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Julio Collado-Vides
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2020 – today
- 2020
- [j44]Carlos-Francisco Méndez-Cruz
, Antonio Blanchet, Alan Godínez
Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties. Database J. Biol. Databases Curation 2020 (2020)
2010 – 2019
- 2019
- [j43]Víctor H. Tierrafría
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. Bioinform. 35(5): 856-864 (2019) - [j42]Oscar Lithgow-Serrano
Similarity corpus on microbial transcriptional regulation. J. Biomed. Semant. 10(1): 8:1-8:14 (2019) - [j41]Oscar Lithgow-Serrano
In the pursuit of semantic similarity for literature on microbial transcriptional regulation. J. Intell. Fuzzy Syst. 36(5): 4777-4786 (2019) - [j40]Alberto Santos-Zavaleta
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) - [c8]Citlalli Mejía-Almonte
Towards the Prokaryotic Regulation Ontology: An Ontological Model to Infer Gene Regulation Physiology from Mechanisms in Bacteria. KEOD 2019: 495-499 - 2018
- [c7]Citlalli Mejía, Julio Collado-Vides:
A Falsification Approach to Create and Check Ontology Definitions. ICBO 2018 - 2017
- [j39]Fabio Rinaldi
Strategies towards digital and semi-automated curation in RegulonDB. Database J. Biol. Databases Curation 2017: bax012 (2017) - [j38]Fabio Rinaldi
Erratum: Strategies towards digital and semi-automated curation in RegulonDB. Database J. Biol. Databases Curation 2017: bax012 (2017) - [j37]Yalbi Itzel Balderas-Martínez
Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. Database J. Biol. Databases Curation 2017: bax030 (2017) - [j36]Carlos-Francisco Méndez-Cruz
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) - [j35]Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res. 45(Database-Issue): D543-D550 (2017) - 2016
- [j34]Socorro Gama-Castro, Heladia Salgado, Alberto Santos-Zavaleta
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 44(Database-Issue): 133-143 (2016) - [j33]Marco Moretto
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. Nucleic Acids Res. 44(Database-Issue): 620-623 (2016) - 2015
- [j32]Fabio Rinaldi, Oscar Lithgow-Serrano, Alejandra López-Fuentes, Socorro Gama-Castro, Yalbi I. Balderas-Martínez, Hilda Solano-Lira, Julio Collado-Vides:
An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database. Polibits 52: 25-31 (2015) - 2014
- [j31]Socorro Gama-Castro, Fabio Rinaldi
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. Database J. Biol. Databases Curation 2014 (2014) - [j30]Pieter Meysman
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic Acids Res. 42(Database-Issue): 649-653 (2014) - 2013
- [j29]Verena Weiss, Alejandra Medina-Rivera
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database J. Biol. Databases Curation 2013 (2013) - [j28]Heladia Salgado, Martín Peralta-Gil
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) - [j27]Ingrid M. Keseler, Amanda Mackie, Martín Peralta-Gil
EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41(Database-Issue): 605-612 (2013) - 2011
- [j26]Socorro Gama-Castro, Heladia Salgado, Martín Peralta-Gil
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) - [j25]Ingrid M. Keseler, Julio Collado-Vides
EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 39(Database-Issue): 583-590 (2011)
2000 – 2009
- 2009
- [j24]Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides
EcoCyc: A comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37(Database-Issue): 464-470 (2009) - 2008
- [j23]Vladimir Espinosa Angarica
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinform. 9 (2008) - [j22]Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil
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) - 2007
- [j21]Bruno Contreras-Moreira
TFmodeller: comparative modelling of protein-DNA complexes. Bioinform. 23(13): 1694-1696 (2007) - [j20]Carlos Rodríguez Penagos
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinform. 8 (2007) - [j19]Abel González Pérez
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. Nucleic Acids Res. 35(Database-Issue): 132-136 (2007) - [j18]Rafael Palacios, Julio Collado-Vides
Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go. PLoS Comput. Biol. 3(9) (2007) - [j17]Osbaldo Resendis-Antonio
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. PLoS Comput. Biol. 3(10) (2007) - [c6]Carlos Rodríguez Penagos
NLP-Based Curation of Bacterial Regulatory Networks. CICLing 2007: 575-586 - 2006
- [j16]Heladia Salgado, Alberto Santos-Zavaleta
The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinform. 7: 5 (2006) - [j15]Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34(Database-Issue): 394-397 (2006) - [c5]Bruno Contreras-Moreira
Comparative footprinting of DNA-binding proteins. ISMB (Supplement of Bioinformatics) 2006: 74-80 - 2005
- [j14]Abel D. González, Vladimir Espinosa Angarica
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. Nucleic Acids Res. 33(Database-Issue): 98-102 (2005) - [j13]Ingrid M. Keseler, Julio Collado-Vides
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33(Database-Issue): 334-337 (2005) - 2004
- [j12]Ernesto Pérez-Rueda
Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput. Biol. Chem. 28(5-6): 341-350 (2004) - [j11]Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Julio Collado-Vides:
Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach. Silico Biol. 5(2): 209-219 (2004) - [j10]Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 32(Database-Issue): 303-306 (2004) - [e2]Julio Collado-Vides, Ralf Hofestädt, Christoph W. Sensen:
Integrative Bioinformatics - Aspects of the Virtual Cell, 04.07. - 09.07.2004. Dagstuhl Seminar Proceedings 04281, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2004 [contents] - [i1]Julio Collado-Vides, Ralf Hofestädt, Christoph W. Sensen:
04281 Abstracts Collection - Integrative Bioinformatics - Aspects of the Virtual Cell. Integrative Bioinformatics - Aspects of the Virtual Cell 2004 - 2002
- [j9]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. Silico Biol. 2(2): 87-95 (2002) - [j8]Peter D. Karp
The EcoCyc Database. Nucleic Acids Res. 30(1): 56-58 (2002) - [c4]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 - [c3]Gabriel Moreno-Hagelsieb, Julio Collado-Vides:
A powerful non-homology method for the prediction of operons in prokaryotes. ISMB 2002: 329-336 - [e1]Julio Collado-Vides, Ralf Hofestädt:
Gene Regulations and Metabolism - Postgenomic Computational Approaches. MIT Press 2002, ISBN 0-262-03297-X [contents] - 2001
- [j7]Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Ernesto Pérez-Rueda
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29(1): 72-74 (2001) - 2000
- [j6]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 Res. 28(1): 65-67 (2000)
1990 – 1999
- 1999
- [j5]Heladia Salgado, Alberto Santos-Zavaleta
RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 27(1): 59-60 (1999) - 1998
- [j4]Denis Thieffry
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinform. 14(5): 391-400 (1998) - [j3]Araceli M. Huerta, Heladia Salgado, Denis Thieffry
RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26(1): 55-59 (1998) - 1996
- [j2]David A. Rosenblueth, Denis Thieffry
Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. 12(5): 415-422 (1996) - [c2]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 - [c1]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 - 1991
- [j1]Julio Collado-Vides
The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars. Comput. Appl. Biosci. 7(3): 321-326 (1991)
Coauthor Index
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