate and reflects lineage history.
Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE.
Cell Volume 148 (2012) p.473-486
DOI: 10.1016/j.cell.2012.01.030

The KUPKB: a novel Web application to access multiomics data on kidney disease.
Klein J, Jupp S, Moulos P, Fernandez M, Buffin-Meyer B, Casemayou A, Chaaya R, Charonis A, Bascands JL, Stevens R, Schanstra JP.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 26 (2012) p.2145-2153
DOI: 10.1096/fj.11-194381

Error-correcting properties of the SOLiD Exact Call Chemistry.
Massingham T, Goldman N.
BMC bioinformatics Volume 13 (2012) p.145
DOI: 10.1186/1471-2105-13-145

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N.
Molecular Biology and Evolution Volume 29 (2012) p.1125-1139
DOI: 10.1093/molbev/msr272

An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.
Sipos B, Massingham T, Stütz AM, Goldman N.
PloS one Volume 7 (2012) p.e43359
DOI: 10.1371/journal.pone.0043359

Large-scale analysis of microRNA evolution.
Guerra-Assunção JA, Enright AJ.
BMC genomics Volume 13 (2012) p.218
DOI: 10.1186/1471-2164-13-218

A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C.
Science (New York, N.Y.) Volume 335 (2012) p.823-828
DOI: 10.1126/science.1215040

Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Schwarz MA, Thornton J, Xu H, Awasthi N, Schwarz RE.
PloS one Volume 7 (2012) p.e33101
DOI: 10.1371/journal.pone.0033101

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A, Vilella AJ, Goldman N.
Bioinformatics Volume 28 (2012) p.1684-1691
DOI: 10.1093/bioinformatics/bts198

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1086-1092
DOI: 10.1093/bioinformatics/bts094

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.
Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 23 (2012) p.641-652
DOI: 10.1007/s00335-012-9428-9

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.
Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJ, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WH, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JR, Platou CG, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney AS, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CN, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Wellcome Trust Case Control Consortium, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Investigators, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Asian Genetic Epidemiology Network–Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.
Nature genetics Volume 44 (2012) p.981-990
DOI: 10.1038/ng.2383

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
Briefings in bioinformatics Volume 13 (2012) p.383-389
DOI: 10.1093/bib/bbr064

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.
Bioinformatics (Oxford, England) Volume 28 (2012) p.3163-3165
DOI: 10.1093/bioinformatics/bts577

Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level.
Fanucchi F, Alpi E, Olivieri S, Cannistraci CV, Bachi A, Alpi A, Alessio M.
Biochimica et biophysica acta Volume 1824 (2012) p.813-825
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High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.
Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K, Amos CI, Padyukov L, Toes RE, Huizinga TW, Wijmenga C, Trynka G, Franke L, Westra HJ, Alfredsson L, Hu X, Sandor C, de Bakker PI, Davila S, Khor CC, Heng KK, Andrews R, Edkins S, Hunt SE, Langford C, Symmons D, Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate, Wellcome Trust Case Control Consortium, Concannon P, Onengut-Gumuscu S, Rich SS, Deloukas P, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Ärlsetig L, Martin J, Rantapää-Dahlqvist S, Plenge RM, Raychaudhuri S, Klareskog L, Gregersen PK, Worthington J.
Nature genetics Volume 44 (2012) p.1336-1340
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All Your Base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.
Genome biology Volume 13 (2012) p.R13
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Populous: a tool for building OWL ontologies from templates.
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BMC bioinformatics Volume 13 Suppl 1 (2012) p.S5
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Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
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PloS one Volume 7 (2012) p.e50881
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In support of the BMRB.
Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S.
Nature structural & molecular biology Volume 19 (2012) p.854-860
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Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
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PLoS Computational Biology Volume 8 (2012) p.e1002403
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Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, 1000 Genomes Project Consortium.
American journal of human genetics Volume 91 (2012) p.1022-1032
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UniProtKB amid the turmoil of plant proteomics research.
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Frontiers in Plant Science Volume 3 (2012) p.270
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Directly e-mailing authors of newly published papers encourages community curation.
Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas024
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ChEMBL: a large-scale bioactivity database for drug discovery.
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Nucleic acids research Volume 40 (2012) p.D1100-7
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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
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Genome research Volume 22 (2012) p.1798-1812
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Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer.
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European journal of mass spectrometry (Chichester, England) Volume 18 (2012) p.505-508
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Modeling gene expression using chromatin features in various cellular contexts.
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Genome biology Volume 13 (2012) p.R53
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Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.
arcOGEN Consortium, arcOGEN Collaborators, Zeggini E, Panoutsopoulou K, Southam L, Rayner NW, Day-Williams AG, Lopes MC, Boraska V, Esko T, Evangelou E, Hoffman A, Houwing-Duistermaat JJ, Ingvarsson T, Jonsdottir I, Jonnson H, Kerkhof HJ, Kloppenburg M, Bos SD, Mangino M, Metrustry S, Slagboom PE, Thorleifsson G, Raine EV, Ratnayake M, Ricketts M, Beazley C, Blackburn H, Bumpstead S, Elliott KS, Hunt SE, Potter SC, Shin SY, Yadav VK, Zhai G, Sherburn K, Dixon K, Arden E, Aslam N, Battley PK, Carluke I, Doherty S, Gordon A, Joseph J, Keen R, Koller NC, Mitchell S, O'Neill F, Paling E, Reed MR, Rivadeneira F, Swift D, Walker K, Watkins B, Wheeler M, Birrell F, Ioannidis JP, Meulenbelt I, Metspalu A, Rai A, Salter D, Stefansson K, Stykarsdottir U, Uitterlinden AG, van Meurs JB, Chapman K, Deloukas P, Ollier WE, Wallis GA, Arden N, Carr A, Doherty M, McCaskie A, Willkinson JM, Ralston SH, Valdes AM, Spector TD, Loughlin J.
Lancet (London, England) Volume 380 (2012) p.815-823
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Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
Su Z, Gay LJ, Strange A, Palles C, Band G, Whiteman DC, Lescai F, Langford C, Nanji M, Edkins S, van der Winkel A, Levine D, Sasieni P, Bellenguez C, Howarth K, Freeman C, Trudgill N, Tucker AT, Pirinen M, Peppelenbosch MP, van der Laan LJ, Kuipers EJ, Drenth JP, Peters WH, Reynolds JV, Kelleher DP, McManus R, Grabsch H, Prenen H, Bisschops R, Krishnadath K, Siersema PD, van Baal JW, Middleton M, Petty R, Gillies R, Burch N, Bhandari P, Paterson S, Edwards C, Penman I, Vaidya K, Ang Y, Murray I, Patel P, Ye W, Mullins P, Wu AH, Bird NC, Dallal H, Shaheen NJ, Murray LJ, Koss K, Bernstein L, Romero Y, Hardie LJ, Zhang R, Winter H, Corley DA, Panter S, Risch HA, Reid BJ, Sargeant I, Gammon MD, Smart H, Dhar A, McMurtry H, Ali H, Liu G, Casson AG, Chow WH, Rutter M, Tawil A, Morris D, Nwokolo C, Isaacs P, Rodgers C, Ragunath K, MacDonald C, Haigh C, Monk D, Davies G, Wajed S, Johnston D, Gibbons M, Cullen S, Church N, Langley R, Griffin M, Alderson D, Deloukas P, Hunt SE, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Anderson M, Brooks C, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood N, Trynka G, Wijmenga C, Cazier JB, Atherfold P, Nicholson AM, Gellatly NL, Glancy D, Cooper SC, Cunningham D, Lind T, Hapeshi J, Ferry D, Rathbone B, Brown J, Love S, Attwood S, MacGregor S, Watson P, Sanders S, Ek W, Harrison RF, Moayyedi P, de Caestecker J, Barr H, Stupka E, Vaughan TL, Peltonen L, Spencer CC, Tomlinson I, Donnelly P, Jankowski JA, Esophageal Adenocarcinoma Genetics Consortium, Wellcome Trust Case Control Consortium 2.
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Seven newly identified loci for autoimmune thyroid disease.
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A database for chemical proteomics: ChEBI.
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Visualizing the drug target landscape.
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Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
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Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.
Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA.
BMC genomics Volume 13 (2012) p.1
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The tomato genome sequence provides insights into fleshy fruit evolution.
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Nature Volume 485 (2012) p.635-641
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Reorganizing the protein space at the Universal Protein Resource (UniProt).
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A parallel systematic-Monte Carlo algorithm for exploring conformational space.
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Current topics in medicinal chemistry Volume 12 (2012) p.1790-1796
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An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS.
Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G, Manske M, Imwong M, Dondorp AM, Kwiatkowski DP, Quail MA, Swerdlow H.
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Paralogous annotation of disease-causing variants in long QT syndrome genes.
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Human mutation Volume 33 (2012) p.1188-1191
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Structure-based classification and ontology in chemistry.
Hastings J, Magka D, Batchelor C, Duan L, Stevens R, Ennis M, Steinbeck C.
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FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM.
Nucleic acids research Volume 40 (2012) p.D776-82
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Natural product-likeness score revisited: an open-source, open-data implementation.
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BMC bioinformatics Volume 13 (2012) p.106
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Annotating Human P-Glycoprotein Bioassay Data.
Zdrazil B, Pinto M, Vasanthanathan P, Williams AJ, Balderud LZ, Engkvist O, Chichester C, Hersey A, Overington JP, Ecker GF.
Molecular informatics Volume 31 (2012) p.599-609
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The UniProt-GO Annotation database in 2011.
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Nucleic acids research Volume 40 (2012) p.D565-70
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Hepatitis B virus in transfusion medicine: still a problem?
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Biologicals : journal of the International Association of Biological Standardization Volume 40 (2012) p.180-186
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The Gene Ontology: enhancements for 2011.
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Structured chemical class definitions and automated matching for chemical ontology evolution.
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Journal of cheminformatics Volume 4 (2012) p.P5-P5

