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)

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; et al. (Gene Regulations and Metabolism, 2002)

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. - Ernesto Pérez-Rueda; Julio Collado-Vides; Lorenzo Segovia (Comput. Biol. Chem., 2004)

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)

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)

Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families. - Sarath Chandra Janga; Ernesto Pérez-Rueda (Comput. Biol. Chem., 2009)

New insights on gene regulation in archaea. - Silvia Tenorio-Salgado; Alejandro Huerta-Saquero; Ernesto Pérez-Rueda (Comput. Biol. Chem., 2011)

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)

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)

Distribution of putative xenogeneic silencers in prokaryote genomes. - Ernesto Pérez-Rueda; J. Antonio Ibarra (Comput. Biol. Chem., 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)

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; et al. (Nucleic Acids Res., 2016)

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)

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability. - André Borges Farias; Gustavo Sganzerla Martinez; Edgardo Galán-Vásquez; Marisa Fabiana Nicolás; Ernesto Pérez-Rueda (Briefings Bioinform., 2024)