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List of works by Julio Collado-Vides

A comparative genomics approach to prediction of new members of regulons

scientific article

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

scientific article

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

scientific article

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

scientific article published in January 2002

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

scientific article published in February 1991

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

scientific article published on 16 August 2018

A web site for the computational analysis of yeast regulatory sequences

article

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

article

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

scientific article

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

scientific article

Bacterial regulatory networks are extremely flexible in evolution

scientific article

Bioinformatics resources for the study of gene regulation in bacteria

scientific article published on 31 October 2008

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

scientific article

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

scientific article published on 19 November 2015

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

article by Ernesto Pérez-Rueda & Julio Collado-Vides published 1 September 2001 in Journal of Molecular Evolution

Comparative Studies of Transcriptional Regulation Mechanisms in a Group of Eight Gamma-proteobacterial Genomes

scientific article published on 04 October 2005

Comparative footprinting of DNA-binding proteins

scientific article published in July 2006

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

scientific article published in January 2005

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes

scientific article published on December 2003

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

scientific article published on 12 October 2007

Correction: Transcription Factors in Escherichia coli Prefer the Holo Conformation.

scientific article published on 22 August 2013

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

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

scientific article

Development of genomic sciences in Mexico: a good start and a long way to go.

scientific article

Distribution of minigenes in the bacteriophage lambda chromosome.

scientific article

Diversification of DNA sequences in the symbiotic genome of Rhizobium etli

scientific article

EcoCyc: a comprehensive database of Escherichia coli biology

scientific article

EcoCyc: a comprehensive database resource for Escherichia coli

scientific article

EcoCyc: a comprehensive view of Escherichia coli biology

scientific article published on 30 October 2008

EcoCyc: fusing model organism databases with systems biology

scientific article

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

scientific article

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

scientific article published on December 2003

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

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

scientific article

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

scientific article published on 17 January 2013

Extracting regulatory networks of Escherichia coli from RegulonDB.

scientific article published in January 2012

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

scientific article

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

scientific article published in January 2017

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

scientific article

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

scientific article published on May 1, 1998

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

scientific article published on 27 October 2008

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

scientific article

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli

scientific article

Genomic position analyses and the transcription machinery.

scientific article published in January 1998

Grammatical model of the regulation of gene expression ⬇️

scientific article published on October 15, 1992

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

scientific article

Identifying global regulators in transcriptional regulatory networks in bacteria

scientific article published on October 2003

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

scientific article

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

scientific article

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

scientific article

In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes

scientific article

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

scientific article published on 20 February 2019

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

scientific article published on 12 January 2007

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

scientific article

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

scientific article published on 01 December 2020

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

scientific article published on 01 July 2019

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

scientific article published in April 2015

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

scientific article

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

scientific article

Modeling and simulation of gene regulation and metabolic pathways

article

Modeling and simulation of metabolic pathways, gene regulation and cell differentiation

article

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

scientific article published in January 2005

Multidimensional annotation of the Escherichia coli K-12 genome

scientific article

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

scientific article

Networks of transcriptional regulation encoded in a grammatical model

article

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

scientific article

Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context.

scientific article published on January 2002

Operons in Escherichia coli: genomic analyses and predictions

scientific article

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

scholarly article by Ernesto Pérez-Rueda et al published December 2004 in Computational Biology and Chemistry

Positional Conservation of Clusters of Overlapping Promoter-Like Sequences in Enterobacterial Genomes

scientific article published in 2006

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

scientific article

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

scientific article published in June 1998

Promoter interference in a bacteriophage lambda control region: effects of a range of interpromoter distances

scientific article

PulmonDB: a curated lung disease gene expression database

scientific article published on 16 January 2020

Redefining fundamental concepts of transcription initiation in bacteria

scientific article published on 14 July 2020

Regulation by transcription factors in bacteria: beyond description

scientific article published on January 2009

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

scientific article published in October 2003

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

scientific article

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

scientific article published on January 2004

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

scientific article

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

scientific article

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

scientific article published in 2022

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

article

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

scientific article

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

scientific article

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

scientific article

RegulonDB: a database on transcriptional regulation in Escherichia coli ⬇️

scientific article published on January 1, 1998

Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes

scientific article published on 12 September 2006

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

scientific article

Similarity corpus on microbial transcriptional regulation

scientific article published on 22 May 2019

Strategies towards digital and semi-automated curation in RegulonDB

Strategies towards digital and semi-automated curation in RegulonDB.

scientific article

Structural and functional map of a bacterial nucleoid

scientific article published on 11 December 2009

Structural properties of prokaryotic promoter regions correlate with functional features

scientific article

Structure and evolution of gene regulatory networks in microbial genomes

scientific article published on 15 October 2007

Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes

article

TFmodeller: comparative modelling of protein-DNA complexes

scientific article

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

scientific article

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The EcoCyc Database

scientific article

The EcoCyc Database

scientific article published on 01 November 2018

The EcoCyc Database.

scientific article

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

scientific article

The complete genome sequence of Escherichia coli K-12

scientific article

The comprehensive updated regulatory network of Escherichia coli K-12.

scientific article

The condition-dependent transcriptional network in Escherichia coli

scientific article published in March 2009

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

scientific article

The growth of random networks as a diffusion process

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

article

Theoretical and empirical quality assessment of transcription factor-binding motifs

scientific article

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

scientific article published on 01 January 2002

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

scientific article

Transcription factors in Escherichia coli prefer the holo conformation

scientific article

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes

scholarly article

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

article

With the finished human genome in hand, what next?

scientific article

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