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National Human Genome Research Institute of the National Institutes of Health [U41HG007234,R01HG004037]; Wellcome Trust [WT222155/Z/20/Z];European Molecular Biology Laboratory. The contentis solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding for open access charge: National Institutes of Health

Analysis of institutional authors

Carbonell-Sala, SilviaAuthorArnan Ros, CarmeAuthorCalvet, FerriolAuthorLagarde, JulienAuthorGuigó Serra, RodericAuthor

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December 12, 2022
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Article

GENCODE: reference annotation for the human and mouse genomes in 2023

Publicated to:Nucleic Acids Research. 51 (D1): D942-D949 - 2023-01-06 51(D1), DOI: 10.1093/nar/gkac1071

Authors: Frankish, A; Carbonell-Sala, S; Diekhans, M; Jungreis, I; Loveland, JE; Mudge, JM; Sisu, C; Wright, JC; Arnan, C; Barnes, I; Banerjee, A; Bennett, R; Berry, A; Bignell, A; Boix, C; Calvet, F; Cerdan-Velez, D; Cunningham, F; Davidson, C; Donaldson, S; Dursun, C; Fatima, R; Giorgetti, S; Giron, CG; Gonzalez, JM; Hardy, M; Harrison, PW; Hourlier, T; Hollis, Z; Hunt, T; James, B; Jiang, YZ; Johnson, R; Kay, M; Lagarde, J; Martin, FJ; Gomez, LM; Nair, S; Ni, PY; Pozo, F; Ramalingam, V; Ruffier, M; Schmitt, BM; Schreiber, JM; Steed, E; Suner, MM; Sumathipala, D; Sycheva, I; Uszczynska-Ratajczak, B; Wass, E; Yang, YT; Yates, A; Zafrulla, Z; Choudhary, JS; Gerstein, M; Guigo, R; Hubbard, TJP; Kellis, M; Kundaje, A; Paten, B; Tress, ML; Flicek, P

Affiliations

Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Dept Bioinformat & Genom, Dr Aiguader 88, Catalonia 08003, Spain - Author
Bern Univ Hosp, Dept Med Oncol, Murtenstr 35, CH-3008 Bern, Switzerland - Author
Broad Inst MIT & Harvard, 415 MainSt, Cambridge, MA 02142 USA - Author
Brunel Univ London, Dept Life Sci, Uxbridge UB8 3PH, England - Author
European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England - Author
Fudan Univ, Inst Sci & Technol Brain Inspired Intelligence, Shanghai 200433, Peoples R China - Author
Guys Hosp, Kings Coll London, Dept Med & Mol Genet, Great Maze Pond, London SE1 9RT, England - Author
Inst Bioorgan Chem, Polish Acad Sci, Computat Biol Noncoding RNA, Noskowskiego 12-14, PL-61704 Poznan, Poland - Author
Inst Canc Res, Div Canc Biol, Funct Prote, 237 Fulham Rd, London SW36JB, England - Author
MIT, Comp Sci & Artificial Intelligence Lab, 32 Vassar St, Cambridge, MA 02139 USA - Author
Spanish Natl Canc Res Ctr CNIO, Bioinformat Unit, Calle Melchor Fernandez Almagro 3, Madrid 28029, Spain - Author
Stanford Univ, Dept Genet, Palo Alto, CA USA - Author
Univ Calif Santa Cruz, UC Santa Cruz Genom Inst, Santa Cruz, CA 95064 USA - Author
Univ Coll Dublin, Sch Biol & Environm Sci, Dublin D04V1W8, Ireland - Author
Univ Pompeu Fabra UPF, Dept Ciencies Expt & Salut, E-08003 Barcelona, Spain - Author
Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA - Author
Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA - Author
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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.

Keywords

AnimalsComputational biologyDatabaseDatabases, geneticGene expression profilingGenome, humanHumansLong noncoding rnasMiceMolecular sequence annotationSequenceTranscriptome

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nucleic Acids Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2023, it was in position 6/313, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology. Notably, the journal is positioned above the 90th percentile.

This publication has been distinguished as a “Highly Cited Paper” by the agencies WoS (ESI, Clarivate) and ESI (Clarivate), meaning that it ranks within the top 1% of the most cited articles in its thematic field during the year of its publication. In terms of the observed impact of the contribution, this work is considered one of the most influential worldwide, as it is recognized as highly cited. (source consulted: ESI Nov 14, 2024)

And this is evidenced by the extremely high normalized impacts through some of the main indicators of this type, which, although dynamic over time and dependent on the set of average global citations at the time of calculation, already indicate that they are well above the average in different agencies:

  • Normalization of citations relative to the expected citation rate (ESI) by the Clarivate agency: 19.73 (source consulted: ESI Nov 14, 2024)
  • Field Citation Ratio (FCR) from Dimensions: 88.07 (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-08, the following number of citations:

  • WoS: 130
  • Europe PMC: 210

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-08-08:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 177.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 254 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 14.2.
  • The number of mentions on the social network X (formerly Twitter): 31 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: China; Poland; Switzerland; United Kingdom; United States of America.