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For: Balaji S, Babu MM, Aravind L. Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli. J Mol Biol 2007;372:1108-1122. [PMID: 17706247 PMCID: PMC2422858 DOI: 10.1016/j.jmb.2007.06.084] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 06/18/2007] [Accepted: 06/26/2007] [Indexed: 01/14/2023]
Number Cited by Other Article(s)
1
Zhou B, Lin X, Li Z, Yao Y, Yang J, Zhu Y. Structure‒function‒pathogenicity analysis of C-terminal myocilin missense variants based on experiments and 3D models. Front Genet 2022;13:1019208. [PMID: 36267417 PMCID: PMC9577182 DOI: 10.3389/fgene.2022.1019208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]  Open
2
The economy of chromosomal distances in bacterial gene regulation. NPJ Syst Biol Appl 2021;7:49. [PMID: 34911953 PMCID: PMC8674286 DOI: 10.1038/s41540-021-00209-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/12/2021] [Indexed: 12/04/2022]  Open
3
Ishihama A, Shimada T. Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators. FEMS Microbiol Rev 2021;45:6312496. [PMID: 34196371 DOI: 10.1093/femsre/fuab032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]  Open
4
Nagy-Staron A, Tomasek K, Caruso Carter C, Sonnleitner E, Kavčič B, Paixão T, Guet CC. Local genetic context shapes the function of a gene regulatory network. eLife 2021;10:e65993. [PMID: 33683203 PMCID: PMC7968929 DOI: 10.7554/elife.65993] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022]  Open
5
Chaiboonchoe A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, Salehi-Ashtiani K. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation. MOLECULAR BIOSYSTEMS 2017;12:2394-407. [PMID: 27357594 DOI: 10.1039/c6mb00237d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
6
Beber ME, Muskhelishvili G, Hütt MT. Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB. Database (Oxford) 2016;2016:baw003. [PMID: 26980514 PMCID: PMC4792529 DOI: 10.1093/database/baw003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 12/12/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022]
7
Van Landeghem S, Van Parys T, Dubois M, Inzé D, Van de Peer Y. Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC Bioinformatics 2016;17:18. [PMID: 26729218 PMCID: PMC4700732 DOI: 10.1186/s12859-015-0863-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/17/2015] [Indexed: 11/30/2022]  Open
8
Santolaya-Forgas J, Townsend R, Santolaya JL, Patel P, Herrera-Garcia G, Castracane VD. The Microbiota and Transgenomic Networks: Potential Implications for Maternal-Fetal Medicine. Fetal Diagn Ther 2016;39:1-3. [DOI: 10.1159/000441452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/23/2015] [Indexed: 01/12/2023]
9
Carson MB, Gu J, Yu G, Lu H. Identification of cancer‐related genes and motifs in the human gene regulatory network. IET Syst Biol 2015;9:128-34. [DOI: 10.1049/iet-syb.2014.0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
10
Imam S, Noguera DR, Donohue TJ. Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet 2014;10:e1004837. [PMID: 25503406 PMCID: PMC4263372 DOI: 10.1371/journal.pgen.1004837] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 10/20/2014] [Indexed: 12/18/2022]  Open
11
Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, Stingl U, Archer JAC, Jankovic BR, Sogin M, Bajic VB, El-Dorry H. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. PLoS One 2014;9:e97338. [PMID: 24921648 PMCID: PMC4055538 DOI: 10.1371/journal.pone.0097338] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/17/2014] [Indexed: 11/19/2022]  Open
12
Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology. Proc Natl Acad Sci U S A 2013;110:7754-9. [PMID: 23610404 DOI: 10.1073/pnas.1217630110] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
13
Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS. Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Brief Bioinform 2013;15:592-611. [DOI: 10.1093/bib/bbs071] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
14
Architecture of the human regulatory network derived from ENCODE data. Nature 2012;489:91-100. [PMID: 22955619 DOI: 10.1038/nature11245] [Citation(s) in RCA: 1111] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 05/22/2012] [Indexed: 12/21/2022]
15
Kosti I, Radivojac P, Mandel-Gutfreund Y. An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PLoS Comput Biol 2012;8:e1002603. [PMID: 22844237 PMCID: PMC3405991 DOI: 10.1371/journal.pcbi.1002603] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 05/24/2012] [Indexed: 11/19/2022]  Open
16
van Dijk ADJ, van Mourik S, van Ham RCHJ. Mutational robustness of gene regulatory networks. PLoS One 2012;7:e30591. [PMID: 22295094 PMCID: PMC3266278 DOI: 10.1371/journal.pone.0030591] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 12/19/2011] [Indexed: 11/18/2022]  Open
17
Iyer LM, Aravind L. Insights from the architecture of the bacterial transcription apparatus. J Struct Biol 2011;179:299-319. [PMID: 22210308 DOI: 10.1016/j.jsb.2011.12.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/14/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
18
Domenzain C, Camarena L, Osorio A, Dreyfus G, Poggio S. Evolutionary origin of the Rhodobacter sphaeroides specialized RpoN sigma factors. FEMS Microbiol Lett 2011;327:93-102. [PMID: 22093079 DOI: 10.1111/j.1574-6968.2011.02459.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 11/29/2022]  Open
19
