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EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.
Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE, R Leach A, Levchenko M, Marques D, McDonagh EM, Mithani A, Parkinson H, Perez-Riverol Y, Perova Z, Sarkans U, Tirunagari S, Tzampatzopoulou E, Venkatesan A, Vizcaino JA, Wingfield B, Zdrazil B, McEntyre J. Thakur M, et al. Among authors: finn rd. Nucleic Acids Res. 2024 Nov 28:gkae1089. doi: 10.1093/nar/gkae1089. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39607697
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: finn rd. Nucleic Acids Res. 2024 Nov 20:gkae1078. doi: 10.1093/nar/gkae1078. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39565199
Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.
Tagirdzhanova G, Saary P, Cameron ES, Allen CCG, Garber AI, Escandón DD, Cook AT, Goyette S, Nogerius VT, Passo A, Mayrhofer H, Holien H, Tønsberg T, Stein LY, Finn RD, Spribille T. Tagirdzhanova G, et al. Among authors: finn rd. PLoS Biol. 2024 Nov 7;22(11):e3002862. doi: 10.1371/journal.pbio.3002862. eCollection 2024 Nov. PLoS Biol. 2024. PMID: 39509454 Free PMC article.
CELEBRIMBOR: core and accessory genes from metagenomes.
Hellewell J, Horsfield ST, von Wachsmann J, Gurbich TA, Finn RD, Iqbal Z, Roberts LW, Lees JA. Hellewell J, et al. Among authors: finn rd. Bioinformatics. 2024 Sep 2;40(9):btae542. doi: 10.1093/bioinformatics/btae542. Bioinformatics. 2024. PMID: 39298479 Free PMC article.
The growing repertoire of phage anti-defence systems.
Murtazalieva K, Mu A, Petrovskaya A, Finn RD. Murtazalieva K, et al. Among authors: finn rd. Trends Microbiol. 2024 Jun 5:S0966-842X(24)00136-7. doi: 10.1016/j.tim.2024.05.005. Online ahead of print. Trends Microbiol. 2024. PMID: 38845267 Free article. Review.
Ensembl 2024.
Harrison PW, Amode MR, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Campbell LI, Martinez MC, Charkhchi M, Chougule K, Cockburn A, Davidson C, De Silva NH, Dodiya K, Donaldson S, El Houdaigui B, Naboulsi TE, Fatima R, Giron CG, Genez T, Grigoriadis D, Ghattaoraya GS, Martinez JG, Gurbich TA, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Lodha D, Marques-Coelho D, Maslen G, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Pérez-Silva JG, Salam AIA, Saraf S, Saraiva-Agostinho N, Sheppard D, Sinha S, Sipos B, Sitnik V, Stark W, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Ware D, Wass E, Willhoft NL, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Keatley J, Loveland JE, Moore B, Mudge JM, Naamati G, Tate J, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Cunningham F, Dyer S, Finn RD, Martin FJ, Yates AD. Harrison PW, et al. Among authors: finn rd. Nucleic Acids Res. 2024 Jan 5;52(D1):D891-D899. doi: 10.1093/nar/gkad1049. Nucleic Acids Res. 2024. PMID: 37953337 Free PMC article.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P. Schmidt TSB, et al. Among authors: finn rd. Nucleic Acids Res. 2024 Jan 5;52(D1):D777-D783. doi: 10.1093/nar/gkad943. Nucleic Acids Res. 2024. PMID: 37897342 Free PMC article.
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.
Zafeiropoulos H, Beracochea M, Ninidakis S, Exter K, Potirakis A, De Moro G, Richardson L, Corre E, Machado J, Pafilis E, Kotoulas G, Santi I, Finn RD, Cox CJ, Pavloudi C. Zafeiropoulos H, et al. Among authors: finn rd. Gigascience. 2022 Dec 28;12:giad078. doi: 10.1093/gigascience/giad078. Epub 2023 Oct 18. Gigascience. 2022. PMID: 37850871 Free PMC article.
268 results