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The Pfam protein families database: embracing AI/ML.
Paysan-Lafosse T, Andreeva A, Blum M, Chuguransky SR, Grego T, Pinto BL, Salazar GA, Bileschi ML, Llinares-López F, Meng-Papaxanthos L, Colwell LJ, Grishin NV, Schaeffer RD, Clementel D, Tosatto SCE, Sonhammer E, Wood V, Bateman A. Paysan-Lafosse T, et al. Among authors: colwell lj. Nucleic Acids Res. 2024 Nov 14:gkae997. doi: 10.1093/nar/gkae997. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39540428
MGnify: the microbiome sequence data analysis resource in 2023.
Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, Burgin J, Caballero-Pérez J, Cochrane G, Colwell LJ, Curtis T, Escobar-Zepeda A, Gurbich TA, Kale V, Korobeynikov A, Raj S, Rogers AB, Sakharova E, Sanchez S, Wilkinson DJ, Finn RD. Richardson L, et al. Among authors: colwell lj. Nucleic Acids Res. 2023 Jan 6;51(D1):D753-D759. doi: 10.1093/nar/gkac1080. Nucleic Acids Res. 2023. PMID: 36477304 Free PMC article.
Hallucinating functional protein sequences.
Belanger D, Colwell LJ. Belanger D, et al. Among authors: colwell lj. Nat Biotechnol. 2023 Aug;41(8):1073-1074. doi: 10.1038/s41587-022-01634-2. Nat Biotechnol. 2023. PMID: 36702894 No abstract available.
A roadmap for the functional annotation of protein families: a community perspective.
de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. de Crécy-Lagard V, et al. Among authors: colwell lj. Database (Oxford). 2022 Aug 12;2022:baac062. doi: 10.1093/database/baac062. Database (Oxford). 2022. PMID: 35961013 Free PMC article.
Using deep learning to annotate the protein universe.
Bileschi ML, Belanger D, Bryant DH, Sanderson T, Carter B, Sculley D, Bateman A, DePristo MA, Colwell LJ. Bileschi ML, et al. Among authors: colwell lj. Nat Biotechnol. 2022 Jun;40(6):932-937. doi: 10.1038/s41587-021-01179-w. Epub 2022 Feb 21. Nat Biotechnol. 2022. PMID: 35190689
41 results