Publications for 2016

2016

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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
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 DOI: 10.1007/s11306-016-1147-x
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Singhal A, Leaman R, Catlett N, Lemberger T, McEntyre J, Polson S, Xenarios I, Arighi C, Lu Z. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw161
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) DOI: 10.1093/database/baw139
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 DOI: 10.1038/nature20802
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 DOI: 10.1186/s12859-016-1402-1
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 DOI: 10.1038/onc.2016.427
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Omics Discovery Index - Discovering and Linking Public Omics Datasets
Perez-Riverol Y, Bai M, Leprevost F, Squizzato S, Park YM, et al. DOI: 10.1101/049205
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On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study
Poux S, Arighi CN, Magrane M, Bateman A, Wei C, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti M, Roechert B. Preprint DOI: 10.1101/094011
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) DOI: 10.12688/f1000research.10221.1
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Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer
Goncalves E, Fraguais A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P. Preprint DOI: 10.1101/093369
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Validation of protein crystal structures
Kleywegt GJ. International Tables for Crystallography, Volume F, Crystallography of biological macromolecules, 2nd edition Wiley DOI: 10.1107/97809553602060000111
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Protein three-dimensional structure validation
Joosten RP, Chinea G, Kleywegt GJ, Vriend G. Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering Elsevier, Waltham, MA DOI: 10.1016/b978-0-12-409547-2.02534-8
Introduction to training with EMBL-EBI
Brooksbank C. DOI: 10.6019/tol.train-w.2016.00001.1
User experience design
Rowland F, Pundir S, Brooksbank C, Hancocks T. DOI: 10.6019/tol.ux-c.2015.00001.1
PDBe: Searching for biological macromolecular structures
Armstrong DR. DOI: 10.6019/tol.pdbe-intr-w.2015.00001.1
Ensembl: Filmed browser workshop
Perry E, Spudich GM, Carvalho-Silva D. DOI: 10.6019/tol.ensfbw-v.2013.00001.1
EBI: Next Generation Sequencing Practical Course
Perry E. DOI: 10.6019/tol.ngs-v.2012.00001.1
Ensembl: Quick tour
Perry E. DOI: 10.6019/tol.ens-qt.2012.00001.1
Ensembl: Filmed API Workshop
Perry E. DOI: 10.6019/tol.ensapi-v.2013.00001.1
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2015.00001.1
Complex Portal: webinar
Meldal BH. DOI: 10.6019/tol.comport-w.2015.00001.1
Bioinformatics for the terrified
Brooksbank C, Cowley A. DOI: 10.6019/tol.bioinfter-c.2016.00001.1
Complex Portal: Quick tour
Meldal BH. DOI: 10.6019/tol.compor-qt.2015.00001.1
Introduction to 1000 Genomes Project and IGSR data resources
Fairley S. DOI: 10.6019/tol.isgr_w.2016.00001.1
Ensembl: Genomic features that regulate genes
Perry E. DOI: 10.6019/tol.ensreg-w.2016.00001.1
Introduction to IntAct - a Protein-Protein Interactions resource
Meldal B, Porras P. DOI: 10.6019/tol.inta-intr-w.2015.00001.1
ArrayExpress: Quick tour
Burke M. DOI: 10.6019/tol.arrex-qt.2011.00001.2
InterPro: functional and structural analysis of protein sequences
Mitchell A, Sangrador-Vegas A, Sehra M. DOI: 10.6019/tol.intp-t.2012.00001.1
EBI Metagenomics resource: Quick tour
Denise H. DOI: 10.6019/tol.mtg-qt.2013.00001.2
Network analysis of protein interaction data: an introduction
Porras P. DOI: 10.6019/tol.networks_t.2016.00001.1
Pfam: Quick tour
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam-qt.2016.00001.1
Phylogenetics: An introduction
Emery L. DOI: 10.6019/tol.phyl.2015.00001.1
UniProt quick tour
Magrane M. DOI: 10.6019/tol.unp-qt.2014.00001.1
Genomics resources: webinar
Emery L. DOI: 10.6019/tol.gen-res-w.2015.00001.1
EBI Metagenomics portal: Submitting metagenomics data to the European Nucleotide Archive
Denise H. DOI: 10.6019/tol.metagensubm-t.2016.00001.1
Protein classification: An introduction to EMBL-EBI resources
Sangrador-Vegas A, Mitchell A. DOI: 10.6019/tol.prc.2011.00001.1
PDBe: quick tour
Velankar S, Battle G. DOI: 10.6019/tol.pdbe-qt.2011.00001.1
IntAct: Molecular Interactions at the EBI
