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For: Studholme DJ, Bentley SD, Kormanec J. Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor. BMC Microbiol 2004;4:14. [PMID: 15072583 PMCID: PMC450296 DOI: 10.1186/1471-2180-4-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Accepted: 04/08/2004] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Anderssen S, Naômé A, Jadot C, Brans A, Tocquin P, Rigali S. AURTHO: Autoregulation of transcription factors as facilitator of cis-acting element discovery. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022;1865:194847. [PMID: 35901946 DOI: 10.1016/j.bbagrm.2022.194847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
2
Dai Z, Iqbal M, Lawrence ND, Rattray M. Efficient inference for sparse latent variable models of transcriptional regulation. Bioinformatics 2018;33:3776-3783. [PMID: 28961802 PMCID: PMC5860323 DOI: 10.1093/bioinformatics/btx508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/25/2017] [Indexed: 12/23/2022]  Open
3
Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015;1849:1017-39. [PMID: 26093238 DOI: 10.1016/j.bbagrm.2015.06.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
4
Iqbal M, Mast Y, Amin R, Hodgson DA, Wohlleben W, Burroughs NJ. Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. Nucleic Acids Res 2012;40:5227-39. [PMID: 22406834 PMCID: PMC3384326 DOI: 10.1093/nar/gks205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
5
Eng C, Asthana C, Aigle B, Hergalant S, Mari JF, Leblond P. A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods. J Comput Biol 2009;16:1211-25. [DOI: 10.1089/cmb.2008.0122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]  Open
6
Liu J, Xu X, Stormo GD. The cis-regulatory map of Shewanella genomes. Nucleic Acids Res 2008;36:5376-90. [PMID: 18701645 PMCID: PMC2532739 DOI: 10.1093/nar/gkn515] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
7
Laing E, Sidhu K, Hubbard SJ. Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics 2008;9:79. [PMID: 18269733 PMCID: PMC2276206 DOI: 10.1186/1471-2164-9-79] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/12/2008] [Indexed: 11/18/2022]  Open
8
Hesketh A, Bucca G, Laing E, Flett F, Hotchkiss G, Smith CP, Chater KF. New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures. BMC Genomics 2007;8:261. [PMID: 17678549 PMCID: PMC2000904 DOI: 10.1186/1471-2164-8-261] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 08/02/2007] [Indexed: 11/10/2022]  Open
9
Rodionov DA. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 2007;107:3467-97. [PMID: 17636889 PMCID: PMC2643304 DOI: 10.1021/cr068309+] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
10
Rokem JS, Lantz AE, Nielsen J. Systems biology of antibiotic production by microorganisms. Nat Prod Rep 2007;24:1262-87. [DOI: 10.1039/b617765b] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
11
Colson S, Stephan J, Hertrich T, Saito A, van Wezel GP, Titgemeyer F, Rigali S. Conserved cis-Acting Elements Upstream of Genes Composing the Chitinolytic System of Streptomycetes Are DasR-Responsive Elements. J Mol Microbiol Biotechnol 2006;12:60-6. [PMID: 17183212 DOI: 10.1159/000096460] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
12
Laing E, Mersinias V, Smith CP, Hubbard SJ. Analysis of gene expression in operons of Streptomyces coelicolor. Genome Biol 2006;7:R46. [PMID: 16749941 PMCID: PMC1779546 DOI: 10.1186/gb-2006-7-6-r46] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 03/03/2006] [Accepted: 05/09/2006] [Indexed: 11/12/2022]  Open
13
Jacques PÉ, Rodrigue S, Gaudreau L, Goulet J, Brzezinski R. Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. BMC Bioinformatics 2006;7:423. [PMID: 17014715 PMCID: PMC1615881 DOI: 10.1186/1471-2105-7-423] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 10/02/2006] [Indexed: 12/03/2022]  Open
14
Bose M, Slick D, Sarto MJ, Roberts D, Roberts J, Barber RD. Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED). ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2006;2:39-49. [PMID: 16877320 PMCID: PMC2685587 DOI: 10.1155/2006/837139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
15
Rigali S, Schlicht M, Hoskisson P, Nothaft H, Merzbacher M, Joris B, Titgemeyer F. Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships. Nucleic Acids Res 2004;32:3418-26. [PMID: 15247334 PMCID: PMC443547 DOI: 10.1093/nar/gkh673] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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