Publications for 2017

2017

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

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

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

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

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.
Tong P, Monahan J, Prendergast JG.
PLoS genetics Volume 13 (2017) p.e1006673

RNA Structure: Advances and Assessment of 3D Structure Prediction.
Miao Z, Westhof E.
Annual review of biophysics Volume 46 (2017) p.483-503

In silico prediction of novel therapeutic targets using gene-disease association data.
Ferrero E, Dunham I, Sanseau P.
Journal of translational medicine Volume 15 (2017) p.182

Literature evidence in open targets - a target validation platform.
Kafkas Ş, Dunham I, McEntyre J.
Journal of biomedical semantics Volume 8 (2017) p.20

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

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 RH, 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

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

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 (2017) p.

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

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, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G.
F1000Research Volume 6 (2017) p.

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data.
Eckes AH, Gubała T, Nowakowski P, Szymczyszyn T, Wells R, Irwin JA, Horro C, Hancock JM, King G, Dyer SC, Jurkowski W.
F1000Research Volume 6 (2017) p.465

Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated.
Ibarra-Soria X, Nakahara TS, Lilue J, Jiang Y, Trimmer C, Souza MA, Netto PH, Ikegami K, Murphy NR, Kusma M, Kirton A, Saraiva LR, Keane TM, Matsunami H, Mainland J, Papes F, Logan DW.
eLife Volume 6 (2017) p.

AIM2-Like Receptors Positively and Negatively Regulate the Interferon Response Induced by Cytosolic DNA.
Nakaya Y, Lilue J, Stavrou S, Moran EA, Ross SR.
mBio Volume 8 (2017) p.

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

Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.
Zaman S, Sarntivijai S, Abernethy DR.
Gene regulation and systems biology Volume 11 (2017) p.1177625017696075

Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.
Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF.
Human molecular genetics Volume 26 (2017) p.519-526

Uncovering novel repositioning opportunities using the Open Targets platform.
Khaladkar M, Koscielny G, Hasan S, Agarwal P, Dunham I, Rajpal D, Sanseau P.
Drug discovery today Volume (2017) p.

A novel community driven software for functional enrichment analysis of extracellular vesicles data.
Pathan M, Keerthikumar S, Chisanga D, Alessandro R, Ang CS, Askenase P, Batagov AO, Benito-Martin A, Camussi G, Clayton A, Collino F, Di Vizio D, Falcon-Perez JM, Fonseca P, Fonseka P, Fontana S, Gho YS, Hendrix A, Hoen EN, Iraci N, Kastaniegaard K, Kislinger T, Kowal J, Kurochkin IV, Leonardi T, Liang Y, Llorente A, Lunavat TR, Maji S, Monteleone F, Øverbye A, Panaretakis T, Patel T, Peinado H, Pluchino S, Principe S, Ronquist G, Royo F, Sahoo S, Spinelli C, Stensballe A, Théry C, van Herwijnen MJC, Wauben M, Welton JL, Zhao K, Mathivanan S.
Journal of extracellular vesicles Volume 6 (2017) p.1321455

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.
Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L, International Mouse Phenotyping Consortium, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wurst W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM.
Nature communications Volume 8 (2017) p.886

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.
PLoS biology Volume 15 (2017) p.e2001414

Prevalence of sexual dimorphism in mammalian phenotypic traits.
Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL, International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK.
Nature communications Volume 8 (2017) p.15475

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.
Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, International Mouse Phenotyping Consortium, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D.
Nature genetics Volume 49 (2017) p.1231-1238

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

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

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

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

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

Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.
Chojnacki S, Cowley A, Lee J, Foix A, Lopez R.
Nucleic acids research Volume (2017) p.

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.

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

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

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

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

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

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

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.

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

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.
Pawlik A, van Gelder CWG, van Gelder CWG, Nenadic A, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Hancock J, Goble C.
F1000Research Volume 6 (2017) p.

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

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

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

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.
Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.
Journal of proteome research Volume 16 (2017) p.831-841

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

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

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

Mechanism-based biomarker discovery.
Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG.
Drug discovery today Volume 22 (2017) p.1209-1215

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

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

The future of metabolomics in ELIXIR.
van Rijswijk M, van Rijswijk M, Beirnaert C, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moschonas NK, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Rosato A, Salek RM, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spicer RA, Spjuth O, Thévenot EA, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Willighagen EL, Zanetti G, Steinbeck C.
F1000Research Volume 6 (2017) p.

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

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

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 (2017) p.

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 (2017) p.

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

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.

The application of project-based learning in bioinformatics training.
Emery LR, Morgan SL.
PLoS Computational Biology Volume 13 (2017) p.e1005620

Expansion of the Gene Ontology knowledgebase and resources.
The Gene Ontology Consortium.
Nucleic acids research Volume 45 (2017) p.D331-D338

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.

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

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

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 (2017) p.

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W.
Cell reports Volume 20 (2017) p.1215-1228

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA.
eLife Volume 6 (2017) p.

