J. Collado-Vides

发表

The complete genome sequence of Escherichia coli K-12.

N. W. Davis, J. Glasner, F. Blattner, 1997, Science.

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

J. Collado-Vides, J. van Helden, B. André, 1998, Journal of molecular biology.

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.

J. Collado-Vides, J. van Helden, J. Helden, 2000, Nucleic acids research.

Minimum information requested in the annotation of biochemical models (MIRIAM)

Hugh D. Spence, H. Sauro, J. Collado-Vides, 2005, Nature Biotechnology.

BioPAX – A community standard for pathway data sharing

Gary D Bader, Alexander R. Pico, Suzanne M. Paley, 2010, Nature Biotechnology.

Integrative Approaches to Molecular Biology

J. Collado-Vides, 1996 .

Modular analysis of the transcriptional regulatory network of E. coli.

J. Collado-Vides, O. Reséndis-Antonio, J. A. Freyre-González, 2005, Trends in genetics : TIG.

Control site location and transcriptional regulation in Escherichia coli

J. Collado-Vides, J. Gralla, B. Magasanik, 1991, Microbiological reviews.

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..

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Araceli M. Huerta, J. Collado-Vides, V. Jiménez-Jacinto, 2009, PloS one.

Theoretical and empirical quality assessment of transcription factor-binding motifs

J. Collado-Vides, J. van Helden, C. Abreu-Goodger, 2010, Nucleic acids research.

Bioinformatics Resources for the Study of Gene Regulation in Bacteria

J. Collado-Vides, Irma Martínez-Flores, V. Jiménez-Jacinto, 2008, Journal of bacteriology.

Networks of transcriptional regulation encoded in a grammatical model.

J. Collado-Vides, R. Gutiérrez-Ríos, G. Bel-Enguix, 1998, Bio Systems.

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes

J. Collado-Vides, M. Babu, S. Janga, 2008, Proceedings of the National Academy of Sciences.

Method DISTILLER : a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

J. Collado-Vides, T. D. Bie, B. De Moor, 2009 .

Redefining fundamental concepts of transcription initiation in bacteria

A. Arkin, J. Collado-Vides, G. Stormo, 2020, Nature Reviews Genetics.

Regulation by transcription factors in bacteria: beyond description

J. Collado-Vides, O. Reséndis-Antonio, S. Encarnación, 2008, FEMS microbiology reviews.

Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors.

Leonardo A. B. Tôrres, J. Collado-Vides, H. Rosu, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes

J. Collado-Vides, Daniela Ledezma-Tejeida, Luis Altamirano-Pacheco, 2019, Nucleic acids research.

Limits to a classic paradigm: Most transcription factors regulate genes in multiple biological processes

J. Collado-Vides, Daniela Ledezma-Tejeida, Luis Altamirano-Pacheco, 2018, bioRxiv.

Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli

J. Collado-Vides, S. Janga, A. Martínez-Antonio, 2007, Nucleic acids research.

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.

Araceli M. Huerta, J. Collado-Vides, D. Thieffry, 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

Araceli M. Huerta, J. Glasner, F. Blattner, 2003, Genome research.

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.

J. Collado-Vides, E. Pérez-Rueda, Ernesto Pérez-Rueda, 2000, Nucleic acids research.

Identifying global regulators in transcriptional regulatory networks in bacteria.

J. Collado-Vides, A. Martínez-Antonio, 2003, Current opinion in microbiology.

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes.

J. Collado-Vides, C. Abreu-Goodger, G. Moreno-Hagelsieb, 2003, Nucleic acids research.

Bacterial regulatory networks are extremely flexible in evolution

J. Collado-Vides, S. Janga, Irma Lozada-Chávez, 2006, Nucleic acids research.

Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.

J. Collado-Vides, S. Janga, A. Martínez-Antonio, 2006, Trends in microbiology.

A web site for the computational analysis of yeast regulatory sequences

J. Collado-Vides, J. van Helden, B. André, 2000, Yeast.

Genomic position analyses and the transcription machinery.

