Literature DB >> 11934610

Mining genome databases to identify and understand new gene regulatory systems.

Gary D Stormo1, Kai Tan.   

Abstract

The availability of a large number of sequenced microbial genomes allows us to conduct systematic studies on microbial gene regulatory systems. Computational methods, using comparative genomics approaches, are powerful tools to understand their mechanisms and evolutionary history. Recent advances in computational methodology for uncovering transcriptional regulatory components and their interactions are discussed.

Mesh：

Year:  2002        PMID： 11934610     DOI： 10.1016/s1369-5274(02)00309-0

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN： 1369-5274            Impact factor:   7.934


  14 in total

Review 1.  In silico identification of metazoan transcriptional regulatory regions.

Authors:  Wyeth W Wasserman; William Krivan
Journal:  Naturwissenschaften       Date:  2003-03-27

2.  Reconciling gene expression data with known genome-scale regulatory network structures.

Authors:  Markus J Herrgård; Markus W Covert; Bernhard Ø Palsson
Journal:  Genome Res       Date:  2003-10-14       Impact factor: 9.043

3.  Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor.

Authors:  Tsz-Kwong Man; Joshua SungWoo Yang; Gary D Stormo
Journal:  Nucleic Acids Res       Date:  2004-08-02       Impact factor: 16.971

Review 4.  Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Authors:  Dmitry A Rodionov
Journal:  Chem Rev       Date:  2007-07-18       Impact factor: 60.622

Review 5.  Tailor-made transcriptional biosensors for optimizing microbial cell factories.

Authors:  Brecht De Paepe; Gert Peters; Pieter Coussement; Jo Maertens; Marjan De Mey
Journal:  J Ind Microbiol Biotechnol       Date:  2016-11-11       Impact factor: 3.346

6.  Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships.

Authors:  Sébastien Rigali; Maximilian Schlicht; Paul Hoskisson; Harald Nothaft; Matthias Merzbacher; Bernard Joris; Fritz Titgemeyer
Journal:  Nucleic Acids Res       Date:  2004-06-24       Impact factor: 16.971

7.  Discovering novel cis-regulatory motifs using functional networks.

Authors:  Laurence M Ettwiller; Johan Rung; Ewan Birney
Journal:  Genome Res       Date:  2003-05       Impact factor: 9.043

8.  Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria.

Authors:  Jiajian Liu; Kai Tan; Gary D Stormo
Journal:  Nucleic Acids Res       Date:  2003-12-01       Impact factor: 16.971

9.  Better estimation of protein-DNA interaction parameters improve prediction of functional sites.

Authors:  Vijayalakshmi H Nagaraj; Ruadhan A O'Flanagan; Anirvan M Sengupta
Journal:  BMC Biotechnol       Date:  2008-12-23       Impact factor: 2.563

10.  The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum.

Authors:  Iris Brune; Hendrikje Werner; Andrea T Hüser; Jörn Kalinowski; Alfred Pühler; Andreas Tauch
Journal:  BMC Genomics       Date:  2006-02-09       Impact factor: 3.969
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