Ernesto Pérez-Rueda

According to our database, Ernesto Pérez-Rueda authored at least 13 papers between 2001 and 2022.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2022

Machine learning and statistics shape a novel path in archaeal promoter annotation.

Gustavo Sganzerla Martinez, Ernesto Pérez-Rueda, Sharmilee Sarkar, Aditya Kumar, Scheila de Avila e Silva

BMC Bioinform., 2022

2016

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

Socorro Gama-Castro, Heladia Salgado, Alberto Santos-Zavaleta, Daniela Ledezma-Tejeida, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Irma Martínez-Flores, Lucia Pannier, Jaime Abraham Castro-Mondragón, Alejandra Medina-Rivera, Hilda Solano-Lira, César Bonavides-Martínez, Ernesto Pérez-Rueda, Shirley Alquicira-Hernández, Liliana Porrón-Sotelo, Alejandra López-Fuentes, Anastasia Hernández-Koutoucheva, Victor del Moral-Chávez, Fabio Rinaldi, Julio Collado-Vides

Nucleic Acids Res., 2016

2015

The functional landscape bound to the transcription factors of Escherichia coli K-12.

Ernesto Pérez-Rueda, Silvia Tenorio-Salgado, Alejandro Huerta-Saquero, Yalbi I. Balderas-Martínez, Gabriel Moreno-Hagelsieb

Comput. Biol. Chem., 2015

Distribution of putative xenogeneic silencers in prokaryote genomes.

Ernesto Pérez-Rueda, J. Antonio Ibarra

Comput. Biol. Chem., 2015

Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families.

Dagoberto Armenta-Medina, Ernesto Pérez-Rueda

BMC Bioinform., 2015

2013

Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.

Julio A. Freyre-González, Alejandra M. Manjarrez-Casas, Enrique Merino, Mario Martinez-Nuñez, Ernesto Pérez-Rueda, Rosa-María Gutiérrez-Ríos

BMC Syst. Biol., 2013

2011

New insights on gene regulation in archaea.

Silvia Tenorio-Salgado, Alejandro Huerta-Saquero, Ernesto Pérez-Rueda

Comput. Biol. Chem., 2011

2009

Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.

Sarath Chandra Janga, Ernesto Pérez-Rueda

Comput. Biol. Chem., 2009

2007

Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins.

Armando Hernandez-Mendoza, Carmen Quinto, Lorenzo Segovia, Ernesto Pérez-Rueda

Comput. Biol. Chem., 2007

2005

TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes.

Abel D. González, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides

Nucleic Acids Res., 2005

2004

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.

Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia

Comput. Biol. Chem., 2004

2002

Genomics of Gene Regulation: The View from Escherichia coli.

Julio Collado-Vides, Gabriel Moreno-Hagelsieb, Ernesto Pérez-Rueda, Heladia Salgado, Araceli M. Huerta, Rosa María Gutiérrez, David A. Rosenblueth, Andrés Christen, Esperanza Benítez-Bellón, Arturo Medrano-Soto, Socorro Gama-Castro, Alberto Santos-Zavaleta, César Bonavides-Martínez, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Dulce María Millá

Proceedings of the Gene Regulations and Metabolism - Postgenomic Computational Approaches, 2002

2001

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

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Ernesto Pérez-Rueda, César Bonavides-Martínez, Julio Collado-Vides

Nucleic Acids Res., 2001