J. Collado-Vides, E. Pérez-Rueda, J. Gralla, 1998, Journal of molecular biology.

Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach

J. Collado-Vides, J. A. Freyre-González, José A Alonso-Pavón, 2008, Genome Biology.

A comparative genomics approach to prediction of new members of regulons.

G D Stormo, J. Collado-Vides, G. Stormo, 2001, Genome research.

Operons in Escherichia coli: genomic analyses and predictions.

Temple F. Smith, T. Smith, J. Collado-Vides, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Effect of genomic distance on coexpression of coregulated genes in E. coli

J. Collado-Vides, K. Marchal, E. Merino, 2017, PloS one.

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.

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.

Internal versus external effector and transcription factor gene pairs differ in their relative chromosomal position in Escherichia coli.

J. Collado-Vides, S. Janga, A. Martínez-Antonio, 2007, Journal of molecular biology.

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.

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.

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.

Grammatical model of the regulation of gene expression.

J. Collado-Vides, J Collado-Vides, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Promoter Interference in a Bacteriophage Lambda Control Region: Effects of a Range of Interpromoter Distances

J. Collado-Vides, P. Dehaseth, M. Strainic, 2000, Journal of bacteriology.

Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli.

J. Collado-Vides, J. A. Freyre-González, Y. Balderas-Martínez, 2015, Molecular bioSystems.

Structural and functional map of a bacterial nucleoid

J. Collado-Vides, A. Martínez-Antonio, A. Medina-Rivera, 2009, Genome Biology.

Syntactic recognition of regulatory regions in Escherichia coli

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

Integrative representations of the regulation of gene expression

J. Collado-Vides, Julio Collado-vides, 1996 .

A linguistic representation of the regulation of transcription initiation. I. An ordered array of complex symbols with distinctive features.

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

Analysis of the Cellular Functions of Escherichia coli Operons and Their Conservation in Bacillus subtilis

A. Valencia, J. Collado-Vides, A. de Daruvar, 2002, Journal of Molecular Evolution.

The elements for a classification of units of genetic information with a combinatorial component.

J. Collado-Vides, J Collado-Vides, 1993, Journal of theoretical biology.

Modeling and simulation of metabolic pathways, gene regulation and cell differentiation. October 22-27, 1995. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany.

R Hofestädt, M Mavrovouniotis, J. Collado-Vides, 1996, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

J. M. Camacho-Zaragoza, J. Collado-Vides, S. Gama-Castro, 2017, bioRxiv.

Modeling and simulation of gene regulation and metabolic pathways.

R Hofestädt, J Collado-Vides, M Mavrovouniotis, 1999, Bio Systems.

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

J. Collado-Vides, Irma Martínez-Flores, H. Salgado, 2016, Scientific Reports.

Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes.

J. Collado-Vides, G. Moreno-Hagelsieb, P. Vinuesa, 2004, Molecular biology and evolution.

Integrative system biology approach for molecular medicine : The case study of Cyclin dependent kinase 5 in neurodegenerative pathologies

C. Sensen, J. Collado-Vides, R. Hofestädt, 2006 .

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

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

Structural Properties of Prokaryotic Promoter Regions Correlate with Functional Features

J. Collado-Vides, K. Laukens, P. Meysman, 2014, PloS one.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

Víctor H. Tierrafría, J. Collado-Vides, J. Galagan, 2022, Microbial genomics.

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

Gary D. Bader, Frank Schacherer, Edgar Wingender, 2010 .

The network of transcriptional interactions imposes linear constrains in the genome.

J. Collado-Vides, S. Janga, Ricardo Menchaca-Méndez, 2005, Omics : a journal of integrative biology.

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

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

The EcoCyc Database.

J. Collado-Vides, P. Midford, P. Karp, 2018, EcoSal Plus.

The EcoCyc Database

Suzanne M. Paley, Socorro Gama-Castro, Julio Collado-Vides, 2002, Nucleic Acids Res..

BioPAX – A community standard for pathway data sharing

Gary D Bader, Alexander R. Pico, Joanne S. Luciano, 2010, Nature Biotechnology.

