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106 results

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Page 1
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S. Deutsch EW, et al. Among authors: frankish a. bioRxiv [Preprint]. 2024 Sep 9:2024.09.09.612016. doi: 10.1101/2024.09.09.612016. bioRxiv. 2024. PMID: 39314370 Free PMC article. Preprint.
Standardized annotation of translated open reading frames.
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Mudge JM, et al. Among authors: frankish a. Nat Biotechnol. 2022 Jul;40(7):994-999. doi: 10.1038/s41587-022-01369-0. Nat Biotechnol. 2022. PMID: 35831657 Free PMC article. No abstract available.
Functional transcriptomics in the post-ENCODE era.
Mudge JM, Frankish A, Harrow J. Mudge JM, et al. Among authors: frankish a. Genome Res. 2013 Dec;23(12):1961-73. doi: 10.1101/gr.161315.113. Epub 2013 Oct 30. Genome Res. 2013. PMID: 24172201 Free PMC article.
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, Frankish A, Kellis M. Mudge JM, et al. Among authors: frankish a. Genome Res. 2019 Dec;29(12):2073-2087. doi: 10.1101/gr.246462.118. Epub 2019 Sep 19. Genome Res. 2019. PMID: 31537640 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. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. doi: 10.1093/nar/gkac1071. Nucleic Acids Res. 2023. PMID: 36420896 Free PMC article.
106 results