González Pérez, Abel, Espinosa Angarica, Vladimir, Collado-Vides, Julio, Vasconcelos, Ana Tereza
Abstract Background The fine tuning of two features of the bacterial regulatory machinery have been known to contribute to the diversity of gene expression within the same regulon: the sequence of...
Lemmens, Karen, De Bie, Tijl, Dhollander, Thomas, De Keersmaecker, Sigrid, Thijs, Inge, Schoofs, Geert, ...
We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase...
Lemmens, Karen, De Bie, Tijl, Dhollander, Thomas, De Keersmaecker, Sigrid C, Thijs, Inge M, Schoofs, Geert, ...
Abstract We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate...
De Bie, Tijl, ...
EcoCyc: A comprehensive view of Escherichia coli biology (2009)
Keseler, Ingrid M., Bonavides-Martínez, César, Collado-Vides, Julio, Gama-Castro, Socorro, Gunsalus, Robert P., Johnson, D. Aaron, ...
EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the...
Freyre-González, Julio A, Alonso-Pavón, José A, Treviño-Quintanilla, Luis G, Collado-Vides, Julio
Abstract Background Previous studies have used different methods in an effort to extract the modular organization of transcriptional regulatory networks. However, these approaches are not natural, as...
Prediction of TF target sites based on atomistic models of protein-DNA complexes (2008)
Angarica, Vladimir, Pérez, Abel, Vasconcelos, Ana T, Collado-Vides, Julio, Contreras-Moreira, Bruno
Abstract Background The specific recognition of genomic cis -regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the...
The role of DNA-binding specificity in the evolution of bacterial regulatory networks (2008)
Lozada-Chávez, Irma, Espinosa Angarica, Vladimir, Collado-Vides, Julio, Contreras-Moreira, Bruno
The definitive version is available at: http://www.sciencedirect.com/science/journal/00222836
footprint benchmark and TFmodeller web server (www.ccg.unam.mx/tfmodeller) (2008)
Bruno Contreras-moreira, Julio Collado-vides, Autónoma México, Cuernavaca Morelos, Fig Fig
Interactions between proteins and DNA molecules lie at the core of fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally described at...
doi:10.1093/bioinformatics/btl215 (2008)
Bruno Contreras-moreira, Julio Collado-vides
Motivation: Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and biotechnology. Traditionally it has been applied to model the structure of...
Denis Thieffry, Araceli M. Huerta, Ernesto Pérez-rueda, Julio Collado-vides
From specific gene regulation to genomic networks: a global analysis of transcriptional
Arturo Medrano-soto, J. Andrés Christen, Julio Collado-vides
Based on mixture models, we present a Bayesian method (called BClass) to classify biological entities (e.g. genes) when variables of quite heterogeneous nature are analyzed. Various statistical...
Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana T, Julio Collado-vides
Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching app... Page 1 of 10 Complementing computationally predicted regulatory sites in
González Pérez, Abel D, González González, Evelyn, Espinosa Angarica, Vladimir, Vasconcelos, Ana, Collado-Vides, Julio
Abstract Background In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative...
Gama-Castro, Socorro, Jiménez-Jacinto, Verónica, Peralta-Gil, Martín, Santos-Zavaleta, Alberto, Peñaloza-Spinola, Mónica I., Contreras-Moreira, Bruno, ...
RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known...
Bayesian Clustering and Prediction in Genetic Data Bases Using Multivariate Mixtures (2007)
J. Andrés Christen, Arturo Medrano-Soto, Julio Collado-Vides, Julio Collado{vides
Based on multivariate mixture models we develop a general approach for clustering and classi cation in data mining of genetic data bases. Using various distributions for the variables in the data...
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli (2007)
Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Ø. Palsson
Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific...
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing (2007)
Rodríguez-Penagos, Carlos, Salgado, Heladia, Martínez-Flores, Irma, Collado-Vides, Julio
Abstract Background Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a...
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli (2007)
Osbaldo Resendis, Jennifer Reed, Sergio Encarnacion, Julio Collado-Vides, Bernhard Palsson
Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific...
TFmodeller: comparative modelling of protein DNA complexes (2007)
Contreras-Moreira, Bruno, Branger, Pierre-Alain, Collado-Vides, Julio
Summary: Interactions between proteins and DNA molecules lie at the core of the fundamental cellular processes such as transcriptional regulation. Some of these interactions have been experimentally...