Toxicogenomics Investigation Under the eTOX Project
Taboureau O, Hersey A, Audouze K, Gautier L, Jacobsen UP, Akhtar R, Atkinson F, Overington JP, Brunak S.
Journal of pharmacogenomics & pharmacoproteomics Volume S7 (2012) p.1-5

Self-organizing ontology of biochemically relevant small molecules.
Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M.
BMC bioinformatics Volume 13 (2012) p.3
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Rhea--a manually curated resource of biochemical reactions.
Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C.
Nucleic acids research Volume 40 (2012) p.D754-60
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Systematic identification of genomic markers of drug sensitivity in cancer cells.
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O'Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH.
Nature Volume 483 (2012) p.570-575
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The genomic basis of adaptive evolution in threespine sticklebacks.
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Nature Volume 484 (2012) p.55-61
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CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J.
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Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke.
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Nature genetics Volume 44 (2012) p.328-333
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Open data for drug discovery: learning from the biological community.
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Future medicinal chemistry Volume 4 (2012) p.1865-1867
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Shouldn't enantiomeric purity be included in the minimum information about a bioactive entity? Response from the MIABE group
Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.
Nature reviews. Drug discovery Volume 11 (2012) p.730
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Data management challenges in three-dimensional EM.
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Nature structural & molecular biology Volume 19 (2012) p.1203-1207
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Extent, causes, and consequences of small RNA expression variation in human adipose tissue.
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PLoS genetics Volume 8 (2012) p.e1002704
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Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.
Schulte I, Batty EM, Pole JC, Blood KA, Mo S, Cooke SL, Ng C, Howe KL, Chin SF, Brenton JD, Caldas C, Howarth KD, Edwards PA.
BMC genomics Volume 13 (2012) p.719
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Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.E944-53
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ISMB 2012 Proceedings Papers Committee. July 15 to July 19, 2012, Long Beach, CA, USA. Editorial.
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Bioinformatics Volume 28 (2012) p.i1
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ACPYPE - AnteChamber PYthon Parser interfacE.
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Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.
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Journey to the genetic interior. Interview by Stephen S Hall.
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Scientific American Volume 307 (2012) p.80-2, 84

Insights into hominid evolution from the gorilla genome sequence.
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Nature Volume 483 (2012) p.169-175
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Isoelectric point optimization using peptide descriptors and support vector machines.
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Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.
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Frontiers in plant science Volume 3 (2012) p.1
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Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.
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Toward interoperable bioscience data.
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First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans?
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Journal of biomolecular structure & dynamics Volume 30 (2012) p.546-558
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Nucleic acids research Volume 40 (2012) p.D790-6
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The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer.
Ng CK, Cooke SL, Howe K, Newman S, Xian J, Temple J, Batty EM, Pole JC, Langdon SP, Edwards PA, Brenton JD.
The Journal of pathology Volume 226 (2012) p.703-712
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Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X, Coffey AJ, Turner DJ, Swerdlow H, Burton J, Quail MA, Conrad DF, Enright AJ, Tyler-Smith C, Xue Y.
Human genetics Volume 131 (2012) p.665-674
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ISMB 2012 PROCEEDINGS PAPERS COMMITTEE.

