Julio Collado-Vides

55 papers A 1C 2Journal 44Unranked 6
YearRankTypeTitle / Venue / Authors
2020 J jnl
Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties.
Database J. Biol. Databases Curation
Carlos-Francisco Méndez-Cruz, Antonio Blanchet, Alan Godínez, Ignacio Arroyo-Fernández, Socorro Gama-Castro, Sara Berenice Martínez-Luna, Cristian González-Colín, Julio Collado-Vides
2019 J jnl
In the pursuit of semantic similarity for literature on microbial transcriptional regulation.
J. Intell. Fuzzy Syst.
Oscar Lithgow-Serrano, Julio Collado-Vides
2019 J jnl
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.
Bioinform.
Víctor H. Tierrafría, Citlalli Mejía-Almonte, J. M. Camacho-Zaragoza, Heladia Salgado, K. Alquicira, Chu Ishida, Socorro Gama-Castro, Julio Collado-Vides
2019 J jnl
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.
Nucleic Acids Res.
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, Victor del Moral-Chávez, César Bonavides-Martínez, Carlos-Francisco Méndez-Cruz, James E. Galagan, Julio Collado-Vides
2019 J jnl
Similarity corpus on microbial transcriptional regulation.
J. Biomed. Semant.
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
2019 C conf
Towards the Prokaryotic Regulation Ontology: An Ontological Model to Infer Gene Regulation Physiology from Mechanisms in Bacteria.
KEOD
Citlalli Mejía-Almonte, Julio Collado-Vides
2018 — conf
A Falsification Approach to Create and Check Ontology Definitions.
ICBO
Citlalli Mejía, Julio Collado-Vides
2017 J jnl
Erratum: Strategies towards digital and semi-automated curation in RegulonDB.
Database J. Biol. Databases Curation
Fabio Rinaldi, 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
2017 J jnl
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes.
Database J. Biol. Databases Curation
Carlos-Francisco Méndez-Cruz, Socorro Gama-Castro, Citlalli Mejía-Almonte, Marco Polo Castillo-Villalba, Luis Muñiz-Rascado, Julio Collado-Vides
2017 J jnl
Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis.
Database J. Biol. Databases Curation
Yalbi Itzel Balderas-Martínez, Fabio Rinaldi, Gabriela Contreras, Hilda Solano-Lira, Mishael Sánchez-Pérez, Julio Collado-Vides, Moisés Selman, Annie Pardo
2017 J jnl
Strategies towards digital and semi-automated curation in RegulonDB.
Database J. Biol. Databases Curation
Fabio Rinaldi, 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
2017 J jnl
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Nucleic Acids Res.
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, Quang Ong, Suzanne M. Paley, Martín Peralta-Gil, Pallavi Subhraveti, David A. Velázquez-Ramírez, Daniel S. Weaver, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp
2016 J jnl
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.
Nucleic Acids Res.
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, Kristof Engelen
2016 J jnl
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.
Nucleic Acids Res.
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
2015 J jnl
An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database.
Polibits
Fabio Rinaldi, Oscar Lithgow-Serrano, Alejandra López-Fuentes, Socorro Gama-Castro, Yalbi I. Balderas-Martínez, Hilda Solano-Lira, Julio Collado-Vides
2014 J jnl
Assisted curation of regulatory interactions and growth conditions of OxyR in
Database J. Biol. Databases Curation
Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez, Simon Clematide, Tilia Renate Ellendorff, Alberto Santos-Zavaleta, Hernani Marques-Madeira, Julio Collado-Vides
2014 J jnl
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.
Nucleic Acids Res.
Pieter Meysman, Paolo Sonego, Luca Bianco, Qiang Fu, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Veerle Liebens, Jan Michiels, Kris Laukens, Kathleen Marchal, Julio Collado-Vides, Kristof Engelen
2013 J jnl
EcoCyc: fusing model organism databases with systems biology.
Nucleic Acids Res.
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, Quang Ong, Suzanne M. Paley, Imke Schröder, Alexander Glennon Shearer, Pallavi Subhraveti, Michael Travers, Deepika Weerasinghe, Verena Weiss, Julio Collado-Vides, Robert P. Gunsalus, Ian T. Paulsen, Peter D. Karp
2013 J jnl
Evidence classification of high-throughput protocols and confidence integration in RegulonDB.
Database J. Biol. Databases Curation
Verena Weiss, Alejandra Medina-Rivera, Araceli M. Huerta, Alberto Santos-Zavaleta, Heladia Salgado, Enrique Morett, Julio Collado-Vides
2013 J jnl
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.
Nucleic Acids Res.
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, Kevin Alquicira-Hernández, Alejandra López-Fuentes, Liliana Porrón-Sotelo, Araceli M. Huerta, César Bonavides-Martínez, Yalbi Itzel 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
2011 J jnl
EcoCyc: a comprehensive database of
Nucleic Acids Res.
