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For: Mrázek J, Xie S, Guo X, Srivastava A. AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes. Bioinformatics 2008;24:1041-8. [PMID: 18304933 DOI: 10.1093/bioinformatics/btn077] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Genomic Insights into Achromobacter mucicolens IA Antibiotic Resistance. Microbiol Spectr 2022;10:e0191621. [PMID: 35377213 PMCID: PMC9045304 DOI: 10.1128/spectrum.01916-21] [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] [Indexed: 11/20/2022]  Open
2
Mrázek J, Karls AC. In silico simulations of occurrence of transcription factor binding sites in bacterial genomes. BMC Evol Biol 2019;19:67. [PMID: 30823869 PMCID: PMC6397444 DOI: 10.1186/s12862-019-1381-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/01/2019] [Indexed: 11/16/2022]  Open
3
Genotoxic, Metabolic, and Oxidative Stresses Regulate the RNA Repair Operon of Salmonella enterica Serovar Typhimurium. J Bacteriol 2018;200:JB.00476-18. [PMID: 30201777 DOI: 10.1128/jb.00476-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022]  Open
4
Novel DNA Binding and Regulatory Activities for σ54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s. J Bacteriol 2017;199:JB.00816-16. [PMID: 28373272 DOI: 10.1128/jb.00816-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/27/2017] [Indexed: 01/13/2023]  Open
5
Yang J, Chen X, McDermaid A, Ma Q. DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. Bioinformatics 2017;33:2586-2588. [DOI: 10.1093/bioinformatics/btx223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/12/2017] [Indexed: 11/14/2022]  Open
6
Tong H, Schliekelman P, Mrázek J. Unsupervised statistical discovery of spaced motifs in prokaryotic genomes. BMC Genomics 2017;18:27. [PMID: 28056763 PMCID: PMC5217627 DOI: 10.1186/s12864-016-3400-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/09/2016] [Indexed: 12/23/2022]  Open
7
Zere TR, Vakulskas CA, Leng Y, Pannuri A, Potts AH, Dias R, Tang D, Kolaczkowski B, Georgellis D, Ahmer BMM, Romeo T. Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. PLoS One 2015;10:e0145035. [PMID: 26673755 PMCID: PMC4682653 DOI: 10.1371/journal.pone.0145035] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/30/2015] [Indexed: 11/30/2022]  Open
8
Huang Y, Mrázek J. Assessing diversity of DNA structure-related sequence features in prokaryotic genomes. DNA Res 2014;21:285-97. [PMID: 24408877 PMCID: PMC4060949 DOI: 10.1093/dnares/dst057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
9
Touzain F, Petit MA, Schbath S, El Karoui M. DNA motifs that sculpt the bacterial chromosome. Nat Rev Microbiol 2011;9:15-26. [PMID: 21164534 DOI: 10.1038/nrmicro2477] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
10
Biggs PJ, Collins LJ. RNA networks in prokaryotes I: CRISPRs and riboswitches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011;722:209-20. [PMID: 21915791 DOI: 10.1007/978-1-4614-0332-6_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
11
Mrázek J. Finding sequence motifs in prokaryotic genomes--a brief practical guide for a microbiologist. Brief Bioinform 2009;10:525-36. [PMID: 19553402 DOI: 10.1093/bib/bbp032] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
The Sac10b homolog in Methanococcus maripaludis binds DNA at specific sites. J Bacteriol 2009;191:2315-29. [PMID: 19168623 DOI: 10.1128/jb.01534-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
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