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Page 1
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. Database (Oxford). 2022 Aug 12;2022:baac062. doi: 10.1093/database/baac062. Database (Oxford). 2022. PMID: 35961013 Free PMC article.
Plant genome annotation methods.
Ouyang S, Thibaud-Nissen F, Childs KL, Zhu W, Buell CR. Ouyang S, et al. Methods Mol Biol. 2009;513:263-82. doi: 10.1007/978-1-59745-427-8_14. Methods Mol Biol. 2009. PMID: 19347655
RefSeq: an update on mammalian reference sequences.
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Pruitt KD, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. doi: 10.1093/nar/gkt1114. Epub 2013 Nov 19. Nucleic Acids Res. 2014. PMID: 24259432 Free PMC article.
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. O'Leary NA, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8. Nucleic Acids Res. 2016. PMID: 26553804 Free PMC article.
RefSeq: an update on prokaryotic genome annotation and curation.
Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD. Haft DH, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860. doi: 10.1093/nar/gkx1068. Nucleic Acids Res. 2018. PMID: 29112715 Free PMC article.
Database resources of the National Center for Biotechnology Information.
Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K, Ketter A, Kim S, Kimchi A, Kitts PA, Kuznetsov A, Lathrop S, Lu Z, McGarvey K, Madden TL, Murphy TD, O'Leary N, Phan L, Schneider VA, Thibaud-Nissen F, Trawick BW, Pruitt KD, Ostell J. Sayers EW, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D9-D16. doi: 10.1093/nar/gkz899. Nucleic Acids Res. 2020. PMID: 31602479 Free PMC article.
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.
Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. Li W, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028. doi: 10.1093/nar/gkaa1105. Nucleic Acids Res. 2021. PMID: 33270901 Free PMC article.
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.
Goldfarb T, Kodali VK, Pujar S, Brover V, Robbertse B, Farrell CM, Oh DH, Astashyn A, Ermolaeva O, Haddad D, Hlavina W, Hoffman J, Jackson JD, Joardar VS, Kristensen D, Masterson P, McGarvey KM, McVeigh R, Mozes E, Murphy MR, Schafer SS, Souvorov A, Spurrier B, Strope PK, Sun H, Vatsan AR, Wallin C, Webb D, Brister JR, Hatcher E, Kimchi A, Klimke W, Marchler-Bauer A, Pruitt KD, Thibaud-Nissen F, Murphy TD. Goldfarb T, et al. Among authors: thibaud nissen f. Nucleic Acids Res. 2024 Nov 11:gkae1038. doi: 10.1093/nar/gkae1038. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39526381
67 results