Julio Collado-Vides

发表

Peter D. Karp, Milton H. Saier, Monica Riley, 2002, Nucleic Acids Res..

The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars

Julio Collado-Vides, J. Collado-Vides, 1991, Comput. Appl. Biosci..

Development of Genomic Sciences in Mexico: A Good Start and a Long Way to Go

Julio Collado-Vides, Rafael Palacios, J. Collado-Vides, 2007, PLoS Comput. Biol..

The comprehensive updated regulatory network of Escherichia coli K-12

Peter D. Karp, Julio Collado-Vides, Socorro Gama-Castro, 2006, BMC Bioinformatics.

First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes

Julio Collado-Vides, Socorro Gama-Castro, Carlos-Francisco Méndez-Cruz, 2017, Database J. Biol. Databases Curation.

A LINGUISTIC INTEGRATION OF A BIOLOGICAL DATABASE

Julio Collado-Vides, J. Collado-Vides, 1993 .

Lisen&Curate: A platform to facilitate knowledge tools for curation of regulation of transcription initiation in bacteria

Fabio Rinaldi, Julio Collado-Vides, Socorro Gama-Castro, 2020 .

Expanding BioPAX format by integrating Gene Regulation

Julio Collado-Vides, Verónica Jiménez-Jacinto, Irma Martínez-Flores, 2010 .

Three Models of Gene Regulation in E.coli

Peter D. Karp, Julio Collado-Vides, Araceli M. Huerta, 1996, German Conference on Bioinformatics.

RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2001, Nucleic Acids Res..

BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data

Julio Collado-Vides, J. Andrés Christen, Arturo Medrano-Soto, 2004 .

RegulonDB: a database on transcriptional regulation in Escherichia coli

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998, Nucleic Acids Res..

04281 Abstracts Collection - Integrative Bioinformatics - Aspects of the Virtual Cell

Ralf Hofestädt, Julio Collado-Vides, Christoph W. Sensen, 2004, Integrative Bioinformatics - Aspects of the Virtual Cell.

EcoCyc: fusing model organism databases with systems biology

Peter D. Karp, Ian T. Paulsen, Julio Collado-Vides, 2012, Nucleic Acids Res..

Prediction of TF target sites based on atomistic models of protein-DNA complexes

Julio Collado-Vides, Ana Tereza Ribeiro de Vasconcelos, Bruno Contreras-Moreira, 2008, BMC Bioinformatics.

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998, Bioinform..

An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database

Fabio Rinaldi, Julio Collado-Vides, Socorro Gama-Castro, 2015, Polytech. Open Libr. Int. Bull. Inf. Technol. Sci..

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2010, Nucleic Acids Res..

Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes

Julio Collado-Vides, Ana Tereza Ribeiro de Vasconcelos, A. T. Vasconcelos, 2006, Nucleic Acids Res..

Towards the Prokaryotic Regulation Ontology: An Ontological Model to Infer Gene Regulation Physiology from Mechanisms in Bacteria

Julio Collado-Vides, Citlalli Mejía-Almonte, 2019, KEOD.

NLP-Based Curation of Bacterial Regulatory Networks

Julio Collado-Vides, Carlos Rodríguez Penagos, Heladia Salgado, 2007, CICLing.

Evidence classification of high-throughput protocols and confidence integration in RegulonDB

Julio Collado-Vides, Heladia Salgado, Alberto Santos-Zavaleta, 2013, Database J. Biol. Databases Curation.

Julio Collado-Vides, Socorro Gama-Castro, Oscar Lithgow-Serrano, 2019, J. Biomed. Semant..

Curation, processing, and data integration of information obtained via high-throughput technologies

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2017 .

Syntactic recognition of regulatory regions in Escherichia coli

Denis Thieffry, Julio Collado-Vides, David A. Rosenblueth, 1996, Comput. Appl. Biosci..

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2007, Nucleic Acids Res..

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2005, Nucleic Acids Res..

A Falsification Approach to Create and Check Ontology Definitions

Julio Collado-Vides, Citlalli Mejía, J. Collado-Vides, 2018, ICBO.

Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context

Julio Collado-Vides, Gabriel Moreno-Hagelsieb, J. Collado-Vides, 2002, Silico Biol..

Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12

Fabio Rinaldi, Simon Clematide, Julio Collado-Vides, 2014, Database J. Biol. Databases Curation.

TFmodeller: comparative modelling of protein-DNA complexes

Julio Collado-Vides, Bruno Contreras-Moreira, Pierre-Alain Branger, 2007, Bioinform..

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

Chiara Romualdi, Luca Bianco, Julio Collado-Vides, 2015, Nucleic Acids Res..

Feedback loops: The wheels of regulatory networks

Julio Collado-Vides, René Thomas, B. Magasanik, 1996 .

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2012, Nucleic Acids Res..

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

Bernhard O. Palsson, Julio Collado-Vides, Jennifer L. Reed, 2007, PLoS Comput. Biol..

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

Peter D. Karp, Ian T. Paulsen, Julio Collado-Vides, 2016, Nucleic Acids Res..

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

Julio Collado-Vides, Carlos Rodríguez Penagos, Heladia Salgado, 2007, BMC Bioinformatics.

MCO: towards an ontology and unified vocabulary for a framework‐based annotation of microbial growth conditions

Julio Collado-Vides, Socorro Gama-Castro, Citlalli Mejía-Almonte, 2018, Bioinform..

Comparative footprinting of DNA-binding proteins

Julio Collado-Vides, Bruno Contreras-Moreira, 2006, ISMB.

A powerful non-homology method for the prediction of operons in prokaryotes

Julio Collado-Vides, Gabriel Moreno-Hagelsieb, J. Collado-Vides, 2002, ISMB.

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2018, Nucleic Acids Res..

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

Julio Collado-Vides, César Bonavides-Martínez, Socorro Gama-Castro, 2004, Nucleic Acids Res..

Strategies towards digital and semi-automated curation in RegulonDB

Fabio Rinaldi, Julio Collado-Vides, Socorro Gama-Castro, 2017, Database : the journal of biological databases and curation.

Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach

Julio Collado-Vides, Ana Tereza Ribeiro de Vasconcelos, A. T. Vasconcelos, 2004, Silico Biol..

RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli

Julio Collado-Vides, Jacques van Helden, Heladia Salgado, 1999, Nucleic Acids Res..

EcoCyc: A comprehensive view of Escherichia coli biology

Peter D. Karp, Ian T. Paulsen, Julio Collado-Vides, 2008, Nucleic Acids Res..

TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes

Julio Collado-Vides, Ana Tereza Ribeiro de Vasconcelos, Ernesto Pérez-Rueda, 2004, Nucleic Acids Res..

Modelling of Living Systems: Learning from Linguistics for Biology

Julio Collado-Vides, J. Collado-Vides, 2009 .

RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12

Julio Collado-Vides, Socorro Gama-Castro, Heladia Salgado, 2000, Nucleic Acids Res..

EcoCyc: a comprehensive database of Escherichia coli biology

Peter D. Karp, Ian T. Paulsen, Julio Collado-Vides, 2010, Nucleic Acids Res..

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia

Kathleen Marchal, Qiang Fu, Luca Bianco, 2013, Nucleic Acids Res..

Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis

Fabio Rinaldi, Julio Collado-Vides, Hilda Solano-Lira, 2017, Database J. Biol. Databases Curation.

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

Fabio Rinaldi, Julio Collado-Vides, César Bonavides-Martínez, 2015, Nucleic Acids Res..

Strategies towards digital and semi-automated curation in RegulonDB

Fabio Rinaldi, Julio Collado-Vides, Socorro Gama-Castro, 2016, Database J. Biol. Databases Curation.

GeDex: A consensus Gene-disease Event Extraction System based on frequency patterns and supervised learning

Julio Collado-Vides, David Velázquez, Carlos-Francisco Méndez-Cruz, 2019, bioRxiv.