Gutierrez-Ríos, Rosa, Freyre-Gonzalez, Julio A, Resendis, Osbaldo, Collado-Vides, Julio, Saier, Milton, Gosset, Guillermo
Abstract Background Glucose is the preferred carbon and energy source for Escherichia coli . A complex regulatory network coordinates gene expression, transport and enzyme activities in response to...
RegulonDB (version 6.0): gene regulation model (2007)
Juan Segura-salazar, Luis Muñiz-rascado, Irma Martínez-flores, Heladia Salgado, César Bonavides-martínez, Cei Abreu-goodger, ...
of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Multidimensional annotation of the Escherichia coli K-12 genome (2007)
Karp, Peter D., Keseler, Ingrid M., Shearer, Alexander, Latendresse, Mario, Krummenacker, Markus, Paley, Suzanne M., ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...
Pérez, Abel González, Angarica, Vladimir Espinosa, Vasconcelos, Ana Tereza R., Collado-Vides, Julio
The version 2.0 of Tractor_DB is now accessible at its three international mirrors: www.bioinfo.cu/Tractor_DB, www.tractor.lncc.br and http://www.ccg.unam.mx/tractorDB. This database contains a...
Multidimensional annotation of the Escherichia coli K-12 genome (2007)
Karp, Peter D, Keseler, Ingrid M, Santos-Zavaleta, Alberto, Peñaloza-Spínola, Mónica I, Bonavides-Martinez, Cesar, Ingraham, John, ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...
Carlos Rodríguez-penagos, Heladia Salgado, Irma Martínez-flores, Julio Collado-vides
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Araceli M. Huerta, M. Pilar Francino, Enrique Morett, Julio Collado-Vides
The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that...
Enrique Morett, Julio Collado-Vides
The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that...
The comprehensive updated regulatory network of Escherichia coliK-12 (2006)
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Peralta-Gil, Martín, Peñaloza-Spínola, Mónica I, Martínez-Antonio, Agustino, ...
Abstract Background Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and...
Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza, R. Vasconcelos, Julio Collado-vides
gamma-proteobacterial genomes
04281 Abstracts Collection -- Integrative Bioinformatics - Aspects of the Virtual Cell (2006)
Collado-Vides, Julio, Hofestädt, Ralf, Sensen, Christoph W.
From 04.07.04 to 09.07.04, the Dagstuhl Seminar 04281 ``Integrative Bioinformatics - Aspects of the Virtual Cell'' was held in the International Conference and Research Center (IBFI), Schloss...
Huerta, Araceli M., Collado-Vides, Julio, Francino, M. Pilar
The selective mechanisms operating in regulatory regions of bacterial genomes are poorly understood. We have previously shown that, in most bacterial genomes, regulatory regions contain high...
Pérez, Abel González, Angarica, Vladimir Espinosa, Vasconcelos, Ana Tereza R., Collado-Vides, Julio
The version 2.0 of Tractor_DB is now accessible at its three international mirrors: www.bioinfo.cu/Tractor_DB, www.tractor.lncc.br and http://www.ccg.unam.mx/tractorDB. This database contains a...
Salgado, Heladia, Gama-Castro, Socorro, Peralta-Gil, Martín, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Santos-Zavaleta, Alberto, ...
RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest...
Huerta, Araceli M., Collado-Vides, Julio, Francino, M. Pilar
The selective mechanisms operating in regulatory regions of bacterial genomes are poorly understood. We have previously shown that, in most bacterial genomes, regulatory regions contain high...
Bacterial regulatory networks are extremely flexible in evolution (2006)
Lozada-Chávez, Irma, Janga, Sarath Chandra, Collado-Vides, Julio
Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche...
Comparative footprinting of DNA-binding proteins (2006)
Contreras-Moreira, Bruno, Collado-Vides, Julio
Motivation: Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and biotechnology. Traditionally it has been applied to model the structure of...
Pérez, Abel González, Angarica, Vladimir Espinosa, Vasconcelos, Ana Tereza R., Collado-Vides, Julio
The version 2.0 of Tractor_DB is now accessible at its three international mirrors: www.bioinfo.cu/Tractor_DB, www.tractor.lncc.br and http://www.ccg.unam.mx/tractorDB. This database contains a...
Minimum information requested in the annotation of biochemical models (MIRIAM) (2005)
Le Novère, Nicolas, Finney, Andrew, Hucka, Michael, Bhalla, Upinder S., Campagne, Fabien, Collado-Vides, Julio, ...
Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The...
