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2010 – 2019
- 2019
[j11]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:
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic Acids Res. 47(Database-Issue): D212-D220 (2019)- 2017
- [j10]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:
Strategies towards digital and semi-automated curation in RegulonDB. Database J. Biol. Databases Curation 2017: bax012 (2017) - [j9]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:
Erratum: Strategies towards digital and semi-automated curation in RegulonDB. Database J. Biol. Databases Curation 2017: bax012 (2017) - [j8]Carlos-Francisco Méndez-Cruz, Socorro Gama-Castro, Citlalli Mejía-Almonte, Marco-Polo Castillo-Villalba, Luis Muñiz-Rascado, Julio Collado-Vides:
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 2017: bax070 (2017) - [j7]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:
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res. 45(Database-Issue): D543-D550 (2017) - 2016
- [j6]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:
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 44(Database-Issue): 133-143 (2016) - 2013
- [j5]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:
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 41(Database-Issue): 203-213 (2013) - [j4]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 Res. 41(Database-Issue): 605-612 (2013) - 2011
- [j3]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 Res. 39(Database-Issue): 98-105 (2011) - [j2]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 Res. 39(Database-Issue): 583-590 (2011)
2000 – 2009
- 2008
- [j1]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 Res. 36(Database-Issue): 120-124 (2008)
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