Bioinformatics Volume 28 (2012) p.i2-i6

PSI-Search: iterative HOE-reduced profile SSEARCH searching.
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1650-1651
DOI: 10.1093/bioinformatics/bts240

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo JB, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara SM, Marsh K, Jiang H, Su XZ, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White NJ, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail MA, Turner DJ, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan JC, Ferdig MT, Amambua-Ngwa A, Conway DJ, Takala-Harrison S, Plowe CV, Rayner JC, Rockett KA, Clark TG, Newbold CI, Berriman M, MacInnis B, Kwiatkowski DP.
Nature Volume 487 (2012) p.375-379
DOI: 10.1038/nature11174

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.
Prins P, Goto N, Yates A, Gautier L, Willis S, Fields C, Katayama T.
Methods in molecular biology (Clifton, N.J.) Volume 856 (2012) p.513-527
DOI: 10.1007/978-1-61779-585-5_21

BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.
Bioinformatics (Oxford, England) Volume 28 (2012) p.2693-2695
DOI: 10.1093/bioinformatics/bts494

Ensembl 2012.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Yates A, Zadissa A, Searle SM.
Nucleic acids research Volume 40 (2012) p.D84-90
DOI: 10.1093/nar/gkr991

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Nucleic acids research Volume 40 (2012) p.D91-7
DOI: 10.1093/nar/gkr895

A suggested new bacteriophage genus: "Viunalikevirus".
Adriaenssens EM, Ackermann HW, Anany H, Blasdel B, Connerton IF, Goulding D, Griffiths MW, Hooton SP, Kutter EM, Kropinski AM, Lee JH, Maes M, Pickard D, Ryu S, Sepehrizadeh Z, Shahrbabak SS, Toribio AL, Lavigne R.
Archives of virology Volume 157 (2012) p.2035-2046
DOI: 10.1007/s00705-012-1360-5

OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR.
Nature methods Volume 9 (2012) p.245-253
DOI: 10.1038/nmeth.1896

WormBase 2012: more genomes, more data, new website.
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic acids research Volume 40 (2012) p.D735-41
DOI: 10.1093/nar/gkr954

graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P.
Bioinformatics Volume 28 (2012) p.1665-1667
DOI: 10.1093/bioinformatics/bts258

WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW.
Worm Volume 1 (2012) p.15-21
DOI: 10.4161/worm.19574

Opportunities for text mining in the FlyBase genetic literature curation workflow.
McQuilton P, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas039
DOI: 10.1093/database/bas039

MetaboLights: towards a new COSMOS of metabolomics data management.
Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL.
Metabolomics Volume 8 (2012) p.757-760
DOI: 10.1007/s11306-012-0462-0

Analysis of variation at transcription factor binding sites in Drosophila and humans.
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E.
Genome biology Volume 13 (2012) p.R49
DOI: 10.1186/gb-2012-13-9-r49

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs.
Manakov SA, Morton A, Enright AJ, Grant SG.
Frontiers in neuroscience Volume 6 (2012) p.156
DOI: 10.3389/fnins.2012.00156

GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.
Britto R, Sallou O, Collin O, Michaux G, Primig M, Chalmel F.
Nucleic acids research Volume 40 (2012) p.W458-65
DOI: 10.1093/nar/gks380

Bioimage informatics: a new category in Bioinformatics.
Peng H, Bateman A, Valencia A, Wren JD.
Bioinformatics Volume 28 (2012) p.1057
DOI: 10.1093/bioinformatics/bts111

The Sequence Read Archive: explosive growth of sequencing data.
Kodama Y, Shumway M, Leinonen R, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 40 (2012) p.D54-6
DOI: 10.1093/nar/gkr854

HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease.
Lam MP, Vivanco F, Scholten A, Hermjakob H, Van Eyk J, Ping P.
Proteomics Volume 12 (2012) p.749-751
DOI: 10.1002/pmic.201270015

Automatic categorization of diverse experimental information in the bioscience literature.
Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold SJ, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW.
BMC bioinformatics Volume 13 (2012) p.16
DOI: 10.1186/1471-2105-13-16

The Origin and Function of Anti-Fungal Peptides in C. elegans: Open Questions.
Pujol N, Davis PA, Ewbank JJ.
Frontiers in immunology Volume 3 (2012) p.237
DOI: 10.3389/fimmu.2012.00237

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks.
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM.
Molecular cell Volume 46 (2012) p.871-883
DOI: 10.1016/j.molcel.2012.05.039

Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N.
Nature Volume 491 (2012) p.705-710
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Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium.
Nature Volume 487 (2012) p.94-98
DOI: 10.1038/nature11041

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D, VectorBase Consortium.
Nucleic acids research Volume 40 (2012) p.D729-34
DOI: 10.1093/nar/gkr1089

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.
Cancers Volume 4 (2012) p.1180-1211
DOI: 10.3390/cancers4041180

BLUEPRINT to decode the epigenetic signature written in blood.
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S.
Nature biotechnology Volume 30 (2012) p.224-226
DOI: 10.1038/nbt.2153

The International Nucleotide Sequence Database Collaboration.
Karsch-Mizrachi I, Nakamura Y, Cochrane G, International Nucleotide Sequence Database Collaboration.
Nucleic acids research Volume 40 (2012) p.D33-7
DOI: 10.1093/nar/gkr1006

Metagenomic analysis: the challenge of the data bonanza.
Hunter CI, Mitchell A, Jones P, McAnulla C, Pesseat S, Scheremetjew M, Hunter S.
Briefings in bioinformatics Volume 13 (2012) p.743-746
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Improvements in the Protein Identifier Cross-Reference service.
Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA.
Nucleic acids research Volume 40 (2012) p.W276-80
DOI: 10.1093/nar/gks338

The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012.
Attwood TK, Coletta A, Muirhead G, Pavlopoulou A, Philippou PB, Popov I, Romá-Mateo C, Theodosiou A, Mitchell AL.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas019
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The 2010 cryo-EM modeling challenge.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W.
Biopolymers Volume 97 (2012) p.651-654
DOI: 10.1002/bip.22081

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.
Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA.
Integrative biology : quantitative biosciences from nano to macro Volume 4 (2012) p.1038-1048
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RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011.
Robbins RJ, Cochrane G, Davies N, Dawyndt P, Kottmann R, Krishtalka LK, Morrison N, Tuama EÓ, San Gil I, Wooley J.
Standards in genomic sciences Volume 7 (2012) p.153-158
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The mammalian gene function resource: the International Knockout Mouse Consortium.
Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 23 (2012) p.580-586
DOI: 10.1007/s00335-012-9422-2

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.
Journal of proteome research Volume 11 (2012) p.1412-1419
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A network-oriented perspective on cardiac calcium signaling.
George CH, Parthimos D, Silvester NC.
American journal of physiology. Cell physiology Volume 303 (2012) p.C897-910
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InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.
Nucleic acids research Volume 40 (2012) p.D306-12
DOI: 10.1093/nar/gkr948

Bioinformatics meets user-centred design: a perspective.
Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C.
PLoS Computational Biology Volume 8 (2012) p.e1002554
DOI: 10.1371/journal.pcbi.1002554

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.
Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG.
PloS one Volume 7 (2012) p.e50085
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An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium.
Nature Volume 489 (2012) p.57-74
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Accessing and using chemical property databases.
Hastings J, Josephs Z, Steinbeck C.
Methods in molecular biology (Clifton, N.J.) Volume 929 (2012) p.193-219
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MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.
Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P.
PloS one Volume 7 (2012) p.e40938
DOI: 10.1371/journal.pone.0040938

