{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T08:04:00Z","timestamp":1776153840045,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2018,10,24]],"date-time":"2018-10-24T00:00:00Z","timestamp":1540339200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U41HG007234"],"award-info":[{"award-number":["U41HG007234"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT108749\/Z\/15\/Z"],"award-info":[{"award-number":["WT108749\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT200990\/Z\/16\/Z"],"award-info":[{"award-number":["WT200990\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,8]]},"DOI":"10.1093\/nar\/gky955","type":"journal-article","created":{"date-parts":[[2018,10,8]],"date-time":"2018-10-08T20:12:25Z","timestamp":1539029545000},"page":"D766-D773","source":"Crossref","is-referenced-by-count":2955,"title":["GENCODE reference annotation for the human and mouse genomes"],"prefix":"10.1093","volume":"47","author":[{"given":"Adam","family":"Frankish","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Mark","family":"Diekhans","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA\u00a095064, USA"}]},{"given":"Anne-Maud","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Center for Integrative Genomics, University of Lausanne, 1015\u00a0Lausanne, Switzerland"}]},{"given":"Rory","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland"},{"name":"Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3197-5367","authenticated-orcid":false,"given":"Irwin","family":"Jungreis","sequence":"additional","affiliation":[{"name":"MIT Computer Science and Artificial Intelligence Laboratory, 32 Vasser St, Cambridge, MA\u00a002139, USA"},{"name":"Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA\u00a002142, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7669-2934","authenticated-orcid":false,"given":"Jane","family":"Loveland","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Jonathan M","family":"Mudge","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Cristina","family":"Sisu","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"},{"name":"Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK"}]},{"given":"James","family":"Wright","sequence":"additional","affiliation":[{"name":"Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK"}]},{"given":"Joel","family":"Armstrong","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA\u00a095064, USA"}]},{"given":"If","family":"Barnes","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Andrew","family":"Berry","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Alexandra","family":"Bignell","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Silvia","family":"Carbonell\u00a0Sala","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003\u00a0Catalonia, Spain"}]},{"given":"Jacqueline","family":"Chrast","sequence":"additional","affiliation":[{"name":"Center for Integrative Genomics, University of Lausanne, 1015\u00a0Lausanne, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7445-2419","authenticated-orcid":false,"given":"Fiona","family":"Cunningham","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2887-815X","authenticated-orcid":false,"given":"Tom\u00e1s","family":"Di\u00a0Domenico","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"}]},{"given":"Sarah","family":"Donaldson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Ian T","family":"Fiddes","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA\u00a095064, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0935-7271","authenticated-orcid":false,"given":"Carlos","family":"Garc\u00eda\u00a0Gir\u00f3n","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Jose Manuel","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Tiago","family":"Grego","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Matthew","family":"Hardy","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4894-7773","authenticated-orcid":false,"given":"Thibaut","family":"Hourlier","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Toby","family":"Hunt","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Osagie G","family":"Izuogu","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Julien","family":"Lagarde","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003\u00a0Catalonia, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1672-050X","authenticated-orcid":false,"given":"Fergal J","family":"Martin","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Laura","family":"Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"}]},{"given":"Shamika","family":"Mohanan","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Paul","family":"Muir","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT\u00a006520, USA"},{"name":"Systems Biology Institute, Yale University, West Haven, CT\u00a006516, USA"}]},{"given":"Fabio C\u00a0P","family":"Navarro","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"}]},{"given":"Anne","family":"Parker","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Baikang","family":"Pei","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"}]},{"given":"Fernando","family":"Pozo","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8386-1580","authenticated-orcid":false,"given":"Magali","family":"Ruffier","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Bianca M","family":"Schmitt","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Eloise","family":"Stapleton","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0380-7171","authenticated-orcid":false,"given":"Marie-Marthe","family":"Suner","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Irina","family":"Sycheva","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Barbara","family":"Uszczynska-Ratajczak","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Warsaw, Poland"}]},{"given":"Jinuri","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"}]},{"given":"Andrew","family":"Yates","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5350-3056","authenticated-orcid":false,"given":"Daniel","family":"Zerbino","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Yan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"},{"name":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH\u00a043210, USA"}]},{"given":"Bronwen","family":"Aken","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Jyoti