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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: uszczynska ratajczak b. Nucleic Acids Res. 2024 Nov 20:gkae1078. doi: 10.1093/nar/gkae1078. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39565199
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.
Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Mądry T, Jungreis I, Arnan C, Lagarde J, Borsari B, Sisu C, Jiang Y, Bennett R, Berry A, Cerdán-Vélez D, Cochran K, Vara C, Davidson C, Donaldson S, Dursun C, González-López S, Gopal Das S, Hardy M, Hollis Z, Kay M, Montañés JC, Ni P, Nurtdinov R, Palumbo E, Pulido-Quetglas C, Suner MM, Yu X, Zhang D, Loveland JE, Albà MM, Diekhans M, Tanzer A, Mudge JM, Flicek P, Martin FJ, Gerstein M, Kellis M, Kundaje A, Paten B, Tress ML, Johnson R, Uszczynska-Ratajczak B, Frankish A, Guigó R. Kaur G, et al. Among authors: uszczynska ratajczak b. bioRxiv [Preprint]. 2024 Oct 31:2024.10.29.620654. doi: 10.1101/2024.10.29.620654. bioRxiv. 2024. PMID: 39554180 Free PMC article. Preprint.
CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing.
Carbonell-Sala S, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R. Carbonell-Sala S, et al. Among authors: uszczynska ratajczak b. bioRxiv [Preprint]. 2023 Jun 18:2023.06.16.543444. doi: 10.1101/2023.06.16.543444. bioRxiv. 2023. Update in: Nat Commun. 2024 Jun 27;15(1):5278. doi: 10.1038/s41467-024-49523-3 PMID: 37398314 Free PMC article. Updated. Preprint.
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: uszczynska ratajczak b. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. doi: 10.1093/nar/gkac1071. Nucleic Acids Res. 2023. PMID: 36420896 Free PMC article.
Author Correction: 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. 2022 May;605(7909):E4. doi: 10.1038/s41586-021-04213-8. Nature. 2022. PMID: 35474002 Free PMC article. No abstract available.
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.
25 results