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 (2017) p.

A Golden Age for Working with Public Proteomics Data.
Martens L, Vizcaíno JA.
Trends in biochemical sciences Volume 42 (2017) p.333-341

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC.
Nature methods Volume 14 (2017) p.565-571

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

Identifying genes for neurobehavioural traits in rodents: progress and pitfalls.
Baud A, Flint J.
Disease models & mechanisms Volume 10 (2017) p.373-383

Testing for differential abundance in mass cytometry data.
Lun ATL, Richard AC, Marioni JC.
Nature methods Volume 14 (2017) p.707-709

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

Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.
Jarnuczak AF, Vizcaíno JA.
Current protocols in bioinformatics Volume 59 (2017) p.13.31.1-13.31.12

Synthetic human proteomes for accelerating protein research.
Perez-Riverol Y, Vizcaíno JA.
Nature methods Volume 14 (2017) p.240-242

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR.
Molecular & cellular proteomics : MCP Volume 16 (2017) p.1275-1285

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

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 (2017) p.

A community proposal to integrate proteomics activities in ELIXIR.
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.
F1000Research Volume 6 (2017) p.

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 (2017) p.

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 (2017) p.

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 (2017) p.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA.
Proteomics Volume 17 (2017) p.

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.

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

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.

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

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

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

ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD.
Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330

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 (2017) p.

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.

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

Effect of pistachio consumption on the modulation of urinary gut microbiota-related metabolites in prediabetic subjects.
Hernández-Alonso P, Cañueto D, Giardina S, Salas-Salvadó J, Cañellas N, Correig X, Bulló M.
The Journal of nutritional biochemistry Volume 45 (2017) p.48-53

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.
Ramos Y, Huerta V, Martín D, Palomares S, Yero A, Pupo D, Gallien S, Martín AM, Pérez-Riverol Y, Sarría M, Guirola O, Chinea G, Domon B, González LJ.
Journal of proteomics Volume (2017) p.

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

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J.
PLoS computational biology Volume 13 (2017) p.e1005297

Dead simple OWL design patterns.
Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C.
Journal of biomedical semantics Volume 8 (2017) p.18

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

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

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

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

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 (2017) p.

Amino Acid Interaction (INTAA) web server.
Galgonek J, Vymetal J, Jakubec D, Vondrášek J.
Nucleic acids research Volume (2017) p.

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

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

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

Compliance with minimum information guidelines in public metabolomics repositories.
Spicer RA, Salek R, Steinbeck C.
Scientific data Volume 4 (2017) p.170137

Automated assembly of species metabolomes through data submission into a public repository.
Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C.
GigaScience Volume 6 (2017) p.1-4

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM.
Bioinformatics (Oxford, England) Volume 33 (2017) p.2598-2600

Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C.
Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.106

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 JM, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis I, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin J, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S.
Analytical chemistry Volume (2017) p.

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

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

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 (2017) p.

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

Global open data management in metabolomics.
Haug K, Salek RM, Steinbeck C.
Current opinion in chemical biology Volume 36 (2017) p.58-63

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.
Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR.
Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.12

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD.
Genome research Volume 27 (2017) p.885-896

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 (2017) p.

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

A chromosome conformation capture ordered sequence of the barley genome.
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N.
Nature Volume 544 (2017) p.427-433

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.
Bolser DM, Staines DM, Perry E, Kersey PJ.
Methods in molecular biology (Clifton, N.J.) Volume 1533 (2017) p.1-31

Erratum to: 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.53

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

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

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes.
Varshney A, Scott LJ, Welch RP, Erdos MR, Chines PS, Narisu N, Albanus RD, Orchard P, Wolford BN, Kursawe R, Vadlamudi S, Cannon ME, Didion JP, Hensley J, Kirilusha A, NISC Comparative Sequencing Program, Bonnycastle LL, Taylor DL, Watanabe R, Mohlke KL, Boehnke M, Collins FS, Parker SC, Stitzel ML.
Proceedings of the National Academy of Sciences of the United States of America Volume 114 (2017) p.2301-2306

BRIE: transcriptome-wide splicing quantification in single cells.
Huang Y, Sanguinetti G.
Genome biology Volume 18 (2017) p.123

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U.
Genome research Volume 27 (2017) p.613-625

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts.
Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS.
Leukemia Volume 31 (2017) p.720-727

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.
Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA.
Oncogene Volume 36 (2017) p.2737-2749

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

Comprehensive pharmacogenomic profiling of malignant pleural mesothelioma identifies a subgroup sensitive to FGFR inhibition.
Quispel-Janssen JM, Badhai J, Schunselaar L, Price S, Brammeld JS, Iorio F, Kolluri KK, Garnett MJ, Berns A, Baas P, McDermott U, Neefjes J, Alifrangis C.
Clinical cancer research : an official journal of the American Association for Cancer Research Volume (2017) p.

