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For: Kannan S, Sharma S, Ciufo S, Clark K, Turner S, Kitts PA, Schoch CL, DiCuccio M, Kimchi A. Collection and curation of prokaryotic genome assemblies from type strains at NCBI. Int J Syst Evol Microbiol 2023;73. [PMID: 36748495 DOI: 10.1099/ijsem.0.005707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
Number Cited by Other Article(s)
1
Elmanzalawi M, Fujisawa T, Mori H, Nakamura Y, Tanizawa Y. DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes. BMC Bioinformatics 2025;26:3. [PMID: 39773409 PMCID: PMC11705978 DOI: 10.1186/s12859-024-06030-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025]  Open
2
Sayers E, Beck J, Bolton E, Brister J, Chan J, Connor R, Feldgarden M, Fine A, Funk K, Hoffman J, Kannan S, Kelly C, Klimke W, Kim S, Lathrop S, Marchler-Bauer A, Murphy T, O’Sullivan C, Schmieder E, Skripchenko Y, Stine A, Thibaud-Nissen F, Wang J, Ye J, Zellers E, Schneider V, Pruitt K. Database resources of the National Center for Biotechnology Information in 2025. Nucleic Acids Res 2025;53:D20-D29. [PMID: 39526373 PMCID: PMC11701734 DOI: 10.1093/nar/gkae979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 10/09/2024] [Accepted: 10/17/2024] [Indexed: 11/16/2024]  Open
3
Renner SS, Scherz MD, Schoch CL, Gottschling M, Vences M. Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains. Syst Biol 2024;73:486-494. [PMID: 37956405 PMCID: PMC11502950 DOI: 10.1093/sysbio/syad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/21/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023]  Open
4
Iyer R, Iken B. Whole genome sequencing data of Acinetobacter venetianus JKSF06 collected from Houston ship channel sediment in La Porte, Texas. Data Brief 2024;53:110117. [PMID: 38348316 PMCID: PMC10859253 DOI: 10.1016/j.dib.2024.110117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024]  Open
5
Frickmann H, Schwinge K, Podbielski A, Warnke P. Preanalytical, Analytical and Postanalytical Analyses on Corynebacterium spp. and Actinomycetaceae in Urine Samples of Patients with Suspected Urinary Tract Infection-A Hypothesis-Forming Observational Study. Diagnostics (Basel) 2024;14:746. [PMID: 38611658 PMCID: PMC11011480 DOI: 10.3390/diagnostics14070746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]  Open
6
Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. FRONTIERS IN BIOINFORMATICS 2024;4:1278228. [PMID: 38560517 PMCID: PMC10978663 DOI: 10.3389/fbinf.2024.1278228] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]  Open
7
Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Brown LC, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol 2024;25:60. [PMID: 38409096 PMCID: PMC10898089 DOI: 10.1186/s13059-024-03198-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]  Open
8
Nguyen SV, Puthuveetil NP, Petrone JR, Kirkland JL, Gaffney K, Tabron CL, Wax N, Duncan J, King S, Marlow R, Reese AL, Yarmosh DA, McConnell HH, Fernandes AS, Bagnoli J, Benton B, Jacobs JL. The ATCC genome portal: 3,938 authenticated microbial reference genomes. Microbiol Resour Announc 2024;13:e0104523. [PMID: 38289057 PMCID: PMC10868203 DOI: 10.1128/mra.01045-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]  Open
9
Sayers E, Beck J, Bolton E, Brister J, Chan J, Comeau D, Connor R, DiCuccio M, Farrell C, Feldgarden M, Fine A, Funk K, Hatcher E, Hoeppner M, Kane M, Kannan S, Katz K, Kelly C, Klimke W, Kim S, Kimchi A, Landrum M, Lathrop S, Lu Z, Malheiro A, Marchler-Bauer A, Murphy T, Phan L, Prasad A, Pujar S, Sawyer A, Schmieder E, Schneider V, Schoch C, Sharma S, Thibaud-Nissen F, Trawick B, Venkatapathi T, Wang J, Pruitt K, Sherry S. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2024;52:D33-D43. [PMID: 37994677 PMCID: PMC10767890 DOI: 10.1093/nar/gkad1044] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023]  Open
10
Haft DH, Badretdin A, Coulouris G, DiCuccio M, Durkin A, Jovenitti E, Li W, Mersha M, O’Neill K, Virothaisakun J, Thibaud-Nissen F. RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes. Nucleic Acids Res 2024;52:D762-D769. [PMID: 37962425 PMCID: PMC10767926 DOI: 10.1093/nar/gkad988] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023]  Open
11
Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD. Rapid and sensitive detection of genome contamination at scale with FCS-GX. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543519. [PMID: 37292984 PMCID: PMC10246020 DOI: 10.1101/2023.06.02.543519] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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