Ernesto Pérez-Rueda

15 papers Journal 14Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0.
Database J. Biol. Databases Curation
Silvia Tenorio-Salgado, Cinthia Rodríguez Maya, Edgardo Galán-Vásquez, André Borges Farias, Dulce Álvarez-López, Jose Luis Villalpando-Aguilar, Alberto J. M. Martin, Leonardo Ledesma-Dominguez, Ernesto Pérez-Rueda
2024 J jnl
Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.
Briefings Bioinform.
André Borges Farias, Gustavo Sganzerla Martinez, Edgardo Galán-Vásquez, Marisa Fabiana Nicolás, Ernesto Pérez-Rueda
2022 J jnl
Machine learning and statistics shape a novel path in archaeal promoter annotation.
BMC Bioinform.
Gustavo Sganzerla Martinez, Ernesto Pérez-Rueda, Sharmilee Sarkar, Aditya Kumar, Scheila de Avila e Silva
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
Distribution of putative xenogeneic silencers in prokaryote genomes.
Comput. Biol. Chem.
Ernesto Pérez-Rueda, J. Antonio Ibarra
2015 J jnl
Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families.
BMC Bioinform.
Dagoberto Armenta-Medina, Ernesto Pérez-Rueda
2015 J jnl
The functional landscape bound to the transcription factors of Escherichia coli K-12.
Comput. Biol. Chem.
Ernesto Pérez-Rueda, Silvia Tenorio-Salgado, Alejandro Huerta-Saquero, Yalbi I. Balderas-Martínez, Gabriel Moreno-Hagelsieb
2013 J jnl
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.
BMC Syst. Biol.
Julio Augusto Freyre-González, Alejandra M. Manjarrez-Casas, Enrique Merino, Mario Martinez-Nuñez, Ernesto Pérez-Rueda, Rosa-María Gutiérrez-Ríos
2011 J jnl
New insights on gene regulation in archaea.
Comput. Biol. Chem.
Silvia Tenorio-Salgado, Alejandro Huerta-Saquero, Ernesto Pérez-Rueda
2009 J jnl
Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families.
Comput. Biol. Chem.
Sarath Chandra Janga, Ernesto Pérez-Rueda
2007 J jnl
Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins.
Comput. Biol. Chem.
Armando Hernandez-Mendoza, Carmen Quinto, Lorenzo Segovia, Ernesto Pérez-Rueda
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 J jnl
Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea.
Comput. Biol. Chem.
Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia
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
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