WormBase: Annotating many nematode genomes
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg P.
Worm Volume 1 (2012) p.15-21

An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
Nelson AC, Pillay N, Henderson S, Presneau N, Tirabosco R, Halai D, Berisha F, Flicek P, Stemple DL, Stern CD, Wardle FC, Flanagan AM.
The Journal of pathology Volume 228 (2012) p.274-285
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Analyses of pig genomes provide insight into porcine demography and evolution.
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.
Nature Volume 491 (2012) p.393-398
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The YARHG domain: an extracellular domain in search of a function.
Coggill P, Bateman A.
PloS one Volume 7 (2012) p.e35575
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The BioSample Database (BioSD) at the European Bioinformatics Institute.
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research Volume 40 (2012) p.D64-70
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Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation.
Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N, Hunter S.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bar068
DOI: 10.1093/database/bar068

MyDas, an extensible Java DAS server.
Salazar GA, García LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.
PloS one Volume 7 (2012) p.e44180
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The Protein Data Bank at 40: reflecting on the past to prepare for the future.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure (London, England : 1993) Volume 20 (2012) p.391-396
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MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.
Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C.
The Journal of biological chemistry Volume 287 (2012) p.29516-29528
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Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P.
Genome research Volume 22 (2012) p.2163-2175
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Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting.
Zheng-Bradley X, Flicek P.
Human mutation Volume 33 (2012) p.1016-1019
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PomBase: a comprehensive online resource for fission yeast.
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Nucleic acids research Volume 40 (2012) p.D695-9
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Modeling signaling networks using high-throughput phospho-proteomics.
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Advances in experimental medicine and biology Volume 736 (2012) p.19-57
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Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.1204-1209
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The making of ENCODE: Lessons for big-data projects.
Birney E.
Nature Volume 489 (2012) p.49-51
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Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.
Proteomics Volume 12 (2012) p.11-20
DOI: 10.1002/pmic.201100562

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H.
Proteomics Volume 12 (2012) p.351-355
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Mapping the human phosphatome on growth pathways.
Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G.
Molecular systems biology Volume 8 (2012) p.603
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De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.
Nature genetics Volume 44 (2012) p.226-232
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A combined functional annotation score for non-synonymous variants.
Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E.
Human heredity Volume 73 (2012) p.47-51
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Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.
BMC bioinformatics Volume 13 (2012) p.324
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Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.
Schmidt D, Schwalie P, Wilson M, Ballester B, Gonçalves Â, Kutter C, Brown G, Marshall A, Flicek P, Odom D.
Cell Volume 148 (2012) p.832-832
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The bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling.
Quin MB, Berrisford JM, Newman JA, Baslé A, Lewis RJ, Marles-Wright J.
Structure (London, England : 1993) Volume 20 (2012) p.350-363
DOI: 10.1016/j.str.2012.01.003

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
Reisinger F, Krishna R, Ghali F, Ríos D, Hermjakob H, Vizcaíno JA, Jones AR.
Proteomics Volume 12 (2012) p.790-794
DOI: 10.1002/pmic.201100577

Analyzing protein-protein interaction networks.
Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE.
Journal of proteome research Volume 11 (2012) p.2014-2031
DOI: 10.1021/pr201211w

PRIDE: quality control in a proteomics data repository.
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas004
DOI: 10.1093/database/bas004

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA.
Molecular & cellular proteomics : MCP Volume 11 (2012) p.1682-1689
DOI: 10.1074/mcp.o112.021543

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.
Proteomics Volume 12 (2012) p.795-798
DOI: 10.1002/pmic.201100578

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT.
Cell Volume 148 (2012) p.335-348
DOI: 10.1016/j.cell.2011.11.058

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I.
PLoS ONE Volume 7 (2012) p.e41762
DOI: 10.1371/journal.pone.0041762

Major submissions tool developments at the European Nucleotide Archive.
Amid C, Birney E, Bower L, Cerdeño-Tárraga A, Cheng Y, Cleland I, Faruque N, Gibson R, Goodgame N, Hunter C, Jang M, Leinonen R, Liu X, Oisel A, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Rivière S, Rossello M, Senf A, Smirnov D, Ten Hoopen P, Vaughan D, Vaughan R, Zalunin V, Cochrane G.
Nucleic acids research Volume 40 (2012) p.D43-7
DOI: 10.1093/nar/gkr946

Annotating cancer variants and anti-cancer therapeutics in reactome.
Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L.
Cancers Volume 4 (2012) p.1180-1211
DOI: 10.3390/cancers4041180

GrameneMart: the BioMart data portal for the Gramene project.
Spooner W, Youens-Clark K, Staines D, Ware D.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bar056
DOI: 10.1093/database/bar056

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.
BMC systems biology Volume 6 (2012) p.29
DOI: 10.1186/1752-0509-6-29

A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR.
Omics : a journal of integrative biology Volume 16 (2012) p.431-442
DOI: 10.1089/omi.2012.0022

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.
Genome research Volume 22 (2012) p.1658-1667
DOI: 10.1101/gr.136838.111

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.
Nucleic acids research Volume 40 (2012) p.D1077-81
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The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.
Nucleic acids research Volume 40 (2012) p.D841-6
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Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC.
PLoS computational biology Volume 8 (2012) p.e1002789
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InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong S.
Nucleic acids research Volume 40 (2012) p.4725-4725
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Predicting the secondary structure of proteins using machine learning algorithms.
Camacho R, Ferreira R, Rosa N, Guimarães V, Fonseca NA, Costa VS, de Sousa M, Magalhães A.
International journal of data mining and bioinformatics Volume 6 (2012) p.571-584
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ADOPS--Automatic Detection Of Positively Selected Sites.
Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Fonseca NA, Vieira J.
Journal of integrative bioinformatics Volume 9 (2012) p.200
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ADOPS - Automatic Detection Of Positively Selected Sites.
Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Fonseca NA, Vieira J.
Journal of integrative bioinformatics Volume 9 (2012) p.18-32
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PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.
Nucleic acids research Volume 40 (2012) p.D445-52
DOI: 10.1093/nar/gkr998

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Nature Volume 491 (2012) p.56-65
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ELIXIR: a distributed infrastructure for European biological data.
Crosswell LC, Thornton JM.
Trends in biotechnology Volume 30 (2012) p.241-242
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State-time spectrum of signal transduction logic models.
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J.
Physical biology Volume 9 (2012) p.045003
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In the beginning there was babble...
Klionsky DJ, Bruford EA, Cherry JM, Hodgkin J, Laulederkind SJ, Singer AG.
Autophagy Volume 8 (2012) p.1165-1167
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Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ.
The Plant cell Volume 24 (2012) p.3530-3557
DOI: 10.1105/tpc.112.102046

