Heladia Salgado

发表

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

Fabio Rinaldi, Julio Collado-Vides, César Bonavides-Martínez, 2015, Nucleic Acids Res..

Extracting regulatory networks of Escherichia coli from RegulonDB.

Julio Collado-Vides, Heladia Salgado, Luis Muñiz-Rascado, 2012, Methods in molecular biology.

Transcription Factors in Escherichia coli Prefer the Holo Conformation

J. Collado-Vides, M. Savageau, E. Pérez-Rueda, 2013, PloS one.

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

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2010, Nucleic Acids Res..

The transcriptional regulator SsrB is involved in a molecular switch controlling virulence lifestyles of Salmonella

Irma Martínez-Flores, H. Salgado, B. Coombes, 2017, PLoS pathogens.

Theoretical and empirical quality assessment of transcription factor-binding motifs

J. Collado-Vides, J. van Helden, C. Abreu-Goodger, 2010, Nucleic acids research.

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Víctor H. Tierrafría, David A. Velázquez-Ramírez, J. Collado-Vides, 2018, BMC Biology.

Towards a unified resource for transcriptional regulation in Escherichia coli K-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB

Víctor H. Tierrafría, David A. Velázquez-Ramírez, J. Collado-Vides, 2017, bioRxiv.

The LysR-Type Transcriptional Regulator LeuO Controls Expression of Several Genes in Salmonella enterica Serovar Typhi

S. Encarnación, I. Hernández-Lucas, E. Calva, 2007, Journal of bacteriology.

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

J. Collado-Vides, Irma Martínez-Flores, H. Salgado, 2016, Scientific Reports.

The LysR-Type Transcriptional Regulator LeuO Controls Expression of Several Genes in Salmonella enterica Serovar Typhi

S. Encarnación, H. Salgado, I. Hernández-Lucas, 2007, Journal of bacteriology.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

Víctor H. Tierrafría, J. Collado-Vides, J. Galagan, 2022, Microbial genomics.

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

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2012, Nucleic Acids Res..

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Araceli M. Huerta, J. Collado-Vides, V. Jiménez-Jacinto, 2009, PloS one.

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2005, Nucleic Acids Res..

RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2001, Nucleic Acids Res..

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli

Julio Collado-Vides, Jacques van Helden, Heladia Salgado, 1999, Nucleic Acids Res..

RegulonDB: a database on transcriptional regulation in Escherichia coli

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998, Nucleic Acids Res..

Operons in Escherichia coli: genomic analyses and predictions.

Temple F. Smith, T. Smith, J. Collado-Vides, 2000, Proceedings of the National Academy of Sciences of the United States of America.

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2018, Nucleic Acids Res..

On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.

J. Collado-Vides, J. Baumbach, A. Pühler, 2012, Integrative biology : quantitative biosciences from nano to macro.

Transcriptional regulation shapes the organization of genes on bacterial chromosomes

Sarath Chandra Janga, Heladia Salgado, Agustino Martínez-Antonio, 2009, Nucleic acids research.

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2007, Nucleic Acids Res..

Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach

Julio Collado-Vides, Socorro Gama-Castro, Verónica Jiménez-Jacinto, 2003, Biotechnology and bioengineering.

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Julio Collado-Vides, Socorro Gama-Castro, Bernhard O Palsson, 2018, BMC Biology.

Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2024, Frontiers in genetics.

A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2023, bioRxiv.

A Golden Standard for Transcription Factor-Gene Regulatory Interactions in Escherichia coli K-12: How reliable are they based on the methods supporting them?

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2023 .

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

J. Collado-Vides, J. Gelpí, S. Gama-Castro, 2023, Nucleic acids research.

The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments

Julio Collado-Vides, Heladia Salgado, Gabriel Moreno-Hagelsieb, 2003, Genome Biology.

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998, Bioinform..

Syntactic recognition of regulatory regions in Escherichia coli

Denis Thieffry, Julio Collado-Vides, David A. Rosenblueth, 1996, Comput. Appl. Biosci..

Using RegulonDB, the Escherichia coli K‐12 Gene Regulatory Transcriptional Network Database

Irma Martínez-Flores, Julio Collado-Vides, Heladia Salgado, 2018, Current protocols in bioinformatics.

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

J. Collado-Vides, S. Janga, A. Martínez-Antonio, 2006, Trends in microbiology.

Bioinformatics Resources for the Study of Gene Regulation in Bacteria

J. Collado-Vides, Irma Martínez-Flores, V. Jiménez-Jacinto, 2008, Journal of bacteriology.

Evidence classification of high-throughput protocols and confidence integration in RegulonDB

Julio Collado-Vides, Heladia Salgado, Alberto Santos-Zavaleta, 2013, Database J. Biol. Databases Curation.