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The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. Ten Hoopen P, et al. Among authors: finn rd. Gigascience. 2017 Aug 1;6(8):1-11. doi: 10.1093/gigascience/gix047. Gigascience. 2017. PMID: 28637310 Free PMC article.
The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. Finn RD, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. doi: 10.1093/nar/gkv1344. Epub 2015 Dec 15. Nucleic Acids Res. 2016. PMID: 26673716 Free PMC article.
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. Finn RD, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899635 Free PMC article.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium; Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Nat Biotechnol. 2017. PMID: 28787424 Free PMC article.
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S, Boland MA, Hunter FMI, Ten Hoopen P, Alako B, Amid C, Wilkinson DJ, Curtis TP, Cochrane G, Finn RD. Mitchell AL, et al. Among authors: finn rd. Nucleic Acids Res. 2018 Jan 4;46(D1):D726-D735. doi: 10.1093/nar/gkx967. Nucleic Acids Res. 2018. PMID: 29069476 Free PMC article.
261 results