Patterns of cis regulatory variation in diverse human populations.
Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.
PLoS genetics Volume 8 (2012) p.e1002639
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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Stegle O, Parts L, Piipari M, Winn J, Durbin R.
Nature protocols Volume 7 (2012) p.500-507
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Women in science.
Dean C, Osborn M, Oshlack A, Thornton J.
Genome biology Volume 13 (2012) p.148
DOI: 10.1186/gb4005

MetaBase--the wiki-database of biological databases.
Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, González V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J.
Nucleic acids research Volume 40 (2012) p.D1250-4
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Gene family matters: expanding the HGNC resource.
Daugherty LC, Seal RL, Wright MW, Bruford EA.
Human genomics Volume 6 (2012) p.4
DOI: 10.1186/1479-7364-6-4

Integrating literature-constrained and data-driven inference of signalling networks.
Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J.
Bioinformatics (Oxford, England) Volume 28 (2012) p.2311-2317
DOI: 10.1093/bioinformatics/bts363

Transcription factors of Lotus: regulation of isoflavonoid biosynthesis requires coordinated changes in transcription factor activity.
Shelton D, Stranne M, Mikkelsen L, Pakseresht N, Welham T, Hiraka H, Tabata S, Sato S, Paquette S, Wang TL, Martin C, Bailey P.
Plant physiology Volume 159 (2012) p.531-547
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Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177
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MageComet--web application for harmonizing existing large-scale experiment descriptions.
Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.
Bioinformatics Volume 28 (2012) p.1402-1403
DOI: 10.1093/bioinformatics/bts148

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S.
Bioinformatics (Oxford, England) Volume 28 (2012) p.246-253
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The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.
Li JW, Robison K, Martin M, Sjödin A, Usadel B, Young M, Olivares EC, Bolser DM.
Nucleic acids research Volume 40 (2012) p.D1313-7
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The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions.
Fonseca NA, Vieira CP, Schlötterer C, Vieira J.
Fly Volume 6 (2012) p.71-74
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Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study.
Budczies J, Denkert C, Müller BM, Brockmöller SF, Klauschen F, Györffy B, Dietel M, Richter-Ehrenstein C, Marten U, Salek RM, Griffin JL, Hilvo M, Orešič M, Wohlgemuth G, Fiehn O.
BMC genomics Volume 13 (2012) p.334
DOI: 10.1186/1471-2164-13-334

Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis.
Masforrol Y, Gil J, González LJ, Pérez-Riverol Y, Fernández-de-Cossío J, Sánchez A, Betancourt LH, Garay HE, Cabrales A, Albericio F, Yang H, Zubarev RA, Besada V, Acosta OR.
ACS combinatorial science Volume 14 (2012) p.145-149
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Low budget analysis of Direct-To-Consumer genomic testing familial data.
Glusman G, Cariaso M, Jimenez R, Swan D, Greshake B, Bhak J, Logan DW, Corpas M.
F1000Research Volume 1 (2012) p.3
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Current challenges in genome annotation through structural biology and bioinformatics.
Furnham N, de Beer TA, Thornton JM.
Current opinion in structural biology Volume 22 (2012) p.594-601
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Blind testing of routine, fully automated determination of protein structures from NMR data.
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM.
Structure (London, England : 1993) Volume 20 (2012) p.227-236
DOI: 10.1016/j.str.2012.01.002

Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery.
Denkert C, Bucher E, Hilvo M, Salek R, Orešič M, Griffin J, Brockmöller S, Klauschen F, Loibl S, Barupal DK, Budczies J, Iljin K, Nekljudova V, Fiehn O.
Genome medicine Volume 4 (2012) p.37

Implementing an X-ray validation pipeline for the Protein Data Bank.
Gore S, Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 68 (2012) p.478-483
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On the need for an international effort to capture, share and use crystallization screening data.
Newman J, Bolton EE, Müller-Dieckmann J, Fazio VJ, Gallagher DT, Lovell D, Luft JR, Peat TS, Ratcliffe D, Sayle RA, Snell EH, Taylor K, Vallotton P, Velanker S, von Delft F.
Acta crystallographica. Section F, Structural biology and crystallization communications Volume 68 (2012) p.253-258
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AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas003
DOI: 10.1093/database/bas003

The mzIdentML data standard for mass spectrometry-based proteomics results.
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.
Molecular & cellular proteomics : MCP Volume 11 (2012) p.M111.014381
DOI: 10.1074/mcp.m111.014381

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.
Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas036
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Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.
Nature methods Volume 9 (2012) p.345-350
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Food for thought ... A toxicology ontology roadmap.
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C.
ALTEX Volume 29 (2012) p.129-137

The future of DNA sequence archiving.
Cochrane G, Cook CE, Birney E.
GigaScience Volume 1 (2012) p.2
DOI: 10.1186/2047-217x-1-2

Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.
Shen PS, Domek MJ, Sanz-García E, Makaju A, Taylor RM, Hoggan R, Culumber MD, Oberg CJ, Breakwell DP, Prince JT, Belnap DM.
Journal of virology Volume 86 (2012) p.7907-7917
DOI: 10.1128/jvi.00407-12

Evaluation of a technology enabled garment for older walkers.
Burns WP, Nugent CD, McCullagh PJ, Finlay DD, Cleland I, Scotney BW, McClean SI, McCann J, Gueldenring D.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2012 (2012) p.2100-2103
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Toxicology ontology perspectives.
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C.
ALTEX Volume 29 (2012) p.139-156

In vitro characterization of the activity of PF-05095808, a novel biological agent for hepatitis C virus therapy.
Lavender H, Brady K, Burden F, Delpuech-Adams O, Denise H, Palmer A, Perkins H, Savic B, Scott S, Smith-Burchnell C, Troke P, Wright JF, Suhy D, Corbau R.
Antimicrobial agents and chemotherapy Volume 56 (2012) p.1364-1375
DOI: 10.1128/aac.05357-11

Outcome of the first electron microscopy validation task force meeting.
Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL.
Structure (London, England : 1993) Volume 20 (2012) p.205-214
DOI: 10.1016/j.str.2011.12.014

HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.
PloS one Volume 7 (2012) p.e31826
DOI: 10.1371/journal.pone.0031826

Safe, long-term hepatic expression of anti-HCV shRNA in a nonhuman primate model.
Suhy DA, Kao SC, Mao T, Whiteley L, Denise H, Souberbielle B, Burdick AD, Hayes K, Wright JF, Lavender H, Roelvink P, Kolykhalov A, Brady K, Moschos SA, Hauck B, Zelenaia O, Zhou S, Scribner C, High KA, Renison SH, Corbau R.
Molecular therapy : the journal of the American Society of Gene Therapy Volume 20 (2012) p.1737-1749
DOI: 10.1038/mt.2012.119

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M.
Genome biology Volume 13 (2012) p.R48
DOI: 10.1186/gb-2012-13-9-r48

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y.
Genome research Volume 22 (2012) p.602-610
DOI: 10.1101/gr.130468.111

Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.
Hödar C, Moreno P, di Genova A, Latorre M, Reyes-Jara A, Maass A, González M, Cambiazo V.
Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine Volume 25 (2012) p.75-93
DOI: 10.1007/s10534-011-9484-8