S","family":"Choudhary","sequence":"additional","affiliation":[{"name":"Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA"},{"name":"Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA"},{"name":"Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA"}]},{"given":"Roderic","family":"Guig\u00f3","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003\u00a0Catalonia, Spain"},{"name":"Universitat Pompeu Fabra (UPF), Barcelona, E-08003\u00a0Catalonia, Spain"}]},{"given":"Tim J\u00a0P","family":"Hubbard","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK"}]},{"given":"Manolis","family":"Kellis","sequence":"additional","affiliation":[{"name":"MIT Computer Science and Artificial Intelligence Laboratory, 32 Vasser St, Cambridge, MA\u00a002139, USA"},{"name":"Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA\u00a002142, USA"}]},{"given":"Benedict","family":"Paten","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA\u00a095064, USA"}]},{"given":"Alexandre","family":"Reymond","sequence":"additional","affiliation":[{"name":"Center for Integrative Genomics, University of Lausanne, 1015\u00a0Lausanne, Switzerland"}]},{"given":"Michael L","family":"Tress","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3897-7955","authenticated-orcid":false,"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]}],"member":"286","published-online":{"date-parts":[[2018,10,24]]},"reference":[{"key":"key\n\t\t\t\t2019010800480568200_B1","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","volume":"306","author":"ENCODE Project Consortium","year":"2004","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010800480568200_B2","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"ENCODE Project Consortium","year":"2007","journal-title":"Nature"},{"issue":"Suppl. 1","key":"key\n\t\t\t\t2019010800480568200_B3","article-title":"GENCODE: producing a reference annotation for ENCODE","volume":"7","author":"Harrow","year":"2006","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019010800480568200_B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010800480568200_B5","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for The ENCODE Project","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B6","doi-asserted-by":"crossref","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","article-title":"Ensembl 2018","volume":"46","author":"Zerbino","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B7","doi-asserted-by":"crossref","first-page":"D762","DOI":"10.1093\/nar\/gkx1020","article-title":"The UCSC Genome Browser database: 2018 update","volume":"46","author":"Casper","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B8","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","author":"GTEx Consortium","year":"2017","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010800480568200_B9","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"International Cancer Genome Consortium","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010800480568200_B10","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/j.cell.2016.11.007","article-title":"The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery","volume":"167","author":"Stunnenberg","year":"2016","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010800480568200_B11","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"1000, Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010800480568200_B12","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019010800480568200_B13","doi-asserted-by":"crossref","first-page":"e27041","DOI":"10.7554\/eLife.27041","article-title":"The Human Cell Atlas","volume":"6","author":"Regev","year":"2017","journal-title":"Elife"},{"key":"key\n\t\t\t\t2019010800480568200_B14","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt Consortium","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B15","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"Schneider","year":"2017","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B16","doi-asserted-by":"crossref","first-page":"D221","DOI":"10.1093\/nar\/gkx1031","article-title":"Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation","volume":"46","author":"Pujar","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B17","doi-asserted-by":"crossref","first-page":"i275","DOI":"10.1093\/bioinformatics\/btr209","article-title":"PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions","volume":"27","author":"Lin","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010800480568200_B18","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1016\/j.cell.2014.11.035","article-title":"A highly conserved program of neuronal microexons is misregulated in autistic brains","volume":"159","author":"Irimia","year":"2014","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010800480568200_B19","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1038\/nbt.3242","article-title":"Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events","volume":"33","author":"Tilgner","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t2019010800480568200_B20","doi-asserted-by":"crossref","first-page":"7070","DOI":"10.1093\/nar\/gky587","article-title":"Loose ends: almost one in five human genes still have unresolved coding status","volume":"46","author":"Abascal","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B21","doi-asserted-by":"crossref","first-page":"5866","DOI":"10.1093\/hmg\/ddu309","article-title":"Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes","volume":"23","author":"Ezkurdia","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"key\n\t\t\t\t2019010800480568200_B22","doi-asserted-by":"crossref","first-page":"D68","DOI":"10.1093\/nar\/gkt1181","article-title":"miRBase: annotating high confidence microRNAs using deep sequencing data","volume":"42","author":"Kozomara","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B23","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B24","doi-asserted-by":"crossref","first-page":"baw093","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","volume":"2016","author":"Aken","year":"2016","journal-title":"Database (Oxford)"},{"key":"key\n\t\t\t\t2019010800480568200_B25","doi-asserted-by":"crossref","first-page":"D335","DOI":"10.1093\/nar\/gkx1038","article-title":"Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families","volume":"46","author":"Kalvari","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B26","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t2019010800480568200_B27","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S0092-8674(02)00727-4","article-title":"Computational