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. BMC Genomics 2011;12 Suppl 1:S4. [PMID: 21810206 PMCID: PMC3223727 DOI: 10.1186/1471-2164-12-s1-s4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
20
Babu MM. Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks. Biochem Soc Trans 2010;38:1155-78. [PMID: 20863280 DOI: 10.1042/bst0381155] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
21
Theodorou EC, Theodorou MC, Samali MN, Kyriakidis DA. Activation of the AtoSC two-component system in the absence of the AtoC N-terminal receiver domain in E. coli. Amino Acids 2010;40:421-30. [DOI: 10.1007/s00726-010-0652-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]
22
Built shallow to maintain homeostasis and persistent infection: insight into the transcriptional regulatory network of the gastric human pathogen Helicobacter pylori. PLoS Pathog 2010;6:e1000938. [PMID: 20548942 PMCID: PMC2883586 DOI: 10.1371/journal.ppat.1000938] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
23
Fu C, Li J, Wang E. Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression. MOLECULAR BIOSYSTEMS 2010;5:1809-16. [PMID: 19593471 DOI: 10.1039/b905382d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
24
Martínez-Núñez MA, Pérez-Rueda E, Gutiérrez-Ríos RM, Merino E. New insights into the regulatory networks of paralogous genes in bacteria. MICROBIOLOGY-SGM 2009;156:14-22. [PMID: 19850620 DOI: 10.1099/mic.0.033266-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
25
Ciandrini L, Maffi C, Motta A, Bassetti B, Cosentino Lagomarsino M. Feedback topology and XOR-dynamics in Boolean networks with varying input structure. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;80:026122. [PMID: 19792215 DOI: 10.1103/physreve.80.026122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 05/28/2009] [Indexed: 05/28/2023]
26
Fadda A, Fierro AC, Lemmens K, Monsieurs P, Engelen K, Marchal K. Inferring the transcriptional network of Bacillus subtilis. MOLECULAR BIOSYSTEMS 2009;5:1840-52. [PMID: 20023724 DOI: 10.1039/b907310h] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
27
Janky R, Helden JV, Babu MM. Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements. Methods 2009;48:277-86. [PMID: 19450688 DOI: 10.1016/j.ymeth.2009.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 04/17/2009] [Accepted: 04/18/2009] [Indexed: 10/20/2022]  Open
28
Bacha J, Brodie JS, Loose MW. myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. BMC DEVELOPMENTAL BIOLOGY 2009;9:33. [PMID: 19500400 PMCID: PMC2702357 DOI: 10.1186/1471-213x-9-33] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 06/06/2009] [Indexed: 11/23/2022]
29
Baumbach J, Wittkop T, Kleindt CK, Tauch A. Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nat Protoc 2009;4:992-1005. [DOI: 10.1038/nprot.2009.81] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
30
Lemmens K, De Bie T, Dhollander T, De Keersmaecker SC, Thijs IM, Schoofs G, De Weerdt A, De Moor B, Vanderleyden J, Collado-Vides J, Engelen K, Marchal K. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol 2009;10:R27. [PMID: 19265557 PMCID: PMC2690998 DOI: 10.1186/gb-2009-10-3-r27] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 01/15/2009] [Accepted: 03/06/2009] [Indexed: 11/13/2022]  Open
31
Balleza E, López-Bojorquez LN, Martínez-Antonio A, Resendis-Antonio O, Lozada-Chávez I, Balderas-Martínez YI, Encarnación S, Collado-Vides J. Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol Rev 2009;33:133-51. [PMID: 19076632 PMCID: PMC2704942 DOI: 10.1111/j.1574-6976.2008.00145.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
32
Lagomarsino MC, Bassetti B, Castellani G, Remondini D. Functional models for large-scale gene regulation networks: realism and fiction. MOLECULAR BIOSYSTEMS 2009;5:335-44. [PMID: 19396369 DOI: 10.1039/b816841p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
33
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC SYSTEMS BIOLOGY 2009;3:8. [PMID: 19146695 PMCID: PMC2653031 DOI: 10.1186/1752-0509-3-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 01/15/2009] [Indexed: 11/10/2022]
34
Sellerio A, Bassetti B, Isambert H, Cosentino Lagomarsino M. A comparative evolutionary study of transcription networks. The global role of feedback and hierachical structures. ACTA ACUST UNITED AC 2009;5:170-9. [DOI: 10.1039/b815339f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
35
Baumbach J, Tauch A, Rahmann S. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Brief Bioinform 2008;10:75-83. [PMID: 19074493 DOI: 10.1093/bib/bbn055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
36
Janga SC, Babu MM. Network-based approaches for linking metabolism with environment. Genome Biol 2008;9:239. [PMID: 19040774 PMCID: PMC2614483 DOI: 10.1186/gb-2008-9-11-239] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
37
Tanous C, Soutourina O, Raynal B, Hullo MF, Mervelet P, Gilles AM, Noirot P, Danchin A, England P, Martin-Verstraete I. The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis. J Biol Chem 2008;283:35551-60. [PMID: 18974048 DOI: 10.1074/jbc.m805951200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
38
Janga SC, Salgado H, Martínez-Antonio A, Collado-Vides J. Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli. Nucleic Acids Res 2007;35:6963-72. [PMID: 17933780 PMCID: PMC2175315 DOI: 10.1093/nar/gkm743] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
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