Access and use of the GUDMAP database of genitourinary development.
Davies JA, Little MH, Aronow B, Armstrong J, Brennan J, Lloyd-MacGilp S, Armit C, Harding S, Piu X, Roochun Y, Haggarty B, Houghton D, Davidson D, Baldock R.
Methods in molecular biology (Clifton, N.J.) Volume 886 (2012) p.185-201
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Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.
Melas IN, Mitsos A, Messinis DE, Weiss TS, Rodriguez JS, Alexopoulos LG.
Molecular bioSystems Volume 8 (2012) p.1571-1584
DOI: 10.1039/c2mb05482e

The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium.
Nature methods Volume 9 (2012) p.459-462
DOI: 10.1038/nmeth.1974

Toward community standards in the quest for orthologs.
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J, Quest for Orthologs Consortium.
Bioinformatics (Oxford, England) Volume 28 (2012) p.900-904
DOI: 10.1093/bioinformatics/bts050

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Bateman A.
Nucleic acids research Volume 40 (2012) p.D343-50
DOI: 10.1093/nar/gkr987

Biocurators and biocuration: surveying the 21st century challenges.
Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios L, Gaudet P.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bar059
DOI: 10.1093/database/bar059

Identification and localisation of the NB-LRR gene family within the potato genome.
Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I.
BMC genomics Volume 13 (2012) p.75
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Extracellular membrane vesicles and immune regulation in the brain.
Cossetti C, Smith JA, Iraci N, Leonardi T, Alfaro-Cervello C, Pluchino S.
Frontiers in physiology Volume 3 (2012) p.117
DOI: 10.3389/fphys.2012.00117

Making your database available through Wikipedia: the pros and cons.
Finn RD, Gardner PP, Bateman A.
Nucleic acids research Volume 40 (2012) p.D9-12
DOI: 10.1093/nar/gkr1195

PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA.
Nature biotechnology Volume 30 (2012) p.135-137
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The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.
Nucleic acids research Volume 40 (2012) p.D290-301
DOI: 10.1093/nar/gkr1065

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.
Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H.
Proteomics Volume 12 (2012) p.2767-2772
DOI: 10.1002/pmic.201270126

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome research Volume 22 (2012) p.2376-2384
DOI: 10.1101/gr.142281.112

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND.
PLoS computational biology Volume 8 (2012) p.e1002330
DOI: 10.1371/journal.pcbi.1002330

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM.
Bioinformatics Volume 28 (2012) p.1001-1008
DOI: 10.1093/bioinformatics/bts081

2011

MiR-221 influences effector functions and actin cytoskeleton in mast cells.
Mayoral RJ, Deho L, Rusca N, Bartonicek N, Saini HK, Enright AJ, Monticelli S.
PloS one Volume 6 (2011) p.e26133
DOI: 10.1371/journal.pone.0026133

Setting the standards for signal transduction research.
Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.
Science signaling Volume 4 (2011) p.pe10
DOI: 10.1126/scisignal.2001844

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".
Griffin JL, Atherton HJ, Steinbeck C, Salek RM.
BMC research notes Volume 4 (2011) p.272
DOI: 10.1186/1756-0500-4-272

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, Murray-Rust P.
Journal of cheminformatics Volume 3 (2011) p.37
DOI: 10.1186/1758-2946-3-37

Revision history aware repositories of computational models of biological systems.
Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PM.
BMC bioinformatics Volume 12 (2011) p.22
DOI: 10.1186/1471-2105-12-22

1,000 structures and more from the MCSG.
Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA.
BMC structural biology Volume 11 (2011) p.2
DOI: 10.1186/1472-6807-11-2

Computational biology for ageing.
Wieser D, Papatheodorou I, Ziehm M, Thornton JM.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.51-63
DOI: 10.1098/rstb.2010.0286

Atomic resolution insights into curli fiber biogenesis.
Taylor JD, Zhou Y, Salgado PS, Patwardhan A, McGuffie M, Pape T, Grabe G, Ashman E, Constable SC, Simpson PJ, Lee WC, Cota E, Chapman MR, Matthews SJ.
Structure (London, England : 1993) Volume 19 (2011) p.1307-1316
DOI: 10.1016/j.str.2011.05.015

Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA.
Nucleic acids research Volume 39 (2011) p.D420-6
DOI: 10.1093/nar/gkq1001

Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A.
Bioinformatics (Oxford, England) Volume 27 (2011) p.973-979
DOI: 10.1093/bioinformatics/btr048

Demographic history and rare allele sharing among human populations.
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, 1000 Genomes Project, Bustamante CD.
Proceedings of the National Academy of Sciences of the United States of America Volume 108 (2011) p.11983-11988
DOI: 10.1073/pnas.1019276108

Using semantic web technologies to manage complexity and change in biomedical data.
Stevens R, Jupp S, Klein J, Schanstra J.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2011 (2011) p.3708-3711
DOI: 10.1109/iembs.2011.6090629

Developing a kidney and urinary pathway knowledge base.
Jupp S, Klein J, Schanstra J, Stevens R.
Journal of biomedical semantics Volume 2 Suppl 2 (2011) p.S7
DOI: 10.1186/2041-1480-2-s5-s7

Crowdsourcing network inference: the DREAM predictive signaling network challenge.
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.
Science signaling Volume 4 (2011) p.mr7
DOI: 10.1126/scisignal.2002212

The functional spectrum of low-frequency coding variation.
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project.
Genome biology Volume 12 (2011) p.R84
DOI: 10.1186/gb-2011-12-9-r84

Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project.
Nature genetics Volume 43 (2011) p.712-714
DOI: 10.1038/ng.862

Comparing signaling networks between normal and transformed hepatocytes using discrete logical models.
Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK.
Cancer research Volume 71 (2011) p.5400-5411
DOI: 10.1158/0008-5472.can-10-4453

genenames.org: the HGNC resources in 2011.
Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA.
Nucleic acids research Volume 39 (2011) p.D514-9
DOI: 10.1093/nar/gkq892

Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature.
Wright MW, Bruford EA.
Human genomics Volume 5 (2011) p.90-98
DOI: 10.1186/1479-7364-5-2-90

Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project.
Nature Volume 470 (2011) p.59-65
DOI: 10.1038/nature09708

Modularization requirements in bio-ontologies: A case study of ChEbi
Hastings J, Batchelor C, Steinbeck C, Schulz S.
Advances in molecular bioinformatics Volume 230 (2011) p.63-70
DOI: 10.3233/978-1-60750-799-4-63

The GUDMAP database--an online resource for genitourinary research.
Harding SD, Armit C, Armstrong J, Brennan J, Cheng Y, Haggarty B, Houghton D, Lloyd-MacGilp S, Pi X, Roochun Y, Sharghi M, Tindal C, McMahon AP, Gottesman B, Little MH, Georgas K, Aronow BJ, Potter SS, Brunskill EW, Southard-Smith EM, Mendelsohn C, Baldock RA, Davies JA, Davidson D.
Development (Cambridge, England) Volume 138 (2011) p.2845-2853
DOI: 10.1242/dev.063594

Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC.
Gut Volume 60 (2011) p.1317-1326
DOI: 10.1136/gut.2010.234179

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y.
PLoS genetics Volume 7 (2011) p.e1001316
DOI: 10.1371/journal.pgen.1001316

Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: evaluation in proteomic studies using peptide-centric database searches.
Betancourt LH, Sánchez A, Pérez Y, Fernandez de Cossio J, Gil J, Toledo P, Iguchi S, Aimoto S, González LJ, Padrón G, Takao T, Besada V.
Journal of proteomics Volume 74 (2011) p.2210-2213
DOI: 10.1016/j.jprot.2011.04.029

Peptide fractionation by acid pH SDS-free electrophoresis.
Ramos Y, Garcia Y, Pérez-Riverol Y, Leyva A, Padrón G, Sánchez A, Castellanos-Serra L, González LJ, Besada V.
Electrophoresis Volume 32 (2011) p.1323-1326
DOI: 10.1002/elps.201000677

Gene expression differences among primates are associated with changes in a histone epigenetic modification.
Cain CE, Blekhman R, Marioni JC, Gilad Y.
Genetics Volume 187 (2011) p.1225-1234
DOI: 10.1534/genetics.110.126177

Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar030
DOI: 10.1093/database/bar030

Genome sequence and analysis of the tuber crop potato.
Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sønderkær M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert Bt, Goverse A, van Ham RC, Visser RG.
Nature Volume 475 (2011) p.189-195
DOI: 10.1038/nature10158

Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors.
Pelé J, Abdi H, Moreau M, Thybert D, Chabbert M.
PloS one Volume 6 (2011) p.e19094
DOI: 10.1371/journal.pone.0019094

UKPMC: a full text article resource for the life sciences.
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, Lewin I, Lyte V, MacIntyre R, Mansoor S, Mason L, McNaught J, Newbold E, Nobata C, Ong E, Pillai S, Rebholz-Schuhmann D, Rosie H, Rowbotham R, Rupp CJ, Stoehr P, Vaughan P.
Nucleic acids research Volume 39 (2011) p.D58-65
DOI: 10.1093/nar/gkq1063

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.
Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F.
BMC microbiology Volume 11 (2011) p.105
DOI: 10.1186/1471-2180-11-105

In silico analysis of accurate proteomics, complemented by selective isolation of peptides.
Perez-Riverol Y, Sánchez A, Ramos Y, Schmidt A, Müller M, Betancourt L, González LJ, Vera R, Padron G, Besada V.
Journal of proteomics Volume 74 (2011) p.2071-2082
DOI: 10.1016/j.jprot.2011.05.034

Minimum Information About a Simulation Experiment (MIASE).
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N.
PLoS computational biology Volume 7 (2011) p.e1001122
DOI: 10.1371/journal.pcbi.1001122

Proteomic temporal profile of human brain endothelium after oxidative stress.
Ning M, Sarracino DA, Kho AT, Guo S, Lee SR, Krastins B, Buonanno FS, Vizcaíno JA, Orchard S, McMullin D, Wang X, Lo EH.
Stroke Volume 42 (2011) p.37-43
DOI: 10.1161/strokeaha.110.585703

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
Holliday GL, Fischer JD, Mitchell JB, Thornton JM.
The FEBS journal Volume 278 (2011) p.3835-3845
DOI: 10.1111/j.1742-4658.2011.08190.x

New developments on the cheminformatics open workflow environment CDK-Taverna.
Truszkowski A, Jayaseelan KV, Neumann S, Willighagen EL, Zielesny A, Steinbeck C.
Journal of cheminformatics Volume 3 (2011) p.54
DOI: 10.1186/1758-2946-3-54

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.
Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D.
BMC plant biology Volume 11 (2011) p.104
DOI: 10.1186/1471-2229-11-104

Quality control in proteomics.
Martens L, Vizcaíno JA, Banks R.
Proteomics Volume 11 (2011) p.1015-1016
DOI: 10.1002/pmic.201190020

EST analysis pipeline: use of distributed computing resources.
González FJ, Vizcaíno JA.
Methods in molecular biology (Clifton, N.J.) Volume 722 (2011) p.103-120
DOI: 10.1007/978-1-61779-040-9_7

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 11 (2011) p.4434-4438
DOI: 10.1002/pmic.201100363

PRIDE and "Database on Demand" as valuable tools for computational proteomics.
Vizcaíno JA, Reisinger F, Côté R, Martens L.
Methods in molecular biology (Clifton, N.J.) Volume 696 (2011) p.93-105
DOI: 10.1007/978-1-60761-987-1_6

The impact of focused Gene Ontology curation of specific mammalian systems.
Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC.
PloS one Volume 6 (2011) p.e27541
DOI: 10.1371/journal.pone.0027541

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.
Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M.
PloS one Volume 6 (2011) p.e25513
DOI: 10.1371/journal.pone.0025513

Submitting proteomics data to PRIDE using PRIDE Converter.
Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.237-253
DOI: 10.1007/978-1-60761-977-2_16

Computational metabolomics – a field at the boundaries of cheminformatics and bioinformatics.
Steinbeck C, Kuhn S, Jayaseelan KV, Moreno P.
Journal of cheminformatics Volume 3 (2011) p.O6-O6
DOI: 10.1186/1758-2946-3-s1-o6

Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.
PLoS computational biology Volume 7 (2011) p.e1001099
DOI: 10.1371/journal.pcbi.1001099

Solving the Problem: Genome Annotation Standards before the Data Deluge.
Klimke W, O'Donovan C, White O, Brister JR, Clark K, Fedorov B, Mizrachi I, Pruitt KD, Tatusova T.
Standards in Genomic Sciences Volume 5 (2011) p.168-193
DOI: 10.4056/sigs.2084864

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.6-8
DOI: 10.1098/rstb.2010.0298

A guide to UniProt for protein scientists.
O'Donovan C, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.25-35
DOI: 10.1007/978-1-60761-977-2_2

The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P, Köhn M.
Biochemistry Volume 50 (2011) p.7579-7590
DOI: 10.1021/bi201095z

Celebrating structural biology.

