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Page 1
GENCODE 2025: reference gene annotation for human and mouse.
Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés LT, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kaur G, Kay M, Mangan RJ, Maquedano M, Gómez LM, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner MM, Uszczynska-Ratajczak B, Wass E, Yang YT, Zhang D, Finn RD, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Birney E, Martin FJ, Frankish A. Mudge JM, et al. Among authors: bignell a. Nucleic Acids Res. 2024 Nov 20:gkae1078. doi: 10.1093/nar/gkae1078. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39565199
GENCODE reference annotation for the human and mouse genomes.
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. Frankish A, et al. Among authors: bignell a. Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955. Nucleic Acids Res. 2019. PMID: 30357393 Free PMC article.
GENCODE 2021.
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P. Frankish A, et al. Among authors: bignell a. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. doi: 10.1093/nar/gkaa1087. Nucleic Acids Res. 2021. PMID: 33270111 Free PMC article.
GENCODE: reference annotation for the human and mouse genomes in 2023.
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, Cerdán-Vélez 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 Y, Johnson R, Kay M, Lagarde J, Martin FJ, Gómez LM, Nair S, Ni P, 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. Frankish A, et al. Among authors: bignell a. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. doi: 10.1093/nar/gkac1071. Nucleic Acids Res. 2023. PMID: 36420896 Free PMC article.
GENCODE: the reference human genome annotation for The ENCODE Project.
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. Harrow J, et al. Among authors: bignell a. Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111. Genome Res. 2012. PMID: 22955987 Free PMC article.
Ensembl 2022.
Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez JG, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh DN, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Pérez-Silva JG, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt SE, IIsley GR, Loveland JE, Martin FJ, Moore B, Mudge JM, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Dyer S, Harrison PW, Howe KL, Yates AD, Zerbino DR, Flicek P. Cunningham F, et al. Among authors: bignell a. Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. doi: 10.1093/nar/gkab1049. Nucleic Acids Res. 2022. PMID: 34791404 Free PMC article.
Ensembl 2023.
Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Bignell A, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Charkhchi M, Cockburn A, Da Rin Fiorretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Ghattaoraya GS, Martinez JG, Guijarro C, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Marques-Coelho D, Marugán JC, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Prosovetskaia I, Pérez-Silva JG, Salam AIA, Saraiva-Agostinho N, Schuilenburg H, Sheppard D, Sinha S, Sipos B, Stark W, Steed E, Sukumaran R, Sumathipala D, Suner MM, Surapaneni L, Sutinen K, Szpak M, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Loveland JE, Moore B, Mudge JM, Tate J, Thybert D, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Ruffier M, Cunningham F, Dyer S, Finn RD, Howe KL, Harrison PW, Yates AD, Flicek P. Martin FJ, et al. Among authors: bignell a. Nucleic Acids Res. 2023 Jan 6;51(D1):D933-D941. doi: 10.1093/nar/gkac958. Nucleic Acids Res. 2023. PMID: 36318249 Free PMC article.
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium; Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Nature. 2020. PMID: 32728249 Free PMC article.
Perspectives on ENCODE.
ENCODE Project Consortium; Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Nature. 2020. PMID: 32728248 Free PMC article.
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium; Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. ENCODE Project Consortium, et al. Nature. 2022 May;605(7909):E3. doi: 10.1038/s41586-021-04226-3. Nature. 2022. PMID: 35474001 Free PMC article. No abstract available.
36 results