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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. Among authors: brover v. 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.
Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov.
Galperin MY, Brover V, Tolstoy I, Yutin N. Galperin MY, et al. Among authors: brover v. Int J Syst Evol Microbiol. 2016 Dec;66(12):5506-5513. doi: 10.1099/ijsem.0.001548. Epub 2016 Oct 7. Int J Syst Evol Microbiol. 2016. PMID: 27902180 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. Among authors: brover v. Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860. doi: 10.1093/nar/gkx1068. Nucleic Acids Res. 2018. PMID: 29112715 Free PMC article.
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates.
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W. Feldgarden M, et al. Among authors: brover v. Antimicrob Agents Chemother. 2019 Oct 22;63(11):e00483-19. doi: 10.1128/AAC.00483-19. Print 2019 Nov. Antimicrob Agents Chemother. 2019. PMID: 31427293 Free PMC article.
Erratum for Feldgarden et al., "Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates".
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W. Feldgarden M, et al. Among authors: brover v. Antimicrob Agents Chemother. 2020 Mar 24;64(4):e00361-20. doi: 10.1128/AAC.00361-20. Print 2020 Mar 24. Antimicrob Agents Chemother. 2020. PMID: 32209564 Free PMC article. No abstract available.
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence.
Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. Feldgarden M, et al. Among authors: brover v. Sci Rep. 2021 Jun 16;11(1):12728. doi: 10.1038/s41598-021-91456-0. Sci Rep. 2021. PMID: 34135355 Free PMC article.
14 results