EcoCyc: a comprehensive database resource for Escherichia coli (2005)
Keseler, Ingrid M., Collado-Vides, Julio, Gama-Castro, Socorro, Ingraham, John, Paley, Suzanne, Paulsen, Ian T., ...
The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both...
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes (2005)
González, Abel D., Espinosa, Vladimir, Vasconcelos, Ana T., Pérez-Rueda, Ernesto, Collado-Vides, Julio
Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (TFs), TFs' binding...
Janga, Sarath Chandra, Collado-Vides, Julio, Moreno-Hagelsieb, Gabriel
Since operons are unstable across Prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. Thus, genes belonging to a given operon in one genome might re-associate in...
Medrano-Soto, Arturo, Moreno-Hagelsieb, Gabriel, Vinuesa, Pablo, Christen, J. Andrés, Collado-Vides, Julio
We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess the selective advantage of imported...
Salgado, Heladia, Gama-Castro, Socorro, Martínez-Antonio, Agustino, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Peralta-Gil, Martín, ...
RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of...
Medrano-Soto, Arturo, Moreno-Hagelsieb, Gabriel, Vinuesa, Pablo, Christen, J. Andrés, Collado-Vides, Julio
We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess the selective advantage of imported...
Medrano-Soto, Arturo, Moreno-Hagelsieb, Gabriel, Vinuesa, Pablo, Christen, J. Andrés, Collado-Vides, Julio
We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess the selective advantage of imported...
With the finished human genome in hand, what next? (2003)
Collado-Vides, Julio, Medrano-Soto, Arturo, Tusié-Luna, Maria
A report on the eighth annual meeting of the Human Genome Organization (HGM2003), Cancun, Mexico, 27-30 April 2003.
González, Víctor, Bustos, Patricia, Ramírez-Romero, Miguel A, Medrano-Soto, Arturo, Salgado, Heladia, Hernández-González, Ismael, ...
Abstract Background Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are...
Gutiérrez-Ríos, Rosa María, Rosenblueth, David A., Loza, José Antonio, Huerta, Araceli M., Glasner, Jeremy D., Blattner, Fred R., ...
The transcriptional network of Escherichia coli may well be the most complete experimentally characterized network of a single cell. A rule-based approach was built to assess the degree of...
Conservation of DNA curvature signals in regulatory regions of prokaryotic genes (2003)
Jáuregui, Ruy, Abreu-Goodger, Cei, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Merino, Enrique
DNA curvature plays a well‐characterized role in many transcriptional regulation mechanisms. We present evidence for the conservation of curvature signals in putative regulatory regions of...
Benítez-Bellón, Esperanza, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio
Abstract Background Sites in DNA that bind regulatory proteins can be detected computationally in various ways. Pattern discovery methods analyze collections of genes suspected to be co-regulated on...
Peter D. Karp, Monica Riley, Milton Saier, Iant. Paulsen, Julio Collado-vides, Suzanne M. Paley, ...
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of E. coli, its enzymes, its transport proteins, and its mechanisms of...
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Collado-Vides, Julio, Paley, Suzanne M., ...
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of...
A powerful non-homology method for the prediction of operons in prokaryotes (2002)
Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio
Motivation: The prediction of the transcription unit organization of genomes is an important clue in the inference of functional relationships of genes, the interpretation and evaluation of...
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Millán-Zárate, Dulce, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, ...
RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers of regulatory elements such...
A Comparative Genomics Approach to Prediction of New Members of Regulons (2001)
Tan, Kai, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Stormo, Gary D.
Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria (2001)
Ramírez-Santos, Jesús, Collado-Vides, Julio, García-Varela, Martin, Gómez-Eichelmann, M. Carmen
The rpoH regulatory region of different members of the enteric bacteria family was sequenced or downloaded from GenBank and compared. In addition, the transcriptional start sites of rpoH of Yersinia...
Strainic, Michael G., Sullivan, Jennifer J., Collado-Vides, Julio, DeHaseth, Pieter L.
The p(R) and p(RM) promoters of bacteriophage lambda direct transcription in divergent directions from start sites separated by 83 phosphodiester bonds. We had previously shown that the presence of...
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads (2000)
Jacques Van Helden, Alma F. Rios, Julio Collado-vides
The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions....
Bayesian Clustering and Prediction in Heterogeneous Data Bases Using Multivariate Mixtures (2000)
J. Andrés Christen, Arturo Medrano-Soto, Julio Collado-Vides, Unidad Morelia, A. P. Xangari, Julio Collado{vides
Based on multivariate mixture models we develop a general approach for clustering and classication. Using various distributions for the variables in the data base to be analyzed, an automatic...
