The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars. - Julio Collado-Vides (Comput. Appl. Biosci., 1991)

Three Models of Gene Regulation in E. coli. - Julio Collado-Vides; Araceli M. Huerta; Kathleen Klose (German Conference on Bioinformatics - Selected Papers, 1996)

Three Models of Gene Regulation in E.coli. - Araceli M. Huerta; Julio Collado-Vides; Peter D. Karp; Kathleen Klose (German Conference on Bioinformatics, 1996)

Syntactic recognition of regulatory regions in Escherichia coli. - David A. Rosenblueth; Denis Thieffry; Araceli M. Huerta; Heladia Salgado; Julio Collado-Vides (Comput. Appl. Biosci., 1996)

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. - Denis Thieffry; Heladia Salgado; Araceli M. Huerta; Julio Collado-Vides (Bioinform., 1998)

RegulonDB: a database on transcriptional regulation in Escherichia coli. - Araceli M. Huerta; Heladia Salgado; Denis Thieffry; Julio Collado-Vides (Nucleic Acids Res., 1998)

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. - Heladia Salgado; Alberto Santos-Zavaleta; Ulises Garza-Ramos; Jacques van Helden; Edgar Díaz-Peredo; Julio Collado-Vides (Nucleic Acids Res., 1999)

RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. - Heladia Salgado; Alberto Santos-Zavaleta; Socorro Gama-Castro; Dulce Millán-Zárate; Frederick R. Blattner; Julio Collado-Vides (Nucleic Acids Res., 2000)

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)

A powerful non-homology method for the prediction of operons in prokaryotes. - Gabriel Moreno-Hagelsieb; Julio Collado-Vides (ISMB, 2002)

Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context. - Gabriel Moreno-Hagelsieb; Julio Collado-Vides (Silico Biol., 2002)

The EcoCyc Database. - Peter D. Karp; Monica Riley; Milton H. Saier Jr.; Ian T. Paulsen; Julio Collado-Vides; Suzanne M. Paley; Alida Pellegrini-Toole; César Bonavides-Martínez; Socorro Gama-Castro (Nucleic Acids Res., 2002)

04281 Abstracts Collection - Integrative Bioinformatics - Aspects of the Virtual Cell. - Julio Collado-Vides; Ralf Hofestädt; Christoph W. Sensen (Integrative Bioinformatics - Aspects of the Virtual Cell, 2004)

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

Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach. - Marylens Hernández Guía; Abel González Pérez; Vladimir Espinosa Angarica; Ana Tereza Ribeiro de Vasconcelos; Julio Collado-Vides (Silico Biol., 2004)

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. - Heladia Salgado; Socorro Gama-Castro; Agustino Martínez-Antonio; Edgar Díaz-Peredo; Fabiola Sánchez-Solano; Martín Peralta-Gil; Delfino Garcia-Alonso; Verónica Jiménez-Jacinto; Alberto Santos-Zavaleta; César Bonavides-Martínez; Julio Collado-Vides (Nucleic Acids Res., 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)

EcoCyc: a comprehensive database resource for Escherichia coli. - Ingrid M. Keseler; Julio Collado-Vides; Socorro Gama-Castro; John Ingraham; Suzanne M. Paley; Ian T. Paulsen; Martín Peralta-Gil; Peter D. Karp (Nucleic Acids Res., 2005)

Comparative footprinting of DNA-binding proteins. - Bruno Contreras-Moreira; Julio Collado-Vides (ISMB (Supplement of Bioinformatics), 2006)

The comprehensive updated regulatory network of Escherichia coli K-12. - Heladia Salgado; Alberto Santos-Zavaleta; Socorro Gama-Castro; Martín Peralta-Gil; Mónica I. Peñaloza-Spínola; Agustino Martínez-Antonio; Peter D. Karp; Julio Collado-Vides (BMC Bioinform., 2006)

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. - Heladia Salgado; Socorro Gama-Castro; Martín Peralta-Gil; Edgar Díaz-Peredo; Fabiola Sánchez-Solano; Alberto Santos-Zavaleta; Irma Martínez-Flores; Verónica Jiménez-Jacinto; César Bonavides-Martínez; Juan Segura-Salazar; Agustino Martínez-Antonio; Julio Collado-Vides (Nucleic Acids Res., 2006)

NLP-Based Curation of Bacterial Regulatory Networks. - Carlos Rodríguez Penagos; Heladia Salgado; Irma Martínez-Flores; Julio Collado-Vides (CICLing, 2007)