PulmonDB: a curated lung disease gene expression database

Luis A. Aguilar, J. Collado-Vides, J. García-Sotelo, 2019, Scientific Reports.

The EcoCyc Database in 2021

Suzanne M. Paley, Víctor H. Tierrafría, J. Collado-Vides, 2021, Frontiers in Microbiology.

Three Models of Gene Regulation in E.coli

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

On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.

J. Collado-Vides, J. Baumbach, A. Pühler, 2012, Integrative biology : quantitative biosciences from nano to macro.

Towards a unified resource for transcriptional regulation in Escherichia coli K-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB

Víctor H. Tierrafría, David A. Velázquez-Ramírez, J. Collado-Vides, 2017, bioRxiv.

fusing model organism databases with systems biology.

Araceli M. Huerta, J. Collado-Vides, P. Karp, 2012 .

Regulation of expression of symbiotic genes in Rhizobium sp. NGR234.

J. Collado-Vides, Hajime Kobayashi, X. Perret, 2003, Indian journal of experimental biology.

Strategies towards digital and semi-automated curation in RegulonDB

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

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..

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.

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.

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.

Feedback loops: The wheels of regulatory networks

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

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.

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.

Modelling of Living Systems: Learning from Linguistics for Biology

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

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

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

A LINGUISTIC INTEGRATION OF A BIOLOGICAL DATABASE

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

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

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

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.

Genomics of Gene Regulation: The View from Escherichia coli

César Bonavides-Martínez, Socorro Gama-Castro, David A. Rosenblueth, 2002, Gene Regulations and Metabolism.

EcoCyc: a comprehensive database of Escherichia coli biology

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

Control site location and transcriptional regulation in Escherichia coli.

J. Collado-Vides, J. Gralla, B. Magasanik, 1991, Microbiological reviews.

A Falsification Approach to Create and Check Ontology Definitions

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

EcoCyc: fusing model organism databases with systems biology

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

Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli

J. Collado-Vides, P. Bustos, D. Piñero, 2005, Journal of bacteriology.

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

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

EcoCyc: a comprehensive database resource for Escherichia coli

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

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.

The EcoCyc Database

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

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..

AR TICLE The Complete Genome Sequence of Escherichia coli K-12

N. W. Davis, J. Glasner, F. Blattner, 2013 .

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.

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..

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..

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..

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

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

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea

Julio Collado-Vides, Lorenzo Segovia, Ernesto Pérez-Rueda, 2004, Comput. Biol. Chem..

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

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

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..

Redefining fundamental concepts of transcription initiation in bacteria

A. Arkin, J. Collado-Vides, G. Stormo, 2020, Nature Reviews Genetics.

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..

Transcription unit conservation in the three domains of life: a perspective from Escherichia coli.

T. Smith, J. Collado-Vides, E. Pérez-Rueda, 2001, Trends in genetics : TIG.

A Golden Standard for Transcription Factor-Gene Regulatory Interactions in Escherichia coli K-12: How reliable are they based on the methods supporting them?

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2023 .

Integrating Bacterial ChIP‐seq and RNA‐seq Data With SnakeChunks

Claire Rioualen, Lucie Charbonnier‐Khamvongsa, Julio Collado‐Vides, 2019, Current protocols in bioinformatics.

Using RegulonDB, the Escherichia coli K‐12 Gene Regulatory Transcriptional Network Database

Irma Martínez-Flores, Julio Collado-Vides, Heladia Salgado, 2018, Current protocols in bioinformatics.

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..

Extracting regulatory networks of Escherichia coli from RegulonDB.

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

Expanding BioPAX format by integrating Gene Regulation

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

A syntactic representation of units of genetic information--a syntax of units of genetic information.

J. Collado-Vides, J Collado-Vides, 1991, Journal of theoretical biology.

A transformational-grammar approach to the study of the regulation of gene expression.

J. Collado-Vides, J Collado-Vides, Julio Collado-Vides, 1989, Journal of theoretical biology.

Structure and evolution of gene regulatory networks in microbial genomes.

