{"doi":"10.1093/nar/gky955","title":"GENCODE reference annotation for the human and mouse genomes","abstract":"The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.","journal":"Nucleic Acids Research","year":2018,"id":7515,"datarank":12.572188519195832,"base_score":8.130059039992796,"endowment":8.130059039992796,"self_citation_contribution":1.2195088559989196,"citation_network_contribution":11.352679663196913,"self_endowment_contribution":1.2195088559989196,"citer_contribution":11.352679663196913,"corpus_percentile":99.2,"corpus_rank":2441,"citation_count":3394,"citer_count":178,"citers_with_citation_signal":178,"citers_with_endowment":178,"datacite_reuse_total":0,"is_dataset":true,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-10-24","authors":[{"id":16842,"name":"Mark Diekhans","orcid":"0000-0002-0430-0989","position":1,"is_corresponding":false},{"id":42975,"name":"Anne-Maud Ferreira","orcid":"0000-0002-4749-746X","position":2,"is_corresponding":false},{"id":11760,"name":"Todd A. Johnson","orcid":"0000-0003-4607-2782","position":3,"is_corresponding":false},{"id":292,"name":"Irwin Jungreis","orcid":"0000-0002-3197-5367","position":4,"is_corresponding":false},{"id":24601,"name":"Jane E Loveland","orcid":"0000-0002-7669-2934","position":5,"is_corresponding":false},{"id":24517,"name":"Shinichi Morishita","orcid":"0000-0002-6201-8885","position":6,"is_corresponding":false},{"id":43162,"name":"Cristina Sisu","orcid":"0000-0001-9371-0797","position":7,"is_corresponding":false},{"id":43209,"name":"James Wright","orcid":null,"position":8,"is_corresponding":false},{"id":42914,"name":"Joel Armstrong","orcid":"0000-0003-2077-4671","position":9,"is_corresponding":false},{"id":18893,"name":"If Barnes","orcid":"0000-0001-9303-4610","position":10,"is_corresponding":false},{"id":42926,"name":"Andrew Berry","orcid":"0000-0001-5096-7701","position":11,"is_corresponding":false},{"id":18895,"name":"Alexandra Bignell","orcid":"0000-0002-5926-7020","position":12,"is_corresponding":false},{"id":59116,"name":"Silvia Carbonell Sala","orcid":null,"position":13,"is_corresponding":false},{"id":11743,"name":"Jacqueline Chrast","orcid":null,"position":14,"is_corresponding":false},{"id":35062,"name":" Fiona Cunningham","orcid":"0000-0002-7445-2419","position":15,"is_corresponding":false},{"id":59117,"name":"Tomás Di Domenico","orcid":"0000-0003-2887-815X","position":16,"is_corresponding":false},{"id":42963,"name":"Sarah Donaldson","orcid":"0000-0002-2576-3173","position":17,"is_corresponding":false},{"id":49022,"name":"Ian T. Fiddes","orcid":"0000-0002-1580-7443","position":18,"is_corresponding":false},{"id":30915,"name":"Carlos García Girón","orcid":"0000-0002-0935-7271","position":19,"is_corresponding":false},{"id":59119,"name":"Tiago Grego","orcid":"0000-0002-7946-7062","position":21,"is_corresponding":false},{"id":36424,"name":"Manoj Hariharan","orcid":"0000-0002-1006-5372","position":22,"is_corresponding":false},{"id":30880,"name":"Thibaut Hourlier","orcid":"0000-0003-4894-7773","position":23,"is_corresponding":false},{"id":18874,"name":"Toby Hunt","orcid":"0000-0001-8377-0841","position":24,"is_corresponding":false},{"id":59121,"name":"Osagie G Izuogu","orcid":null,"position":25,"is_corresponding":false},{"id":11723,"name":"Julien Lagarde","orcid":"0000-0002-0290-7445","position":26,"is_corresponding":false},{"id":24505,"name":"Fergal J. Martin","orcid":"0000-0002-1672-050X","position":27,"is_corresponding":false},{"id":98907,"name":"Laura Martinez-Gomez","orcid":null,"position":28,"is_corresponding":false},{"id":59123,"name":"Shamika Mohanan","orcid":"0000-0001-8126-2747","position":29,"is_corresponding":false},{"id":59124,"name":"Paul Muir","orcid":"0000-0002-3645-6822","position":30,"is_corresponding":false},{"id":13855,"name":"Fabio