TFmodeller: comparative modelling of protein-DNA complexes. - Bruno Contreras-Moreira; Pierre-Alain Branger; Julio Collado-Vides (Bioinform., 2007)

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. - Carlos Rodríguez Penagos; Heladia Salgado; Irma Martínez-Flores; Julio Collado-Vides (BMC Bioinform., 2007)

Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. - Abel González Pérez; Vladimir Espinosa Angarica; Ana Tereza Ribeiro de Vasconcelos; Julio Collado-Vides (Nucleic Acids Res., 2007)

Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go. - Rafael Palacios; Julio Collado-Vides (PLoS Comput. Biol., 2007)

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. - Osbaldo Resendis-Antonio; Jennifer L. Reed; Sergio Encarnación; Julio Collado-Vides; Bernhard Ø. Palsson (PLoS Comput. Biol., 2007)

Prediction of TF target sites based on atomistic models of protein-DNA complexes. - Vladimir Espinosa Angarica; Abel González Pérez; Ana Tereza Ribeiro de Vasconcelos; Julio Collado-Vides; Bruno Contreras-Moreira (BMC Bioinform., 2008)

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. - Socorro Gama-Castro; Verónica Jiménez-Jacinto; Martín Peralta-Gil; Alberto Santos-Zavaleta; Mónica I. Peñaloza-Spínola; Bruno Contreras-Moreira; Juan Segura-Salazar; Luis Muñiz-Rascado; Irma Martínez-Flores; Heladia Salgado; César Bonavides-Martínez; Cei Abreu-Goodger; et al. (Nucleic Acids Res., 2008)

EcoCyc: A comprehensive view of Escherichia coli biology. - Ingrid M. Keseler; César Bonavides-Martínez; Julio Collado-Vides; Socorro Gama-Castro; Robert P. Gunsalus; D. Aaron Johnson; Markus Krummenacker; Laura M. Nolan; Suzanne M. Paley; Ian T. Paulsen; Martín Peralta-Gil; Alberto D. Santos-Zavaleta; et al. (Nucleic Acids Res., 2009)

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). - Socorro Gama-Castro; Heladia Salgado; Martín Peralta-Gil; Alberto Santos-Zavaleta; Luis Muñiz-Rascado; Hilda Solano-Lira; Verónica Jiménez-Jacinto; Verena Weiss; Jair S. García-Sotelo; Alejandra López-Fuentes; Liliana Porrón-Sotelo; Shirley Alquicira-Hernández; et al. (Nucleic Acids Res., 2011)

EcoCyc: a comprehensive database of Escherichia coli biology. - Ingrid M. Keseler; Julio Collado-Vides; Alberto Santos-Zavaleta; Martín Peralta-Gil; Socorro Gama-Castro; Luis Muñiz-Rascado; César Bonavides-Martínez; Suzanne M. Paley; Markus Krummenacker; Tomer Altman; Pallavi Kaipa; Aaron Spaulding; et al. (Nucleic Acids Res., 2011)

Evidence classification of high-throughput protocols and confidence integration in RegulonDB. - Verena Weiss; Alejandra Medina-Rivera; Araceli M. Huerta; Alberto Santos-Zavaleta; Heladia Salgado; Enrique Morett; Julio Collado-Vides (Database J. Biol. Databases Curation, 2013)

EcoCyc: fusing model organism databases with systems biology. - Ingrid M. Keseler; Amanda Mackie; Martín Peralta-Gil; Alberto Santos-Zavaleta; Socorro Gama-Castro; César Bonavides-Martínez; Carol A. Fulcher; Araceli M. Huerta; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Luis Muñiz-Rascado; et al. (Nucleic Acids Res., 2013)

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. - Heladia Salgado; Martín 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; et al. (Nucleic Acids Res., 2013)

Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. - Socorro Gama-Castro; Fabio Rinaldi 001; Alejandra López-Fuentes; Yalbi Itzel Balderas-Martínez; Simon Clematide; Tilia Renate Ellendorff; Alberto Santos-Zavaleta; Hernani Marques-Madeira; Julio Collado-Vides (Database J. Biol. Databases Curation, 2014)

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. - Pieter Meysman; Paolo Sonego; Luca Bianco; Qiang Fu 009; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Veerle Liebens; Jan Michiels; Kris Laukens; Kathleen Marchal; Julio Collado-Vides; Kristof Engelen (Nucleic Acids Res., 2014)

