ArticleNucleic acids research2025
GENCODE 2025: reference gene annotation for human and mouse.
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Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 268 papers.
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268citing papers in PubMed
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268 citing papers in PubMed.
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- A trio-based long-read sequencing workflow identifies a pathogenic transposable element insertion in a previously undiagnosed patient.Journal of human genetics · 2026Article
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Lack of evidence for transcription-to-RNA maturation lags across G1-to-G2-phase boundary in fibroblasts.Life science alliance · 2026Article
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- The novel transcripts we keep rediscovering.Nature biotechnology · 2026Article
- Molecular underpinnings of metastatic small renal masses.JCI insight · 2026Article
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- Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Pervasive tissue specificity of driver genes revealed by mutational analysis of 265 cancer types.iScience · 2026Article
- A Real-Data-Driven Framework for Evaluating Differential Transcript Usage Methods Across Long-Read Bulk, Single-Cell, and Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Sex Steroid Hormone Signaling Tunes Metabolic and Neuronal Programs in Human Cortical Development.Research square · 2026Article
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- The dark genome in cardiovascular medicine.European heart journal · 2026Review
- Atlastin-2-mediated endoplasmic reticulum membrane tethering is critical for flavivirus replication.PLoS biology · 2026Article
- IFN-α and IFN-β inhibit NLRP1-driven PANoptosis.EMBO reports · 2026Article
208 more citing papers are in PubMed but not listed here.
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Authors and funding
56 authors.
Jonathan M MudgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0003-4789-7495
Sílvia Carbonell-SalaCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain.
Mark DiekhansUC Santa Cruz Genomics Institute, 2300 Delaware Avenue, University of California, Santa Cruz, CA 95060, USA.ORCID 0000-0002-0430-0989
Jose Gonzalez MartinezEuropean 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.
Irwin JungreisComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 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
Carme ArnanCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 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.
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.
Daniel Cerdán-VélezBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Kelly CochranDepartment of Computer Science, Stanford University, 353 Jane Stanford Way, Stanford, CA, USA.
Lucas T CortésEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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 DursunProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Reham FatimaEuropean 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.
Prajna HebbarUC Santa Cruz Genomics Institute, 2300 Delaware Avenue, University of California, Santa Cruz, CA 95060, USA.
Zoe HollisEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Benjamin T JamesComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 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.
Gazaldeep KaurCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain.
Mike KayEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Riley J ManganComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.
Miguel MaquedanoBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Laura Martínez GómezBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Nourhen MathlouthiEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Ryan MerrittEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Pengyu NiProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Emilio PalumboCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain.
Tamara PerteghellaCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain.
Fernando PozoBioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
Shriya RajEuropean 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.
Emily SteedEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Dulika SumathipalaEuropean 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
Barbara Uszczynska-RatajczakDepartment of Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego12/14, 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.
Dingyao ZhangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Robert D FinnEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0001-8626-2148
Mark GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 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 KellisComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.
Anshul KundajeDepartment of Computer Science, Stanford University, 353 Jane Stanford Way, Stanford, CA, USA.ORCID 0000-0003-3084-2287
Benedict PatenUC Santa Cruz Genomics Institute, 2300 Delaware Avenue, University of California, Santa Cruz, CA 95060, 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
Ewan BirneyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0001-8314-8497
Fergal J MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-1672-050X
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-4333-628X
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
$16.1MTRAINING GRANT IN GENETICST32GM007748 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI Anne O'Donnell-Luria, Louise Wilkins-Haug · 1985 to 2026
$12.0MGenerating a full-length reference transcriptome for human protein-coding genesU24HG011451 · NHGRI · DANA-FARBER CANCER INST · PI David E. Hill, Marc Vidal · 2022 to 2026
$3.3MEuropean Molecular Biology LaboratoryNational Science Center 2021/42/E/NZ2/00434NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24HG007234NHGRI NIH HHS U24 HG011451NHGRI NIH HHS U41 HG007234NIGMS NIH HHS T32 GM007748NIH HHSWellcome TrustWellcome Trust WT222155/Z/20/Z
Abstract
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species' genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate annotations throughout multiple human and mouse genomes, as we enter the pangenome era. Our resources are freely available at our web portal www.gencodegenes.org, and via the Ensembl and UCSC genome browsers.
Indexed as
Molecular Sequence AnnotationAnimalsDatabases, GeneticGenomeGenomicsHumansMiceRNA, Long NoncodingSoftwareTranscriptomeRNA, Long Noncoding
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