Strategies towards digital and semi-automated curation in RegulonDB

Fabio Rinaldi, Julio Collado-Vides, Socorro Gama-Castro, 2017, Database J. Biol. Databases Curation.

Monitoring the genetic regulation process with a nonlinear software sensor

Julio Collado-Vides, Lizeth Torres, Vrani Ibarra-Junquera, 2004 .

EcoCyc: a comprehensive database resource for Escherichia coli

Peter D. Karp, Ian T. Paulsen, Julio Collado-Vides, 2004, Nucleic Acids Res..

Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes.

Julio Collado-Vides, Araceli M. Huerta, A. T. Vasconcelos, 2005, Journal of molecular biology.

Report on the International Conference & Meetings EMBnet-RIBio 2009

Julio Collado-Vides, César Bonavides-Martínez, Lucia Nikolaia López-Bojórquez, 2010 .

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Kei-Hoi Cheung, Frank Schacherer, Edgar Wingender, 2010 .

Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.

Julio Collado-Vides, Araceli M. Huerta, Araceli M Huerta, 2003, Journal of molecular biology.

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters

Julio Collado-Vides, A. T. Vasconcelos, Ana Tereza Ribeiro Vasconcelos, 2009, BMC Molecular Biology.

Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons

Julio Collado-Vides, Sarath Chandra Janga, Gabriel Moreno-Hagelsieb, 2005, Nucleic acids research.

The role of DNA-binding specificity in the evolution of bacterial regulatory networks.

Julio Collado-Vides, Bruno Contreras-Moreira, Irma Lozada-Chávez, 2008, Journal of molecular biology.

RegulonDB: A database on transcriptional regulation

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998 .

Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach

Julio Collado-Vides, Socorro Gama-Castro, Verónica Jiménez-Jacinto, 2003, Biotechnology and bioengineering.

Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes

Julio Collado-Vides, Enrique Morett, Araceli M Huerta, 2006, PLoS genetics.

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes.

Julio Collado-Vides, Araceli M Huerta, J. Collado-Vides, 2006, Molecular biology and evolution.

Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli

Julio Collado-Vides, Osbaldo Resendis, Milton Saier, 2007, BMC Microbiology.

Multidimensional annotation of the Escherichia coli K-12 genome

Peter D. Karp, Julio Collado-Vides, Suzanne M. Paley, 2007, Nucleic acids research.

GETools: gene expression tool for analysis of transcriptome experiments in E. coli

Julio Collado-Vides, Jeremy D. Glasner, Araceli M. Huerta, 2002 .

Extracting regulatory networks of Escherichia coli from RegulonDB.

Julio Collado-Vides, Heladia Salgado, Luis Muñiz-Rascado, 2012, Methods in molecular biology.

The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments

Julio Collado-Vides, Heladia Salgado, Gabriel Moreno-Hagelsieb, 2003, Genome Biology.

Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA

Julio Collado-Vides, Gabriel Moreno-Hagelsieb, Esperanza Benítez-Bellón, 2002, Genome Biology.

Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet).

Julio Collado-Vides, Reynaldo Vargas, J. Collado-Vides, 2002, Applied bioinformatics.

The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942))

Kei-Hoi Cheung, Gary D. Bader, Frank Schacherer, 2012 .

Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli

Julio Collado-Vides, Daniela Ledezma-Tejeida, Cecilia Ishida, 2017, Front. Microbiol..

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria

Julio Collado-Vides, A. T. Vasconcelos, J. Collado-Vides, 2008, BMC Genomics.

Common History at the Origin of the Position–Function Correlation in Transcriptional Regulators in Archaea and Bacteria

Julio Collado-Vides, Ernesto Pérez-Rueda, J. Collado-Vides, 2001, Journal of Molecular Evolution.

The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons.

Julio Collado-Vides, Verónica Jiménez-Jacinto, Sarath Chandra Janga, 2006, Proceedings of the National Academy of Sciences of the United States of America.

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Julio Collado-Vides, Socorro Gama-Castro, Bernhard O Palsson, 2018, BMC Biology.