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Millán-Zárate, Dulce, Blattner, Frederick R., Collado-Vides, Julio
RegulonDB is a database on transcription regulation and operon organization in Escherichia coli. The current version describes regulatory signals of transcription initiation, promoters, regulatory...
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads (2000)
Helden, Jacques Van, Rios, Alma. F., Collado-Vides, Julio
The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions....
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12 (2000)
Pérez-Rueda, Ernesto, Collado-Vides, Julio
Using a combination of several approaches we estimated and characterized a total of 314 regulatory DNA-binding proteins in Escherichia coli, which might represent its minimal set of transcription...
Prediction of transcriptional regulatory sites in the complete genome sequence of E.coli (1998)
Thieffry,Denis, Salgado,Heladia, Huerta,Araceli M., Collado-Vides,Julio
RegulonDB: A database on transcriptional regulation (1998)
Huerta,Araceli M., Salgado,Heladia, Thieffry,Denis, Collado-Vides,Julio
Prediction of transcriptional regulatory sites in the complete genome sequence of E.coli (1998)
Thieffry, Denis, Salgado, Heladia, Huerta, Araceli M., Collado-Vides, Julio
RegulonDB: A database on transcriptional regulation (1998)
Huerta, Araceli M., Salgado, Heladia, Thieffry, Denis, Collado-Vides, Julio
RegulonDB: a database on transcriptional regulation in Escherichia coli (1998)
Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-vides
RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli, as well as knowledge on the organization of the genes...
RegulonDB: a database on transcriptional regulation in Escherichia Coli (1998)
Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides
RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli, as well as knowledge on the organization of the genes...
Syntactic recognition of regulatory regions in Escherichia coli (1996)
Rosenblueth, David A., Thieffry, Denis, Huerta, Araceli M., Salgado, Heladia, Collado-Vides, Julio
Motivation One of the most common methodologies identify cis-regulatory sites in regulatory regions in the DNA is that of weight matrices, as testified by several articles this issue. An alternative...
No one questions the important practical contributions of computer sciences to molecular biology. It may well be that one day theoretical contributions also will become useful. One example of this...
Operons in Escherichia coli: Genomic analyses and predictions
Salgado, Heladia, Moreno-Hagelsieb, Gabriel, Smith, Temple F., Collado-Vides, Julio
The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of...
Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria
Ramírez-Santos, Jesús, Collado-Vides, Julio, García-Varela, Martin, Gómez-Eichelmann, M. Carmen
The rpoH regulatory region of different members of the enteric bacteria family was sequenced or downloaded from GenBank and compared. In addition, the transcriptional start sites of rpoH of Yersinia...
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Millán-Zárate, Dulce, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, ...
RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers of regulatory elements such...
Strainic, Michael G., Sullivan, Jennifer J., Collado-Vides, Julio, DeHaseth, Pieter L.
The pR and pRM promoters of bacteriophage lambda direct transcription in divergent directions from start sites separated by 83 phosphodiester bonds. We had previously shown that the presence of an...
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Collado-Vides, Julio, Paley, Suzanne M., ...
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of...
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Millán-Zárate, Dulce, Blattner, Frederick R., Collado-Vides, Julio
RegulonDB is a database on transcription regulation and operon organization in Escherichia coli. The current version describes regulatory signals of transcription initiation, promoters, regulatory...
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
Pérez-Rueda, Ernesto, Collado-Vides, Julio
Using a combination of several approaches we estimated and characterized a total of 314 regulatory DNA-binding proteins in Escherichia coli, which might represent its minimal set of transcription...
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
Helden, Jacques Van, Rios, Alma. F., Collado-Vides, Julio
The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions....
González, Víctor, Bustos, Patricia, Ramírez-Romero, Miguel A, Medrano-Soto, Arturo, Salgado, Heladia, Hernández-González, Ismael, ...
In rhizobia, essential genes for symbiosis are compartmentalized in symbiotic plasmids or in chromosomal symbiotic islands. The complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a...
With the finished human genome in hand, what next?
Collado-Vides, Julio, Medrano-Soto, Arturo, Tusié-Luna, Maria Teresa
A report on the eighth annual meeting of the Human Genome Organization (HGM2003), Cancun, Mexico, 27-30 April 2003.
