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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: fiddes it. Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955. Nucleic Acids Res. 2019. PMID: 30357393 Free PMC article.
Whole-Genome Alignment and Comparative Annotation.
Armstrong J, Fiddes IT, Diekhans M, Paten B. Armstrong J, et al. Among authors: fiddes it. Annu Rev Anim Biosci. 2019 Feb 15;7:41-64. doi: 10.1146/annurev-animal-020518-115005. Epub 2018 Oct 31. Annu Rev Anim Biosci. 2019. PMID: 30379572 Free PMC article. Review.
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: fiddes it. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. doi: 10.1093/nar/gkaa1087. Nucleic Acids Res. 2021. PMID: 33270111 Free PMC article.
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Lilue J, et al. Among authors: fiddes it. Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1. Nat Genet. 2018. PMID: 30275530 Free PMC article.
The UCSC Genome Browser database: 2018 update.
Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. Casper J, et al. Among authors: fiddes it. Nucleic Acids Res. 2018 Jan 4;46(D1):D762-D769. doi: 10.1093/nar/gkx1020. Nucleic Acids Res. 2018. PMID: 29106570 Free PMC article.
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Thybert D, et al. Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21. Genome Res. 2018. PMID: 29563166 Free PMC article.
The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.
Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG. Sarsani VK, et al. Among authors: fiddes it. G3 (Bethesda). 2019 Jun 5;9(6):1795-1805. doi: 10.1534/g3.119.400071. G3 (Bethesda). 2019. PMID: 30996023 Free PMC article.
Progressive Cactus is a multiple-genome aligner for the thousand-genome era.
Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B. Armstrong J, et al. Among authors: fiddes it. Nature. 2020 Nov;587(7833):246-251. doi: 10.1038/s41586-020-2871-y. Epub 2020 Nov 11. Nature. 2020. PMID: 33177663 Free PMC article.
43 results