Nature structural & molecular biology Volume 18 (2011) p.1304-1316
DOI: 10.1038/nsmb1211-1304

Towards automated metabolome assembly: application of text mining to correlate small molecules, targets and tissues.
Moreno P, Jayaseelan K, Steinbeck C.
Journal of cheminformatics Volume 3 (2011) p.P19-P19
DOI: 10.1186/1758-2946-3-s1-p19

A common layer of interoperability for biomedical ontologies based on OWL EL.
Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV.
Bioinformatics Volume 27 (2011) p.1001-1008
DOI: 10.1093/bioinformatics/btr058

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P.
BMC research notes Volume 4 (2011) p.313
DOI: 10.1186/1756-0500-4-313

Integrating systems biology models and biomedical ontologies.
Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV.
BMC systems biology Volume 5 (2011) p.124
DOI: 10.1186/1752-0509-5-124

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.
BMC bioinformatics Volume 12 (2011) p.104
DOI: 10.1186/1471-2105-12-104

"4D Biology for health and disease" workshop report.
Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ.
New biotechnology Volume 28 (2011) p.291-293
DOI: 10.1016/j.nbt.2010.10.003

Ensembl 2011.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM.
Nucleic acids research Volume 39 (2011) p.D800-6
DOI: 10.1093/nar/gkq1064

Autism candidate genes via mouse phenomics.
Meehan TF, Carr CJ, Jay JJ, Bult CJ, Chesler EJ, Blake JA.
Journal of biomedical informatics Volume 44 Suppl 1 (2011) p.S5-11
DOI: 10.1016/j.jbi.2011.03.003

A revised nomenclature for transcribed human endogenous retroviral loci.
Mayer J, Blomberg J, Seal RL.
Mobile DNA Volume 2 (2011) p.7
DOI: 10.1186/1759-8753-2-7

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2156-2158
DOI: 10.1093/bioinformatics/btr330

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic acids research Volume 39 (2011) p.D214-9
DOI: 10.1093/nar/gkq1020

Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily.
Bingle CD, Seal RL, Craven CJ.
Biochemical Society transactions Volume 39 (2011) p.977-983
DOI: 10.1042/bst0390977

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M.
Bioinformatics Volume 27 (2011) p.589-591
DOI: 10.1093/bioinformatics/btq693

Logical development of the cell ontology.
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD.
BMC bioinformatics Volume 12 (2011) p.6
DOI: 10.1186/1471-2105-12-6

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, MolPAGE Consortium, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan KT, Spector TD, Nicholson JK, Lindon JC, Baunsgaard D, Holmes E, McCarthy MI, Holmes CC.
PLoS genetics Volume 7 (2011) p.e1002270
DOI: 10.1371/journal.pgen.1002270

Anatomy ontologies and potential users: bridging the gap.
Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H.
Journal of biomedical semantics Volume 2 Suppl 4 (2011) p.S3
DOI: 10.1186/2041-1480-2-s5-s3

Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts.
Malone CM, Domaschenz R, Amagase Y, Dunham I, Murai K, Jones PH.
Experimental cell research Volume 317 (2011) p.1590-1602
DOI: 10.1016/j.yexcr.2011.03.023

Data standards for Omics data: the basis of data sharing and reuse.
Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA.
Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.31-69
DOI: 10.1007/978-1-61779-027-0_2

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.
BMC bioinformatics Volume 12 (2011) p.218
DOI: 10.1186/1471-2105-12-218

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.
Genome research Volume 21 (2011) p.1757-1767
DOI: 10.1101/gr.121541.111

Contributions of the EMERALD project to assessing and improving microarray data quality.
Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.
BioTechniques Volume 50 (2011) p.27-31
DOI: 10.2144/000113591

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.
Genome research Volume 21 (2011) p.2224-2241
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PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.
Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, Fonseca NA.
International journal of legal medicine Volume 125 (2011) p.629-636
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Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.
Kosiol C, Goldman N.
Journal of molecular biology Volume 411 (2011) p.910-923
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Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited.
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PloS one Volume 6 (2011) p.e22783
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Hematopoietic cell types: prototype for a revised cell ontology.
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ.
Journal of biomedical informatics Volume 44 (2011) p.75-79
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Structural annotation of Mycobacterium tuberculosis proteome.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R, OSDD Consortium, Brahmachari SK, Chandra N.
PloS one Volume 6 (2011) p.e27044
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LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
Journal of chemical information and modeling Volume 51 (2011) p.2778-2786
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What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.
Lakner C, Holder MT, Goldman N, Naylor GJ.
Systematic biology Volume 60 (2011) p.161-174
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RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA (New York, N.Y.) Volume 17 (2011) p.578-594
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Protein structure databases.
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Molecular biotechnology Volume 48 (2011) p.183-198
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Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.O111.015446
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A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.
Camacho R, Pereira M, Costa VS, Fonseca NA, Adriano C, Simões CJ, Brito RM.
Journal of integrative bioinformatics Volume 8 (2011) p.182
DOI: 10.2390/biecoll-jib-2011-182

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.
de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL.
Journal of theoretical biology Volume 271 (2011) p.136-144
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Predicting Malignancy from Mammography Findings and Surgical Biopsies.
Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Volume 2011 (2011) p.
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A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics Volume 27 (2011) p.867-869
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Omics technologies, data and bioinformatics principles.
Schneider MV, Orchard S.
Methods in molecular biology (Clifton, N.J.) Volume 719 (2011) p.3-30
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Reactome: a database of reactions, pathways and biological processes.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.
Nucleic acids research Volume 39 (2011) p.D691-7
DOI: 10.1093/nar/gkq1018

Effects of BMI and abdominal volume on the accuracy of step count obtained from a tri-axial accelerometer.
Cleland I, Nugent CD, Finlay DD, Burns W, Bougourd J, Stevens K, Armitage R.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2011 (2011) p.3656-3659
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The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.
Morris C, Pajon A, Griffiths SL, Daniel E, Savitsky M, Lin B, Diprose JM, da Silva AW, Pilicheva K, Troshin P, van Niekerk J, Isaacs N, Naismith J, Nave C, Blake R, Wilson KS, Stuart DI, Henrick K, Esnouf RM.
Acta crystallographica. Section D, Biological crystallography Volume 67 (2011) p.249-260
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Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.
Nature Volume 477 (2011) p.419-423
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Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D.
Nucleic acids research Volume 39 (2011) p.D1085-94
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easyDAS: automatic creation of DAS servers.
Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H.
BMC bioinformatics Volume 12 (2011) p.23
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The Reactome BioMart.
Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar031
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Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H.
Bioinformatics Volume 27 (2011) p.2616-2617
DOI: 10.1093/bioinformatics/btr433

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs.
Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC.
Nucleic acids research Volume 39 (2011) p.W190-6
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The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements.
De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D.
Nature Volume 480 (2011) p.259-263
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DAS writeback: a collaborative annotation system.
Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.
BMC bioinformatics Volume 12 (2011) p.143
DOI: 10.1186/1471-2105-12-143

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.
Nucleic acids research Volume 39 (2011) p.D1002-4
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Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar047
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Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R.
Genome biology Volume 12 (2011) p.402
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Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.
Proteomics. Clinical applications Volume 5 (2011) p.580-589
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mzML--a community standard for mass spectrometry data.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.
Molecular & cellular proteomics : MCP Volume 10 (2011) p.R110.000133
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Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H.
Proteomics Volume 11 (2011) p.4284-4290
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Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.
Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.
Molecular & cellular prote