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, John Pacheco, Mario Latendresse, Carol A. Fulcher, Malabika Sarker, Alexander Glennon Shearer, Amanda Mackie, Ian T. Paulsen, Robert P. Gunsalus, Peter D. Karp
2011 J jnl
RegulonDB version 7.0: transcriptional regulation of
Nucleic Acids Res.
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, 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
2009 J jnl
EcoCyc: A comprehensive view of
Nucleic Acids Res.
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, Alexander Glennon Shearer, Peter D. Karp
2008 J jnl
Prediction of TF target sites based on atomistic models of protein-DNA complexes.
BMC Bioinform.
Vladimir Espinosa Angarica, Abel González Pérez, Ana Tereza Ribeiro de Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira
2008 J jnl
RegulonDB (version 6.0): gene regulation model of
Nucleic Acids Res.
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, Carlos Rodríguez Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, Julio Collado-Vides
2007 J jnl
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing.
BMC Bioinform.
Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides
2007 J jnl
Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go.
PLoS Comput. Biol.
Rafael Palacios, Julio Collado-Vides
2007 J jnl
Metabolic Reconstruction and Modeling of Nitrogen Fixation in
PLoS Comput. Biol.
Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson
2007 C conf
NLP-Based Curation of Bacterial Regulatory Networks.
CICLing
Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides
2007 J jnl
TFmodeller: comparative modelling of protein-DNA complexes.
Bioinform.
Bruno Contreras-Moreira, Pierre-Alain Branger, Julio Collado-Vides
2007 J jnl
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes.
Nucleic Acids Res.
Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Julio Collado-Vides
2006 — conf
Comparative footprinting of DNA-binding proteins.
ISMB (Supplement of Bioinformatics)
Bruno Contreras-Moreira, Julio Collado-Vides
2006 J jnl
RegulonDB (version 5.0):
Nucleic Acids Res.
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
2006 J jnl
The comprehensive updated regulatory network of
BMC Bioinform.
Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I. Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D. Karp, Julio Collado-Vides
2005 J jnl
EcoCyc: a comprehensive database resource for
Nucleic Acids Res.
Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp
2005 J jnl
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes.
Nucleic Acids Res.
Abel D. González, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides
2004 — conf
04281 Abstracts Collection - Integrative Bioinformatics - Aspects of the Virtual Cell.
Integrative Bioinformatics - Aspects of the Virtual Cell
Julio Collado-Vides, Ralf Hofestädt, Christoph W. Sensen
2004 J jnl
Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach.
Silico Biol.
Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Julio Collado-Vides
2004 — ed.
Integrative Bioinformatics - Aspects of the Virtual Cell, 04.07. - 09.07.2004
Integrative Bioinformatics - Aspects of the Virtual Cell
Julio Collado-Vides, Ralf Hofestädt, Christoph W. Sensen
2004 J jnl
Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.
Comput. Biol. Chem.
Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia
2004 J jnl
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.
Nucleic Acids Res.
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
2002 A conf
A powerful non-homology method for the prediction of operons in prokaryotes.
ISMB
Gabriel Moreno-Hagelsieb, Julio Collado-Vides
2002 — ed.
Gene Regulations and Metabolism - Postgenomic Computational Approaches
Gene Regulations and Metabolism
Julio Collado-Vides, Ralf Hofestädt
2002 — conf
Genomics of Gene Regulation: The View from Escherichia coli.
Gene Regulations and Metabolism
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
2002 J jnl
Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context.
Silico Biol.
Gabriel Moreno-Hagelsieb, Julio Collado-Vides
2002 J jnl
The EcoCyc Database.
Nucleic Acids Res.
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
2001 J jnl
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.
Nucleic Acids Res.
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
2000 J jnl
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.
Nucleic Acids Res.
Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Frederick R. Blattner, Julio Collado-Vides
1999 J jnl
RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli.
Nucleic Acids Res.
Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides
1998 J jnl
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.
Bioinform.
Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides
1998 J jnl
RegulonDB: a database on transcriptional regulation in Escherichia coli.
Nucleic Acids Res.
Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides
1996 J jnl
Syntactic recognition of regulatory regions in Escherichia coli.
Comput. Appl. Biosci.
David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides
1996 — conf
Three Models of Gene Regulation in E. coli.
German Conference on Bioinformatics - Selected Papers
Julio Collado-Vides, Araceli M. Huerta, Kathleen Klose
1996 — conf
Three Models of Gene Regulation in E.coli.
German Conference on Bioinformatics
Araceli M. Huerta, Julio Collado-Vides, Peter D. Karp, Kathleen Klose
1991 J jnl
The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars.
Comput. Appl. Biosci.
Julio Collado-Vides