GENCODE 2025: reference gene annotation for human and mouse.

Autor:	Mudge JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Carbonell-Sala S; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain., Diekhans M; UC Santa Cruz Genomics Institute, 2300 Delaware Avenue, University of California, Santa Cruz, CA 95060, USA., Martinez JG; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Hunt T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Jungreis I; Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA., Loveland JE; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Arnan C; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain., Barnes I; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Bennett R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Berry A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Bignell A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Cerdán-Vélez D; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain., Cochran K; Department of Computer Science, Stanford University, 353 Jane Stanford Way, Stanford, CA, USA., Cortés LT; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Davidson C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Donaldson S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Dursun C; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Fatima R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Hardy M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Hebbar P; UC Santa Cruz Genomics Institute, 2300 Delaware Avenue, University of California, Santa Cruz, CA 95060, USA., Hollis Z; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., James BT; Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA., Jiang Y; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Johnson R; Department of Medical Oncology, Bern University Hospital, Murtenstrasse 35, 3008 Bern, Switzerland.; School of Biology and Environmental Science, University College Dublin,, Belfield, Dublin 4 D04 V1W8, Ireland., Kaur G; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain., Kay M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Mangan RJ; Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.; Genetics Training Program, Harvard Medical School, Boston, MA 02115, USA., Maquedano M; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain., Gómez LM; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain., Mathlouthi N; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Merritt R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Ni P; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Palumbo E; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain., Perteghella T; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain.; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Carrer de la Mercè, 12, Ciutat Vella 08002 Barcelona, Spain., Pozo F; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain., Raj S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Sisu C; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.; Department of Life Sciences, Brunel University London, Kingston Lane, Uxbridge, London UB8 3PH, UK., Steed E; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Sumathipala D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Suner MM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Uszczynska-Ratajczak B; Department of Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego12/14, 61-704 Poznan, Poland., Wass E; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Yang YT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, 220 Handan Road, Shanghai 200433, China., Zhang D; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Finn RD; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Gerstein M; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Guigó R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003 Catalonia, Spain.; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Carrer de la Mercè, 12, Ciutat Vella 08002 Barcelona, Spain., Hubbard TJP; Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK.; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Kellis M; Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA.; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA., Kundaje A; Department of Computer Science, Stanford University, 353 Jane Stanford Way, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA., Paten B; UC Santa Cruz Genomics Institute, 2300 Delaware Avenue, University of California, Santa Cruz, CA 95060, USA., Tress ML; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain., Birney E; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Martin FJ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Frankish A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Nov 20. Date of Electronic Publication: 2024 Nov 20.
DOI:	10.1093/nar/gkae1078
Abstrakt:	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. (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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