ArticleNucleic acids research2019
GENCODE reference annotation for the human and mouse genomes.
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Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,996 papers, 1 of them a synthesis that pooled it.
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1,996 citing papers in PubMed, 1 synthesis or guideline pooled it.
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Authors and funding
55 authors.
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Mark DiekhansUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Anne-Maud FerreiraCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
Rory JohnsonDepartment of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland.
Irwin JungreisMIT Computer Science and Artificial Intelligence Laboratory, 32 Vasser St, Cambridge, MA 02139, USA.
Jane LovelandEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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 WrightFunctional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK.
Joel ArmstrongUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
If BarnesEuropean 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.
Silvia Carbonell SalaCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.
Jacqueline ChrastCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
Fiona CunninghamEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Tomás Di DomenicoBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Sarah DonaldsonEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Ian T FiddesUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Carlos García GirónEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jose Manuel GonzalezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Tiago GregoEuropean 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.
Thibaut HourlierEuropean 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.
Osagie G IzuoguEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Julien LagardeCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Laura MartínezBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Shamika MohananEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Paul MuirDepartment of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA.
Fabio C P NavarroDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Anne ParkerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Baikang PeiDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Fernando PozoBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Magali RuffierEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Bianca M SchmittEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Eloise StapletonEuropean 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.
Irina SychevaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Barbara Uszczynska-RatajczakCentre of New Technologies, University of Warsaw, Warsaw, Poland.
Jinuri XuDepartment 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.
Daniel ZerbinoEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Yan ZhangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Bronwen AkenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jyoti S ChoudharyFunctional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK.
Mark GersteinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-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 Vasser St, Cambridge, MA 02139, USA.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Alexandre ReymondCenter for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
Michael L TressBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Funding
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MNHGRI NIH HHS U41 HG007234Wellcome TrustWellcome Trust WT108749/Z/15/ZWellcome Trust WT200990/Z/16/Z
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.
Indexed as
Databases, GeneticGenomicsAnimalsComputational BiologyGenome, HumanHumansInternetMiceMolecular Sequence AnnotationPseudogenesSoftware
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.