Literature DB >> 17996425

Structure and evolution of gene regulatory networks in microbial genomes.

Sarath Chandra Janga1, J Collado-Vides.   

Abstract

With the availability of genome sequences for hundreds of microbial genomes, it has become possible to address several questions from a comparative perspective to understand the structure and function of regulatory systems, at least in model organisms. Recent studies have focused on topological properties and the evolution of regulatory networks and their components. Our understanding of natural networks is paving the way to embedding synthetic regulatory systems into organisms, allowing us to expand the natural diversity of living systems to an extent we had never before anticipated.

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Year:  2007        PMID: 17996425      PMCID: PMC5696542          DOI: 10.1016/j.resmic.2007.09.001

Source DB:  PubMed          Journal:  Res Microbiol        ISSN: 0923-2508            Impact factor:   3.992


  68 in total

1.  Combining phylogenetic data with co-regulated genes to identify regulatory motifs.

Authors:  Ting Wang; Gary D Stormo
Journal:  Bioinformatics       Date:  2003-12-12       Impact factor: 6.937

Review 2.  Multiple sigma subunits and the partitioning of bacterial transcription space.

Authors:  Tanja M Gruber; Carol A Gross
Journal:  Annu Rev Microbiol       Date:  2003       Impact factor: 15.500

3.  A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.

Authors:  Martha L Bulyk; Abigail M McGuire; Nobuhisa Masuda; George M Church
Journal:  Genome Res       Date:  2004-02       Impact factor: 9.043

Review 4.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

5.  Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.

Authors:  Agustino Martínez-Antonio; Sarath Chandra Janga; Heladia Salgado; Julio Collado-Vides
Journal:  Trends Microbiol       Date:  2005-11-28       Impact factor: 17.079

6.  Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.

Authors:  L McCue; W Thompson; C Carmack; M P Ryan; J S Liu; V Derbyshire; C E Lawrence
Journal:  Nucleic Acids Res       Date:  2001-02-01       Impact factor: 16.971

7.  Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

Authors:  S D Bentley; K F Chater; A-M Cerdeño-Tárraga; G L Challis; N R Thomson; K D James; D E Harris; M A Quail; H Kieser; D Harper; A Bateman; S Brown; G Chandra; C W Chen; M Collins; A Cronin; A Fraser; A Goble; J Hidalgo; T Hornsby; S Howarth; C-H Huang; T Kieser; L Larke; L Murphy; K Oliver; S O'Neil; E Rabbinowitsch; M-A Rajandream; K Rutherford; S Rutter; K Seeger; D Saunders; S Sharp; R Squares; S Squares; K Taylor; T Warren; A Wietzorrek; J Woodward; B G Barrell; J Parkhill; D A Hopwood
Journal:  Nature       Date:  2002-05-09       Impact factor: 49.962

8.  Prediction of transcription terminators in bacterial genomes.

Authors:  M D Ermolaeva; H G Khalak; O White; H O Smith; S L Salzberg
Journal:  J Mol Biol       Date:  2000-08-04       Impact factor: 5.469

9.  The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.

Authors:  S Mangan; S Itzkovitz; A Zaslaver; U Alon
Journal:  J Mol Biol       Date:  2005-12-19       Impact factor: 5.469

10.  A novel method for prokaryotic promoter prediction based on DNA stability.

Authors:  Aditi Kanhere; Manju Bansal
Journal:  BMC Bioinformatics       Date:  2005-01-05       Impact factor: 3.169

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  23 in total

Review 1.  Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

Authors:  Sacha A F T van Hijum; Marnix H Medema; Oscar P Kuipers
Journal:  Microbiol Mol Biol Rev       Date:  2009-09       Impact factor: 11.056

2.  Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.

Authors:  Haythem Latif; Merve Sahin; Janna Tarasova; Yekaterina Tarasova; Vasiliy A Portnoy; Juan Nogales; Karsten Zengler
Journal:  Appl Environ Microbiol       Date:  2015-06-05       Impact factor: 4.792

3.  Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.

Authors:  Fuyi Li; Jinxiang Chen; Zongyuan Ge; Ya Wen; Yanwei Yue; Morihiro Hayashida; Abdelkader Baggag; Halima Bensmail; Jiangning Song
Journal:  Brief Bioinform       Date:  2021-03-22       Impact factor: 11.622

4.  RAIL: A new tool for defining bacterial promoter regions.

Authors:  Jyl S Matson
Journal:  J Bacteriol       Date:  2018-03-12       Impact factor: 3.490

5.  Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels.

Authors:  Mauricio Latorre; Jessica Galloway-Peña; Jung Hyeob Roh; Marko Budinich; Angélica Reyes-Jara; Barbara E Murray; Alejandro Maass; Mauricio González
Journal:  Metallomics       Date:  2014-01-02       Impact factor: 4.526

6.  Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.

Authors:  Ernesto Pérez-Rueda; Sarath Chandra Janga
Journal:  Mol Biol Evol       Date:  2010-02-01       Impact factor: 16.240

7.  Reconstructing genome trees of prokaryotes using overlapping genes.

Authors:  Chih-Hsien Cheng; Chung-Han Yang; Hsien-Tai Chiu; Chin Lung Lu
Journal:  BMC Bioinformatics       Date:  2010-02-24       Impact factor: 3.169

8.  Fractal topology of gene promoter networks at phase transitions.

Authors:  Preston R Aldrich; Robert K Horsley; Yousuf A Ahmed; Joseph J Williamson; Stefan M Turcic
Journal:  Gene Regul Syst Bio       Date:  2010-07-28

9.  Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.

Authors:  Sarath Chandra Janga; Bruno Contreras-Moreira
Journal:  Nucleic Acids Res       Date:  2010-07-14       Impact factor: 16.971

Review 10.  Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks.

Authors:  Yann S Dufour; Timothy J Donohue
Journal:  Adv Microb Physiol       Date:  2012       Impact factor: 3.517

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