An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database. - Fabio Rinaldi 001; Oscar Lithgow-Serrano; Alejandra López-Fuentes; Socorro Gama-Castro; Yalbi I. Balderas-Martínez; Hilda Solano-Lira; Julio Collado-Vides (Polibits, 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)

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. - Marco Moretto; Paolo Sonego; Nicolas Dierckxsens; Matteo Brilli; Luca Bianco; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Marco Galardini; Chiara Romualdi; Kris Laukens; Julio Collado-Vides; Pieter Meysman; et al. (Nucleic Acids Res., 2016)

Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. - Yalbi Itzel Balderas-Martínez; Fabio Rinaldi 001; Gabriela Contreras; Hilda Solano-Lira; Mishael Sánchez-Pérez; Julio Collado-Vides; Moisés Selman; Annie Pardo (Database J. Biol. Databases Curation, 2017)

First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes. - Carlos-Francisco Méndez-Cruz; Socorro Gama-Castro; Citlalli Mejía-Almonte; Marco-Polo Castillo-Villalba; Luis Muñiz-Rascado; Julio Collado-Vides (Database J. Biol. Databases Curation, 2017)

Strategies towards digital and semi-automated curation in RegulonDB. - Fabio Rinaldi 001; Oscar Lithgow-Serrano; Socorro Gama-Castro; Hilda Solano-Lira; Alejandra López-Fuentes; Luis Muñiz-Rascado; Cecilia Ishida-Gutiérrez; Carlos-Francisco Méndez-Cruz; Julio Collado-Vides (Database J. Biol. Databases Curation, 2017)

Erratum: Strategies towards digital and semi-automated curation in RegulonDB. - Fabio Rinaldi 001; Oscar Lithgow-Serrano; Socorro Gama-Castro; Hilda Solano-Lira; Alejandra López-Fuentes; Luis Muñiz-Rascado; Cecilia Ishida-Gutiérrez; Carlos-Francisco Méndez-Cruz; Julio Collado-Vides (Database J. Biol. Databases Curation, 2017)

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. - Ingrid M. Keseler; Amanda Mackie; Alberto Santos-Zavaleta; Richard Billington; César Bonavides-Martínez; Ron Caspi; Carol A. Fulcher; Socorro Gama-Castro; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Luis Muñiz-Rascado; et al. (Nucleic Acids Res., 2017)

A Falsification Approach to Create and Check Ontology Definitions. - Citlalli Mejía; Julio Collado-Vides (ICBO, 2018)

Towards the Prokaryotic Regulation Ontology: An Ontological Model to Infer Gene Regulation Physiology from Mechanisms in Bacteria. - Citlalli Mejía-Almonte; Julio Collado-Vides (KEOD, 2019)

MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. - Víctor H. Tierrafría; Citlalli Mejía-Almonte; J. M. Camacho-Zaragoza; Heladia Salgado; K. Alquicira; Chu Ishida; Socorro Gama-Castro; Julio Collado-Vides (Bioinform., 2019)

Similarity corpus on microbial transcriptional regulation. - Oscar Lithgow-Serrano; Socorro Gama-Castro; Cecilia Ishida-Gutiérrez; Citlalli Mejía-Almonte; Víctor H. Tierrafría; Sara Martínez-Luna; Alberto Santos-Zavaleta; David A. Velázquez-Ramírez; Julio Collado-Vides (J. Biomed. Semant., 2019)

In the pursuit of semantic similarity for literature on microbial transcriptional regulation. - Oscar Lithgow-Serrano; Julio Collado-Vides (J. Intell. Fuzzy Syst., 2019)

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. - Alberto Santos-Zavaleta; Heladia Salgado; Socorro Gama-Castro; Mishael Sánchez-Pérez; Laura Gómez-Romero; Daniela Ledezma-Tejeida; Jair Santiago García-Sotelo; Kevin Alquicira-Hernández; Luis Muñiz-Rascado; Pablo Peña-Loredo; Cecilia Ishida-Gutiérrez; David A. Velázquez-Ramírez; et al. (Nucleic Acids Res., 2019)

Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties. - Carlos-Francisco Méndez-Cruz; Antonio Blanchet; Alan Godínez; Ignacio Arroyo-Fernández; Socorro Gama-Castro; Sara Berenice Martínez-Luna; Cristian González-Colín; Julio Collado-Vides (Database J. Biol. Databases Curation, 2020)