C. P. Navarro","orcid":null,"position":31,"is_corresponding":false},{"id":59125,"name":"Anne Parker","orcid":null,"position":32,"is_corresponding":false},{"id":37964,"name":"Baikang Pei","orcid":null,"position":33,"is_corresponding":false},{"id":59126,"name":"Fernando Pozo","orcid":null,"position":34,"is_corresponding":false},{"id":29376,"name":"Magali Ruffier","orcid":"0000-0002-8386-1580","position":35,"is_corresponding":false},{"id":59128,"name":"Bianca M. Schmitt","orcid":"0000-0003-4341-2972","position":36,"is_corresponding":false},{"id":59129,"name":"Eloise Stapleton","orcid":null,"position":37,"is_corresponding":false},{"id":43173,"name":"Balaji Sundararaman","orcid":"0000-0001-8559-1660","position":38,"is_corresponding":false},{"id":59130,"name":"Irina Sycheva","orcid":"0000-0002-1931-4531","position":39,"is_corresponding":false},{"id":43182,"name":"Barbara Uszczynska-Ratajczak","orcid":null,"position":40,"is_corresponding":false},{"id":43212,"name":"Jie Xu","orcid":"0000-0002-1503-1104","position":41,"is_corresponding":false},{"id":59133,"name":"Andrew Yates","orcid":"0000-0002-8886-4772","position":42,"is_corresponding":false},{"id":32862,"name":"Vyacheslav Amstislavskiy","orcid":"0000-0002-1384-7599","position":43,"is_corresponding":false},{"id":12202,"name":"Yan Zhang","orcid":"0000-0002-9173-7029","position":44,"is_corresponding":false},{"id":37972,"name":"Bronwen Aken","orcid":"0000-0002-3032-4095","position":45,"is_corresponding":false},{"id":17805,"name":"Jyoti Sharma Choudhary","orcid":"0000-0003-0881-5477","position":46,"is_corresponding":false},{"id":42990,"name":"Grigorios Georgolopoulos","orcid":"0000-0002-9906-4797","position":47,"is_corresponding":false},{"id":59323,"name":"Simon G. Gregory","orcid":"0000-0002-7805-1743","position":48,"is_corresponding":false},{"id":14693,"name":"Sharon L. R. Kardia","orcid":"0000-0002-9853-3379","position":50,"is_corresponding":false},{"id":30899,"name":"Nathan D. Olson","orcid":"0000-0003-2585-3037","position":51,"is_corresponding":false},{"id":11786,"name":"Alexandre Reymond","orcid":"0000-0003-1030-8327","position":52,"is_corresponding":false},{"id":13168,"name":"Liis Uusküla-Reimand","orcid":"0000-0002-5322-5524","position":53,"is_corresponding":false},{"id":20075,"name":"David B. Jaffe","orcid":"0000-0001-8739-568X","position":54,"is_corresponding":false},{"id":43288,"name":"James C. Wright","orcid":"0000-0001-6950-4328","position":55,"is_corresponding":false},{"id":59135,"name":"Sílvia Carbonell Sala","orcid":"0000-0001-7956-6215","position":56,"is_corresponding":false},{"id":37971,"name":"Jose Manuel Gonzalez","orcid":"0000-0001-5569-0705","position":57,"is_corresponding":false},{"id":43255,"name":"Matthew P. Hardy","orcid":"0000-0001-6420-1715","position":58,"is_corresponding":false},{"id":43032,"name":"Osagie Izuogu","orcid":"0000-0003-3116-2558","position":59,"is_corresponding":false},{"id":59136,"name":"Laura Martínez Gómez","orcid":"0000-0001-9843-1332","position":60,"is_corresponding":false},{"id":14412,"name":"Fábio C. P. Navarro","orcid":"0000-0002-5640-9070","position":61,"is_corresponding":false},{"id":59137,"name":"Fernando Campo del Pozo","orcid":"0000-0001-7688-6045","position":62,"is_corresponding":false},{"id":43283,"name":"Barbara Uszczyńska-Ratajczak","orcid":"0000-0003-0150-3841","position":63,"is_corresponding":false},{"id":43213,"name":"Jinrui Xu","orcid":"0000-0003-1944-2821","position":64,"is_corresponding":false},{"id":2131,"name":"Tim Hubbard","orcid":"0000-0002-1767-9318","position":65,"is_corresponding":false},{"id":29021,"name":"Michael G. FitzGerald","orcid":"0000-0002-0488-0530","position":0,"is_corresponding":true}],"reference_count":48,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}