genomics of noncoding RNA genes","volume":"109","author":"Eddy","year":"2002","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019010800480568200_B28","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1101\/gr.132159.111","article-title":"The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression","volume":"22","author":"Derrien","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B29","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1038\/nmeth.3958","article-title":"Spliced synthetic genes as internal controls in RNA sequencing experiments","volume":"13","author":"Hardwick","year":"2016","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010800480568200_B30","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/nmeth.2714","article-title":"Assessment of transcript reconstruction methods for RNA-seq","volume":"10","author":"Steijger","year":"2013","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t2019010800480568200_B31","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1038\/ng.3988","article-title":"High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing","volume":"49","author":"Lagarde","year":"2017","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010800480568200_B32","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/s41576-018-0017-y","article-title":"Towards a complete map of the human long non-coding RNA transcriptome","volume":"19","author":"Uszczynska-Ratajczak","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t2019010800480568200_B33","doi-asserted-by":"crossref","first-page":"4686","DOI":"10.1021\/acs.jproteome.6b00765","article-title":"Flexible Data Analysis Pipeline for High-Confidence Proteogenomics","volume":"15","author":"Weisser","year":"2016","journal-title":"J Proteome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B34","doi-asserted-by":"crossref","first-page":"176","DOI":"10.4172\/jpb.1000404","article-title":"DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics","volume":"9","author":"Wright","year":"2016","journal-title":"J Proteomics Bioinform"},{"key":"key\n\t\t\t\t2019010800480568200_B35","doi-asserted-by":"crossref","first-page":"11778","DOI":"10.1038\/ncomms11778","article-title":"Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow","volume":"7","author":"Wright","year":"2016","journal-title":"Nat. Commun."},{"key":"key\n\t\t\t\t2019010800480568200_B36","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1101\/gr.134478.111","article-title":"Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome","volume":"22","author":"Howald","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B37","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1101\/gr.233460.117","article-title":"Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation","volume":"28","author":"Fiddes","year":"2018","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B38","doi-asserted-by":"crossref","DOI":"10.1038\/s41588-018-0223-8","article-title":"Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci","author":"Lilue","year":"2018","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t2019010800480568200_B39","doi-asserted-by":"crossref","first-page":"aae0344","DOI":"10.1126\/science.aae0344","article-title":"Long-read sequence assembly of the gorilla genome","volume":"352","author":"Gordon","year":"2016","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010800480568200_B40","doi-asserted-by":"crossref","first-page":"eaar6343","DOI":"10.1126\/science.aar6343","article-title":"High-resolution comparative analysis of great ape genomes","volume":"360","author":"Kronenberg","year":"2018","journal-title":"Science"},{"key":"key\n\t\t\t\t2019010800480568200_B41","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1101\/gr.123356.111","article-title":"Cactus: algorithms for genome multiple sequence alignment","volume":"21","author":"Paten","year":"2011","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B42","doi-asserted-by":"crossref","first-page":"3388","DOI":"10.1093\/bioinformatics\/btw494","article-title":"Simultaneous gene finding in multiple genomes","volume":"32","author":"K\u00f6nig","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010800480568200_B43","doi-asserted-by":"crossref","first-page":"D110","DOI":"10.1093\/nar\/gks1058","article-title":"APPRIS: annotation of principal and alternative splice isoforms","volume":"41","author":"Rodriguez","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B44","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1021\/pr501286b","article-title":"Most highly expressed protein-coding genes have a single dominant isoform","volume":"14","author":"Ezkurdia","year":"2015","journal-title":"J. Proteome Res."},{"key":"key\n\t\t\t\t2019010800480568200_B45","doi-asserted-by":"crossref","first-page":"D213","DOI":"10.1093\/nar\/gkx997","article-title":"APPRIS 2017: principal isoforms for multiple gene sets","volume":"46","author":"Rodriguez","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t2019010800480568200_B46","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1093\/bioinformatics\/btl116","article-title":"PseudoPipe: an automated pseudogene identification pipeline","volume":"22","author":"Zhang","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019010800480568200_B47","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1186\/1471-2164-9-466","article-title":"Retrocopy contributions to the evolution of the human genome","volume":"9","author":"Baertsch","year":"2008","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t2019010800480568200_B48","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1093\/bioinformatics\/btt104","article-title":"RCPedia: a database of retrocopied genes","volume":"29","author":"Navarro","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/D1\/D766\/27436288\/gky955.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T19:36:46Z","timestamp":1693942606000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/D1\/D766\/5144133"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,24]]},"references-count":48,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2018,10,24]]},"published-print":{"date-parts":[[2019,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky955","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1,8]]},"published":{"date-parts":[[2018,10,24]]}}}