Literature DB >> 18978060

Bioinformatics resources for the study of gene regulation in bacteria.

Julio Collado-Vides1, Heladia Salgado, Enrique Morett, Socorro Gama-Castro, Verónica Jiménez-Jacinto, Irma Martínez-Flores, Alejandra Medina-Rivera, Luis Muñiz-Rascado, Martín Peralta-Gil, Alberto Santos-Zavaleta.   

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Year:  2008        PMID： 18978060      PMCID： PMC2612416          DOI： 10.1128/JB.01017-08

Source DB:  PubMed          Journal:  J Bacteriol        ISSN： 0021-9193            Impact factor:   3.490


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  112 in total

1.  Improved prediction of bacterial transcription start sites.

Authors:  J J Gordon; M W Towsey; J M Hogan; S A Mathews; P Timms
Journal:  Bioinformatics       Date:  2005-11-15       Impact factor: 6.937

2.  Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.

Authors:  Richard Münch; Karsten Hiller; Andreas Grote; Maurice Scheer; Johannes Klein; Max Schobert; Dieter Jahn
Journal:  Bioinformatics       Date:  2005-08-18       Impact factor: 6.937

3.  Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.

Authors:  Lena Strömbäck; Patrick Lambrix
Journal:  Bioinformatics       Date:  2005-10-18       Impact factor: 6.937

4.  Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor.

Authors:  Ferenc Marincs; Iain W Manfield; Jonathan A Stead; Kenneth J McDowall; Peter G Stockley
Journal:  Biochem J       Date:  2006-06-01       Impact factor: 3.857

5.  Evolutionary dynamics of prokaryotic transcriptional regulatory networks.

Authors:  M Madan Babu; Sarah A Teichmann; L Aravind
Journal:  J Mol Biol       Date:  2006-02-28       Impact factor: 5.469

6.  Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis.

Authors:  François Enault; Karsten Suhre; Jean-Michel Claverie
Journal:  BMC Bioinformatics       Date:  2005-10-12       Impact factor: 3.169

7.  An approach for clustering gene expression data with error information.

Authors:  Brian Tjaden
Journal:  BMC Bioinformatics       Date:  2006-01-12       Impact factor: 3.169

8.  Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons.

Authors:  Bettina Harr; Christian Schlötterer
Journal:  Nucleic Acids Res       Date:  2006-01-23       Impact factor: 16.971

9.  A classification based framework for quantitative description of large-scale microarray data.

Authors:  Dipen P Sangurdekar; Friedrich Srienc; Arkady B Khodursky
Journal:  Genome Biol       Date:  2006-04-20       Impact factor: 13.583

10.  Low degree metabolites explain essential reactions and enhance modularity in biological networks.

Authors:  Areejit Samal; Shalini Singh; Varun Giri; Sandeep Krishna; Nandula Raghuram; Sanjay Jain
Journal:  BMC Bioinformatics       Date:  2006-03-08       Impact factor: 3.169
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  10 in total

1.  It is computation time for bacteriology!

Authors:  Igor B Zhulin
Journal:  J Bacteriol       Date:  2008-10-31       Impact factor: 3.490

2.  Insights from the architecture of the bacterial transcription apparatus.

Authors:  Lakshminarayan M Iyer; L Aravind
Journal:  J Struct Biol       Date:  2011-12-24       Impact factor: 2.867

Review 3.  Antibiotic Resistance and Epigenetics: More to It than Meets the Eye.

Authors:  Dipannita Ghosh; Balaji Veeraraghavan; Ravikrishnan Elangovan; Perumal Vivekanandan
Journal:  Antimicrob Agents Chemother       Date:  2020-01-27       Impact factor: 5.191

4.  The Antiactivator of Type III Secretion, OspD1, Is Transcriptionally Regulated by VirB and H-NS from Remote Sequences in Shigella flexneri.

Authors:  Joy A McKenna; Helen J Wing
Journal:  J Bacteriol       Date:  2020-04-27       Impact factor: 3.490

5.  Lack of conservation of bacterial type promoters in plastids of Streptophyta.

Authors:  Vassily A Lyubetsky; Lev I Rubanov; Alexandr V Seliverstov
Journal:  Biol Direct       Date:  2010-05-10       Impact factor: 4.540

6.  Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.

Authors:  Heladia Salgado; Irma Martínez-Flores; Víctor H Bustamante; Kevin Alquicira-Hernández; Jair S García-Sotelo; Delfino García-Alonso; Julio Collado-Vides
Journal:  Curr Protoc Bioinformatics       Date:  2018-03

7.  In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes.

Authors:  Luary C Martínez; Irma Martínez-Flores; Heladia Salgado; Marcos Fernández-Mora; Alejandra Medina-Rivera; José L Puente; Julio Collado-Vides; Víctor H Bustamante
Journal:  J Bacteriol       Date:  2013-11-01       Impact factor: 3.490

8.  RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

Authors:  Socorro Gama-Castro; Heladia Salgado; Martin Peralta-Gil; Alberto Santos-Zavaleta; Luis Muñiz-Rascado; Hilda Solano-Lira; Verónica Jimenez-Jacinto; Verena Weiss; Jair S García-Sotelo; Alejandra López-Fuentes; Liliana Porrón-Sotelo; Shirley Alquicira-Hernández; Alejandra Medina-Rivera; Irma Martínez-Flores; Kevin Alquicira-Hernández; Ruth Martínez-Adame; César Bonavides-Martínez; Juan Miranda-Ríos; Araceli M Huerta; Alfredo Mendoza-Vargas; Leonardo Collado-Torres; Blanca Taboada; Leticia Vega-Alvarado; Maricela Olvera; Leticia Olvera; Ricardo Grande; Enrique Morett; Julio Collado-Vides
Journal:  Nucleic Acids Res       Date:  2010-11-04       Impact factor: 16.971

9.  RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

Authors:  Heladia Salgado; Martin Peralta-Gil; Socorro Gama-Castro; Alberto Santos-Zavaleta; Luis Muñiz-Rascado; Jair S García-Sotelo; Verena Weiss; Hilda Solano-Lira; Irma Martínez-Flores; Alejandra Medina-Rivera; Gerardo Salgado-Osorio; Shirley Alquicira-Hernández; Kevin Alquicira-Hernández; Alejandra López-Fuentes; Liliana Porrón-Sotelo; Araceli M Huerta; César Bonavides-Martínez; Yalbi I Balderas-Martínez; Lucia Pannier; Maricela Olvera; Aurora Labastida; Verónica Jiménez-Jacinto; Leticia Vega-Alvarado; Victor Del Moral-Chávez; Alfredo Hernández-Alvarez; Enrique Morett; Julio Collado-Vides
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971

10.  Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.

Authors:  Patricia Oliver; Martín Peralta-Gil; María-Luisa Tabche; Enrique Merino
Journal:  BMC Genomics       Date:  2016-08-27       Impact factor: 3.969
  10 in total

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