ArticleNucleic acids research2021
GENCODE 2021.
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Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 894 papers.
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894citing papers in PubMed
–field-weighted citation impact
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Who cites it
894 citing papers in PubMed.
- Olaparib, durvalumab, and cyclophosphamide, and a prognostic blood signature in platinum-sensitive ovarian cancer: the randomized phase 2 SOLACE2 trial.Nature communications · 2025Trial
- Pan-cancer multi-omics analysis reveals upregulation of the POLE2 subunit of DNA polymerase epsilon and its associations with patient survival and cellular pathways beyond DNA replication.NAR genomics and bioinformatics · 2026Article
- Paternal cytokine administration alters sperm small ncRNAs and offspring brain and behavior.Molecular psychiatry · 2026Article
- Fast and slow gene expression changes in blood following acute social stress.Brain, behavior, & immunity - health · 2026Article
- Species-specific inflammatory responses of chondrocytes: Toward evidence-based model selection in OA research.iScience · 2026Article
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
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- Genotype-driven variations in lncRNA expression underlie predisposition to high-grade serous ovarian cancer.Journal of advanced research · 2026Article
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- Global Regulatory Functions of the Human CCR4-NOT Complex in mRNA Deadenylation and Decay.bioRxiv : the preprint server for biology · 2026Article
- A knockout screening platform for interferon-stimulated genes in respiratory cells identifies LY6E as a dominant antiviral effector against coronaviruses.bioRxiv : the preprint server for biology · 2026Article
- A systematic single-cell analysis of enhancer RNAs across human and mouse.Nucleic acids research · 2026Article
- Codon optimality predicts mRNA half-life but does not transfer to lncRNAs.Molecular genetics and genomics : MGG · 2026Article
- An atlas of transcription factor cooperation reveals how motif readers shape regulatory output.bioRxiv : the preprint server for biology · 2026Article
- Spindle Cell Tumors with aInternational journal of molecular sciences · 2026Article
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- Batch- and Composition-Controlled Reanalysis of Bulk and Single-Nucleus Transcriptomes Reveals Co-Enrichment of Glial Complement and of Translational Signatures in Parkinson's Disease and Amyotrophic Lateral Sclerosis.International journal of molecular sciences · 2026Article
- The molecular basis of transcription initiation by RNA polymerase II.Nature reviews. Molecular cell biology · 2026Review
- The insulin/IGF axis is critically important for controlling gene transcription in the podocyte.eLife · 2026Article
- Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans.NAR genomics and bioinformatics · 2026Article
834 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
56 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.
Irwin JungreisMIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.
Julien LagardeCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.
Jane E 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 C WrightFunctional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, 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.
Carles BoixMIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.
Silvia Carbonell SalaCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.
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.
Kevin L HoweEuropean 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.
Rory JohnsonDepartment of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland.
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.
Ferriol Calvet RieraEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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.
Maxim Y WolfDepartment of Biomedical Informatics at Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA 02115, USA.
Jinuri XuDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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.
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.
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 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 Vassar St, Cambridge, MA 02139, USA.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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
$20.3MGraduate Training in Computational and Systems BiologyT32GM087237 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BURGE, CHRISTOPHER B · 2009 to 2023
$4.6MNHGRI NIH HHS U41 HG007234NIGMS NIH HHS T32 GM087237Wellcome TrustWellcome Trust WT108749/Z/15/ZWellcome Trust WT200990/Z/16/Z
Abstract
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
Indexed as
Databases, GeneticAnimalsComputational BiologyCOVID-19EpidemicsGenomicsHumansInternetMiceMolecular Sequence AnnotationPseudogenesRNA, Long NoncodingSARS-CoV-2Transcription, GeneticRNA, Long Noncoding
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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.