Julio Collado-Vides

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 I. 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: RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Research 41(Database-Issue): 203-213 (2013)

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: EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Research 41(Database-Issue): 605-612 (2013)

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: RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Research 39(Database-Issue): 98-105 (2011)

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: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Research 39(Database-Issue): 583-590 (2011)

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: EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Research 37(Database-Issue): 464-470 (2009)

Vladimir Espinosa Angarica, Abel González Pérez, Ana Tereza R. Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira: Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics 9 (2008)

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: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research 36(Database-Issue): 120-124 (2008)

Bruno Contreras-Moreira, Pierre-Alain Branger, Julio Collado-Vides: TFmodeller: comparative modelling of protein-DNA complexes. Bioinformatics 23(13): 1694-1696 (2007)

Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides: Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics 8 (2007)

Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides: Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. Nucleic Acids Research 35(Database-Issue): 132-136 (2007)

Rafael Palacios, Julio Collado-Vides: Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go. PLoS Computational Biology 3(9) (2007)

Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson: Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. PLoS Computational Biology 3(10) (2007)

Carlos Rodríguez Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides: NLP-Based Curation of Bacterial Regulatory Networks. CICLing 2007: 575-586

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I. Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D. Karp, Julio Collado-Vides: The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics 7: 5 (2006)

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: RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Research 34(Database-Issue): 394-397 (2006)

Bruno Contreras-Moreira, Julio Collado-Vides: Comparative footprinting of DNA-binding proteins. ISMB (Supplement of Bioinformatics) 2006: 74-80

Abel D. González, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides: TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Research 33(Database-Issue): 98-102 (2005)

Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research 33(Database-Issue): 334-337 (2005)

Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia: Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Computational Biology and Chemistry 28(5-6): 341-350 (2004)

Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides: Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach. In Silico Biology 5 (2004)

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: RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Research 32(Database-Issue): 303-306 (2004)

Gabriel Moreno-Hagelsieb, Julio Collado-Vides: Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context. In Silico Biology 2: 8 (2002)

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: The EcoCyc Database. Nucleic Acids Research 30(1): 56-58 (2002)

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: Genomics of Gene Regulation: The View from Escherichia coli. Gene Regulations and Metabolism 2002: 103-128

Gabriel Moreno-Hagelsieb, Julio Collado-Vides: A powerful non-homology method for the prediction of operons in prokaryotes. ISMB 2002: 329-336

Julio Collado-Vides, Ralf Hofestädt (Eds.): Gene Regulations and Metabolism - Postgenomic Computational Approaches. MIT Press 2002, isbn 0-262-03297-X

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: RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Research 29(1): 72-74 (2001)

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Frederick R. Blattner, Julio Collado-Vides: RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Research 28(1): 65-67 (2000)

Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides: RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Research 27(1): 59-60 (1999)

Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides: Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics 14(5): 391-400 (1998)

Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides: RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Research 26(1): 55-59 (1998)

David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides: Syntactic recognition of regulatory regions in Escherichia coli. Computer Applications in the Biosciences 12(5): 415-422 (1996)

Araceli M. Huerta, Julio Collado-Vides, Peter D. Karp, Kathleen Klose: Three Models of Gene Regulation in E.coli. German Conference on Bioinformatics 1996: 64-67

Julio Collado-Vides, Araceli M. Huerta, Kathleen Klose: Three Models of Gene Regulation in E. coli. German Conference on Bioinformatics - Selected Papers 1996: 72-78

Julio Collado-Vides: The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars. Computer Applications in the Biosciences 7(3): 321-326 (1991)