Sarath Chandra Janga, J. Collado-Vides, S. Janga, 2007, Research in microbiology.

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

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

Towards a unified grammatical model of sigma 70 and sigma 54 bacterial promoters.

J. Collado-Vides, J Collado-Vides, 1996, Biochimie.

Some ideas towards a grammatical model of the /spl sigma//sup 54/ bacterial promoters

J. Collado-Vides, 1995, Proceedings First International Symposium on Intelligence in Neural and Biological Systems. INBS'95.

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..

The comprehensive updated regulatory network of Escherichia coli K-12

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

RegulonDB: a database on transcriptional regulation in Escherichia coli

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

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

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

EcoCyc: A comprehensive view of Escherichia coli biology

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

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.

Missing Links Between Gene Function and Physiology in Genomics

J. Collado-Vides, V. de Lorenzo, P. Gaudet, 2022, Frontiers in Physiology.

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.

A linguistic representation of the regulation of transcription initiation. II. Distinctive features of sigma 70 promoters and their regulatory binding sites.

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

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

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

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.

Multidimensional annotation of the Escherichia coli K-12 genome

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

Sensory Systems and Transcriptional Regulation in Escherichia coli

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2022, Frontiers in bioengineering and biotechnology.

Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria.

J. Collado-Vides, M. García-Varela, M. Gómez‐Eichelmann, 2001, Nucleic acids research.

Regulatory promoter architectures in the hands of thermodynamic modelling

J. Collado-Vides, 2023, Nature Reviews Genetics.

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.

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.

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.

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..

In Silico Identification and Experimental Characterization of Regulatory Elements Controlling the Expression of the Salmonella csrB and csrC Genes

J. Collado-Vides, Irma Martínez-Flores, H. Salgado, 2013, Journal of bacteriology.

Genes csrC and csrB Salmonella Controlling the Expression of the Characterization of Regulatory Elements Identification and Experimental In Silico

J. Collado-Vides, Irma Martínez-Flores, H. Salgado, 2013 .

A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2023, bioRxiv.

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

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

Transcription Factors in Escherichia coli Prefer the Holo Conformation

J. Collado-Vides, M. Savageau, E. Pérez-Rueda, 2013, PloS one.

Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

Socorro Gama-Castro, Julio Collado-Vides, Carlos-Francisco Méndez-Cruz, 2020, Database J. Biol. Databases Curation.

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.

Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria.

J. Collado-Vides, Fabio Rinaldi, S. Gama-Castro, 2021, Biochimica et biophysica acta. Gene regulatory mechanisms.

TFmodeller: comparative modelling of protein-DNA complexes

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

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

J. Collado-Vides, B. De Moor, K. Marchal, 2009, Genome Biology.

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..

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..

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.

The growth of random networks as a diffusion process

J. Collado-Vides, O. Reséndis-Antonio, 2004 .

L-Regulon: A novel “soft-curation” approach supported by a semantic enriched reading for RegulonDB literature

Socorro Gama-Castro, Julio Collado-Vides, Oscar Lithgow-Serrano, 2020, bioRxiv.

Microbial computational genomics of gene regulation

J. Collado-Vides, G. Moreno-Hagelsieb, A. Medrano-Soto, 2002 .

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.

J. Collado-Vides, J. Helden, Alma. F. Rios, 2000, Nucleic Acids Research.

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

Víctor H. Tierrafría, David A. Velázquez-Ramírez, J. Collado-Vides, 2018, BMC Biology.

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

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

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..

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..

A web site for the computational analysis of yeast regulatory sequences

J. Collado-Vides, B. André, J. Helden, 2000, Yeast.

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

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

Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types

Víctor H. Tierrafría, J. Collado-Vides, S. Gama-Castro, 2024, Frontiers in genetics.

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

J. Collado-Vides, J. Gelpí, S. Gama-Castro, 2023, Nucleic acids research.

The EcoCyc Database

Suzanne M. Paley, Araceli M. Huerta, Daniel S. Weaver, 2014, EcoSal Plus.