Orchard S. DOI: 10.6019/tol.inta-t.2012.00001.1
Protein interactions and their importance
Porras P, Sehra M. DOI: 10.6019/tol.pro-int.2012.00001.1
Array Express: Exploring functional genomics data quickly and easily
Füllgrabe A. DOI: 10.6019/tol.aex-t.2016.00001.2
IntAct quick tour
Porras P. DOI: 10.6019/tol.inta-qt.2011.00001.1
UniProt: Exploring protein sequence and functional information - webinar
Pundir S. DOI: 10.6019/tol.unp-expl-w.2015.00001.1
InterPro: quick tour
Mitchell A. DOI: 10.6019/tol.intp-qt.2011.00001.1
Proteomics: An introduction to EMBL-EBI resources
Orchard S, Charles PD. DOI: 10.6019/tol.pms.2011.00001.1
PRIDE: Quick tour
Vizcaino JA. DOI: 10.6019/tol.pride-qt.2014.00001.1
ArrayExpress: why and how to submit your data
Burke M. DOI: 10.6019/tol.aesub-w.2016.00001.1
BioSamples RDF: webinar
Brandizi M, Hancocks T. DOI: 10.6019/tol.bsa-rdf-w.2015.00001.1
Biomedical data: Ethical, legal and social implications
Morgan SL, Hancocks T. DOI: 10.6019/tol.elsi-c.2015.00001.1
UniProt: Exploring protein sequence and fucntional information
Magrane M, Pundir S. DOI: 10.6019/tol.unp-t.2014.00001.1
Cellular Microscopy Phenotype Ontology (CMPO): Quick tour
Rustici G, Hancocks T. DOI: 10.6019/tol.cmpo-qt.2015.00001.1
Ensembl Variant Effect Predictor (VEP): webinar
Moore B. DOI: 10.6019/tol.ensvep-w.2016.00001.1
European Nucleotide Archive (ENA) quick tour
Amid C, Cochrane G. DOI: 10.6019/tol.ena-qt.2011.00001.1
Ensembl browser webinar series (2016)
Perry E, Carvalho-Silva D, Moore B, Sparrow H. DOI: 10.6019/tol.ensbrows-w.2016.00001.1
EMBL-EBI resources: An introduction
Gopalasingam P. DOI: 10.6019/tol.intr-ebi-res-w.2015.00001.1
BioSamples quick tour
Faulconbridge A. DOI: 10.6019/tol.bsa-qt.2014.00001.1
Biomacromolecular structures
Argasinska J, Symmons MF, Gutmanas A, Kleywegt GJ, . DOI: 10.6019/tol.bms.2011.00001.1
ProteomeXchange submissions via PRIDE
Vizcaino JA, Ternent T, Sehra M, Csordas A. DOI: 10.6019/tol.pxd-t.2014.00001.1
PRIDE and ProteomeXchange: webinar
Vizcaino JA. DOI: 10.6019/tol.pride-px-w.2015.00001.1
UniProt peptide search and website updates: webinar
Pichler K. DOI: 10.6019/tol.unp-peptide-pub-w.2016.00001.1
UniProt: Programmatic access to UniProtKB: webinar
Pichler K. DOI: 10.6019/tol.unp-program-w.2015.00001.1
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 DOI: 10.1093/nar/gkw1089
Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ. Proteins Volume 85 (2017) p.359-377 DOI: 10.1002/prot.25215
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
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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
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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
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 DOI: 10.1093/gigascience/giw002
An atlas of human kinase regulation.
Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P. Molecular systems biology Volume 12 (2016) p.888 DOI: 10.15252/msb.20167295
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BiologicalWeb services: Integration, optimization, and reasoning
Benedikt M,  Lopez Serrano R,  Tsamoura E. CEUR workshop proceedings (2016) p.21-27 DOI: https://pdfs.semanticscholar.org/9983/e953294f45436c49f28d173ba078b15e4545.pdf
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
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 DOI: 10.1038/ncomms13555
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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
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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
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
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
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
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
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
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
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
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
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
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The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo-Salas RE, Swedlow J. Preprint DOI: 10.1101/089359
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 DOI: 10.1038/hortres.2016.56
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 DOI: 10.1038/nmicrobiol.2016.216
The BLUEPRINT Data Analysis Portal.
Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, BLUEPRINT Consortium, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. Cell systems Volume 3 (2016) p.491-495.e5 DOI: 10.1016/j.cels.2016.10.021
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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 MR, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Preprint DOI: 10.1101/087239
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 DOI: 10.1186/s13007-016-0144-4
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GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Iotchkova V, Ritchie GRS, Geihs M, Morganella S, Min JL, Walter K, Timpson NJ, UK10K Consortium, Dunham I, Birney E, Soranzo N. Preprint DOI: 10.1101/085738
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
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS. Journal of cheminformatics Volume 8 (2016) p.61 DOI: 10.1186/s13321-016-0174-y
The Mighty Fruit Fly Moves into Outbred Genetics.
Birney E. PLoS genetics Volume 12 (2016) p.e1006388 DOI: 10.1371/journal.pgen.1006388
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 DOI: 10.1016/j.cpb.2016.12.005
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 DOI: 10.1038/nmeth.4077
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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 DOI: 10.1097/j.pain.0000000000000678
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
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RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
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The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
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RNAcentral: a comprehensive database of non-coding RNA sequences.
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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
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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
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Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
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Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.
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Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA. Journal of molecular biology Volume 428 (2016) p.3131-3146 DOI: 10.1016/j.jmb.2016.07.003
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Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
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Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining.
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A Landscape of Pharmacogenomic Interactions in Cancer.
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Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
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The Evolutionary Fates of a Large Segmental Duplication in Mouse.
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Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.
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Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
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Birney E, Smith GD, Greally JM. PLoS genetics Volume 12 (2016) p.e1006105 DOI: 10.1371/journal.pgen.1006105
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Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
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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
Databases and Archiving for CryoEM.
Patwardhan A, Lawson CL. Methods in enzymology Volume 579 (2016) p.393-412 DOI: 10.1016/bs.mie.2016.04.015
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 DOI: 10.1186/s13059-016-0992-2
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 DOI: 10.1038/srep27740
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 DOI: 10.3389/fpls.2016.00835
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The Ensembl Variant Effect Predictor.
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Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
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Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
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Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements.
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Genomic Classification and Prognosis in Acute Myeloid Leukemia.
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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
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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 DOI: 10.1021/acs.jproteome.5b01008
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
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Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
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Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.
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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 DOI: 10.1002/ijc.30142
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 DOI: 10.1093/nar/gkw368
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Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci
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The topography of mutational processes in breast cancer genomes.
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From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
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Organization, evolution and functions of the human and mouse Ly6/uPAR family genes.
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Omics Discovery Index - Discovering and Linking Public Omics Datasets
Perez-Riverol Y, Bai M, Leprevost F, Squizzato S, Mi Park Y, Haug O, Carroll AJ, Spalding D, Paschall J, Wang M, del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch E, Campbell DS, Beavis RC, Salek R, Nesvizhskii A, Sansone S, Steinbeck C, Lopez R, Vizcaino J, Ping P, Hermjakob H. Preprint DOI: 10.1101/049205
Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
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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 DOI: 10.1186/s13326-016-0061-5
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 DOI: 10.1186/s12859-016-1008-7
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
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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
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 DOI: 10.1371/journal.pcbi.1004862
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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 DOI: 10.1038/nmeth.3830
ProbOnto: ontology and knowledge base of probability distributions.
Swat MJ, Grenon P, Wimalaratne S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2719-2721 DOI: 10.1093/bioinformatics/btw170
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 DOI: 10.1111/mec.13596
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 DOI: 10.1186/s13326-016-0055-3
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Structure (London, England : 1993) Volume 24 (2016) p.502-508 DOI: 10.1016/j.str.2016.02.017
UniProt Tools.
Pundir S, Martin MJ, O'Donovan C, UniProt Consortium. Current protocols in bioinformatics Volume 53 (2016) p.1.29.1-15 DOI: 10.1002/0471250953.bi0129s53
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
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J. Journal of biomedical semantics Volume 7 (2016) p.8 DOI: 10.1186/s13326-016-0051-7
EMPIAR: a public archive for raw electron microscopy image data.
Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A. Nature methods Volume 13 (2016) p.387-388 DOI: 10.1038/nmeth.3806
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) DOI: 10.1093/database/baw027
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
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) DOI: 10.1093/database/bav127
Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.
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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 DOI: 10.1093/bioinformatics/btw114
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Genomic epidemiology of artemisinin resistant malaria.
MalariaGEN Plasmodium falciparum Community Project. eLife Volume 5 (2016) DOI: 10.7554/elife.08714
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 DOI: 10.1371/journal.pbio.1002364
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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) DOI: 10.3835/plantgenome2015.06.0038
libChEBI: an API for accessing the ChEBI database.
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. Journal of cheminformatics Volume 8 (2016) p.11 DOI: 10.1186/s13321-016-0123-9
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 DOI: 10.18632/oncotarget.7255
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The ORFeome Collaboration: a genome-scale human ORF-clone resource.
ORFeome Collaboration. Nature methods Volume 13 (2016) p.191-192 DOI: 10.1038/nmeth.3776
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 DOI: 10.1016/j.cell.2016.01.047
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 DOI: 10.1091/mbc.e15-10-0682
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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 (Oxford, England) Volume 32 (2016) p.2041-2043 DOI: 10.1093/bioinformatics/btw110
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 DOI: 10.1093/jhered/esw010
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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.
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Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. RNA (New York, N.Y.) Volume 22 (2016) p.667-676 DOI: 10.1261/rna.055301.115
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
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
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) DOI: 10.1093/database/bav120
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) DOI: 10.1093/database/bav096
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 DOI: 10.1038/srep21518
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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
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
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) DOI: 10.1093/database/bav119
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) DOI: 10.3390/metabo6010008
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 DOI: 10.1371/journal.pcbi.1004743
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.7911.1
Web-based volume slicer for 3D electron-microscopy data from EMDB.
Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A. Journal of structural biology Volume 194 (2016) p.164-170 DOI: 10.1016/j.jsb.2016.02.012
MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC. Bioinformatics (Oxford, England) Volume 32 (2016) p.1905-1906 DOI: 10.1093/bioinformatics/btw056
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
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 DOI: 10.1186/s13326-016-0050-8
Value, but high costs in post-deposition data curation.
ten Hoopen P, Amid C, Buttigieg PL, Pafilis E, Bravakos P, Cerdeño-Tárraga AM, Gibson R, Kahlke T, Legaki A, Narayana Murthy K, Papastefanou G, Pereira E, Rossello M, Luisa Toribio A, Cochrane G. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav126
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 DOI: 10.3390/ijms17020171
Characterising Complex Enzyme Reaction Data.
Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. PloS one Volume 11 (2016) p.e0147952 DOI: 10.1371/journal.pone.0147952
Exploring the chemistry and evolution of the isomerases.
Martínez Cuesta S, Rahman SA, Thornton JM. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.1796-1801 DOI: 10.1073/pnas.1509494113
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 DOI: 10.1186/s40246-016-0062-6
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 DOI: 10.1016/j.mce.2016.01.027
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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
Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A. Cell reports Volume 14 (2016) p.1246-1257 DOI: 10.1016/j.celrep.2016.01.008
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 DOI: 10.1128/jcm.02717-15
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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)
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 DOI: 10.1093/nar/gkw022
Structure of bacterial respiratory complex I.
Berrisford JM, Baradaran R, Sazanov LA. Biochimica et biophysica acta Volume 1857 (2016) p.892-901 DOI: 10.1016/j.bbabio.2016.01.012
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 DOI: 10.1371/journal.pgen.1005772
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 DOI: 10.1021/acs.jproteome.5b00885
The EMBL-EBI channel.
McEntyre J, Birney E. F1000Research Volume 5 (2016) p.52 DOI: 10.12688/f1000research.7764.1
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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 DOI: 10.1038/ncomms10415
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 DOI: 10.1038/nmeth.3728
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
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.
Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study, Wright CF. Human molecular genetics Volume 25 (2016) p.927-935 DOI: 10.1093/hmg/ddv625
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
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 DOI: 10.12688/wellcomeopenres.10210.2
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
Protein Structure Databases.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.31-53 DOI: 10.1007/978-1-4939-3572-7_2