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

Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE.
Nature genetics Volume 49 (2017) p.550-558

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

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

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.
Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ.
Genome research Volume 27 (2017) p.1300-1311

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

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

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P.
Scientific data Volume 4 (2017) p.170093

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 (2017) p.

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

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

UniEuk: Time to Speak a Common Language in Protistology!
Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C.
The Journal of eukaryotic microbiology Volume 64 (2017) p.407-411

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.
Methods in molecular biology (Clifton, N.J.) Volume 1607 (2017) p.627-641

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

Data management: A global coalition to sustain core data.
Anderson WP, Global Life Science Data Resources Working Group.
Nature Volume 543 (2017) p.179

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.370-375

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

Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.
Amato R, Lim P, Miotto O, Amaratunga C, Dek D, Pearson RD, Almagro-Garcia J, Neal AT, Sreng S, Suon S, Drury E, Jyothi D, Stalker J, Kwiatkowski DP, Fairhurst RM.
The Lancet. Infectious diseases Volume 17 (2017) p.164-173

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

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

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

BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution.
Psomopoulos FE, Vitsios DM, Baichoo S, Ouzounis CA.
Bioinformatics (Oxford, England) Volume (2017) p.

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

A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data.
Ogeh D, Badge R.
Bioinformatics (Oxford, England) Volume 33 (2017) p.650-653

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 (2017) p.

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

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

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

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.
Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P.
Nucleic acids research Volume 45 (2017) p.D854-D859

Fifty important research questions in microbial ecology.
Antwis RE, Griffiths SM, Harrison XA, Aranega-Bou P, Arce A, Bettridge AS, Brailsford FL, de Menezes A, Devaynes A, Forbes KM, Fry EL, Goodhead I, Haskell E, Heys C, James C, Johnston SR, Lewis GR, Lewis Z, Macey MC, McCarthy A, McDonald JE, Mejia-Florez NL, O'Brien D, Orland C, Pautasso M, Reid WDK, Robinson HA, Wilson K, Sutherland WJ.
FEMS microbiology ecology Volume 93 (2017) p.

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

From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB.
Zaru R, Magrane M, O'Donovan C, UniProt Consortium.
The Biochemical journal Volume 474 (2017) p.493-515

ProtVista: visualization of protein sequence annotations.
Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium.
Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041

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

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

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 (2017) p.

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

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

Two forms of death in ageing Caenorhabditis elegans.
Zhao Y, Gilliat AF, Ziehm M, Turmaine M, Wang H, Ezcurra M, Yang C, Phillips G, McBay D, Zhang WB, Partridge L, Pincus Z, Gems D.
Nature communications Volume 8 (2017) p.15458

Drug repurposing for aging research using model organisms.
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM.
Aging cell Volume 16 (2017) p.1006-1015

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

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

RNAcentral: a comprehensive database of non-coding RNA sequences.
The RNAcentral Consortium.
Nucleic acids research Volume 45 (2017) p.D128-D134

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

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 PM, 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

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

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

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.

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

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

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

Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.
Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y.
Journal of proteome research Volume 16 (2017) p.1825-1830

UniProt: the universal protein knowledgebase.
The UniProt Consortium.
Nucleic acids research Volume 45 (2017) p.D158-D169

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

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.
Pundir S, Onwubiko J, Zaru R, Rosanoff S, Antunes R, Bingley M, Watkins X, O'Donovan C, Martin MJ.
Protein engineering, design & selection : PEDS Volume 30 (2017) p.245-251

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

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

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

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 FS.
Nucleic acids research Volume (2017) p.

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.

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

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

Applications of the 1000 Genomes Project resources.
Zheng-Bradley X, Flicek P.
Briefings in functional genomics Volume 16 (2017) p.163-170

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.

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.

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.

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

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

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

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

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

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

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.
Journal of Clinical Investigation Volume 127 (2017) p.4090-4103

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 (2017) p.

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

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

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

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

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

Variation and functional impact of Neanderthal ancestry in Western Asia.
Taskent RO, Alioglu D, Fer E, Donertas HM, Somel M, Gokcumen O.
Genome Biology and Evolution Volume (2017) p.

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

AmyPro: a database of proteins with validated amyloidogenic regions.
Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R.
Nucleic acids research Volume (2017) p.

UniProt Protein Knowledgebase.
Pundir S, Martin MJ, O'Donovan C.
Methods in molecular biology (Clifton, N.J.) Volume 1558 (2017) p.41-55

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

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

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

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 (2017) p.

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.

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

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ.
Proteins Volume 85 (2017) p.359-377

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

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

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

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

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

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

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.

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

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

General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J.
F1000Research Volume 6 (2017) p.273

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

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

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.

The use of novel selectivity metrics in kinase research.
Bosc N, Meyer C, Bonnet P.
BMC bioinformatics Volume 18 (2017) p.17

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O.
Genome biology Volume 18 (2017) p.212

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

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 (2017) p.

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.

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

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

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

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

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

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

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

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

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.
F1000Research Volume 6 (2017) p.

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