ArticleNucleic acids research2023
GENCODE: reference annotation for the human and mouse genomes in 2023.
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Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 349 papers, 1 of them a synthesis that pooled it.
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349citing papers in PubMed, 1 pooled it
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Who cites it
349 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genetic mechanisms of mitotic error in 840,853 blood genomes.medRxiv : the preprint server for health sciences · 2026Article
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- Article
289 more citing papers are in PubMed but not listed here.
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Authors and funding
62 authors.
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-4333-628X
Sílvia Carbonell-SalaDepartment of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Mark DiekhansUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.ORCID 0000-0002-0430-0989
Irwin JungreisMIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.ORCID 0000-0002-3197-5367
Jane E LovelandEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-7669-2934
Jonathan M MudgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Cristina SisuDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
James C WrightFunctional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
Carme ArnanDepartment of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.ORCID 0000-0002-7431-2088
If BarnesEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Abhimanyu BanerjeeDepartment of Genetics, Stanford University, Palo Alto, CA, USA.
Ruth BennettEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Andrew BerryEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Alexandra BignellEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Carles BoixMIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Ferriol CalvetDepartment of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Daniel Cerdán-VélezBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Fiona CunninghamEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-7445-2419
Claire DavidsonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Sarah DonaldsonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Cagatay DursunDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Reham FatimaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Stefano GiorgettiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Carlos Garcıa GironEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-0935-7271
Jose Manuel GonzalezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Matthew HardyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Peter W HarrisonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-4007-2899
Thibaut HourlierEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0003-4894-7773
Zoe HollisEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Toby HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Benjamin JamesMIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Yunzhe JiangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Rory JohnsonDepartment of Medical Oncology, Bern University Hospital, Murtenstrasse 35, 3008 Bern, Switzerland.ORCID 0000-0003-4607-2782
Mike KayEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Julien LagardeDepartment of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-1672-050X
Laura Martínez GómezBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Surag NairDepartment of Genetics, Stanford University, Palo Alto, CA, USA.ORCID 0000-0002-6216-2457
Pengyu NiDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Fernando PozoBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Vivek RamalingamDepartment of Genetics, Stanford University, Palo Alto, CA, USA.
Magali RuffierEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-8386-1580
Bianca M SchmittEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jacob M SchreiberDepartment of Genetics, Stanford University, Palo Alto, CA, USA.
Emily SteedEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Marie-Marthe SunerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-0380-7171
Dulika SumathipalaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Irina SychevaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Barbara Uszczynska-RatajczakComputational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Elizabeth WassEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Yucheng T YangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Andrew YatesEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-8886-4772
Zahoor ZafrullaDepartment of Genetics, Stanford University, Palo Alto, CA, USA.
Jyoti S ChoudharyFunctional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
Mark GersteinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Roderic GuigoDepartment of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Tim J P HubbardDepartment of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK.
Manolis KellisMIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Anshul KundajeDepartment of Genetics, Stanford University, Palo Alto, CA, USA.ORCID 0000-0003-3084-2287
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.ORCID 0000-0001-8863-3539
Michael L TressBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.ORCID 0000-0001-9046-6370
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-3897-7955
Funding
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MRegulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9MNHGRI NIH HHS R01 HG004037NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U41 HG007234Wellcome Trust
Abstract
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
Indexed as
Computational BiologyGenome, HumanAnimalsDatabases, GeneticGene Expression ProfilingHumansMiceMolecular Sequence AnnotationTranscriptome
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