Conservation of DNA curvature signals in regulatory regions of prokaryotic genes
Jáuregui, Ruy, Abreu-Goodger, Cei, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Merino, Enrique
DNA curvature plays a well-characterized role in many transcriptional regulation mechanisms. We present evidence for the conservation of curvature signals in putative regulatory regions of several...
Salgado, Heladia, Gama-Castro, Socorro, Martínez-Antonio, Agustino, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Peralta-Gil, Martín, ...
RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of...
A Comparative Genomics Approach to Prediction of New Members of Regulons
Tan, Kai, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Stormo, Gary D.
Identifying the complete transcriptional regulatory network for an organism is a major challenge. For each regulatory protein, we want to know all the genes it regulates, that is, its regulon....
Gutiérrez-Ríos, Rosa María, Rosenblueth, David A., Loza, José Antonio, Huerta, Araceli M., Glasner, Jeremy D., Blattner, Fred R., ...
The transcriptional network of Escherichia coli may well be the most complete experimentally characterized network of a single cell. A rule-based approach was built to assess the degree of...
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes
González, Abel D., Espinosa, Vladimir, Vasconcelos, Ana T., Pérez-Rueda, Ernesto, Collado-Vides, Julio
Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (TFs), TFs' binding...
EcoCyc: a comprehensive database resource for Escherichia coli
Keseler, Ingrid M., Collado-Vides, Julio, Gama-Castro, Socorro, Ingraham, John, Paley, Suzanne, Paulsen, Ian T., ...
The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both...
Janga, Sarath Chandra, Collado-Vides, Julio, Moreno-Hagelsieb, Gabriel
Since operons are unstable across Prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. Thus, genes belonging to a given operon in one genome might re-associate in...
Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli
Flores, Margarita, Morales, Lucia, Avila, Agustín, González, Víctor, Bustos, Patricia, García, Delfino, ...
Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually...
Salgado, Heladia, Gama-Castro, Socorro, Peralta-Gil, Martín, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Santos-Zavaleta, Alberto, ...
RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest...
The comprehensive updated regulatory network of Escherichia coli K-12
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Peralta-Gil, Martín, Peñaloza-Spínola, Mónica I, Martínez-Antonio, Agustino, ...
Bacterial regulatory networks are extremely flexible in evolution
Lozada-Chávez, Irma, Janga, Sarath Chandra, Collado-Vides, Julio
Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche...
González, Víctor, Santamaría, Rosa I., Bustos, Patricia, Hernández-González, Ismael, Medrano-Soto, Arturo, Moreno-Hagelsieb, Gabriel, ...
We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium Rhizobium etli. Six large plasmids comprise one-third of the total genome size. The chromosome encodes...
Huerta, Araceli M, Francino, M. Pilar, Morett, Enrique, Collado-Vides, Julio
The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that...
Operons in Escherichia coli: Genomic analyses and predictions
Salgado, Heladia, Moreno-Hagelsieb, Gabriel, Smith, Temple F., Collado-Vides, Julio
The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of...
Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria
Ramírez-Santos, Jesús, Collado-Vides, Julio, García-Varela, Martin, Gómez-Eichelmann, M. Carmen
The rpoH regulatory region of different members of the enteric bacteria family was sequenced or downloaded from GenBank and compared. In addition, the transcriptional start sites of rpoH of Yersinia...
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Millán-Zárate, Dulce, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, ...
RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers of regulatory elements such...
Strainic, Michael G., Sullivan, Jennifer J., Collado-Vides, Julio, DeHaseth, Pieter L.
The pR and pRM promoters of bacteriophage lambda direct transcription in divergent directions from start sites separated by 83 phosphodiester bonds. We had previously shown that the presence of an...
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Collado-Vides, Julio, Paley, Suzanne M., ...
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of...
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Millán-Zárate, Dulce, Blattner, Frederick R., Collado-Vides, Julio
RegulonDB is a database on transcription regulation and operon organization in Escherichia coli. The current version describes regulatory signals of transcription initiation, promoters, regulatory...
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
Pérez-Rueda, Ernesto, Collado-Vides, Julio
Using a combination of several approaches we estimated and characterized a total of 314 regulatory DNA-binding proteins in Escherichia coli, which might represent its minimal set of transcription...
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
Helden, Jacques Van, Rios, Alma. F., Collado-Vides, Julio
The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions....
González, Víctor, Bustos, Patricia, Ramírez-Romero, Miguel A, Medrano-Soto, Arturo, Salgado, Heladia, Hernández-González, Ismael, ...
In rhizobia, essential genes for symbiosis are compartmentalized in symbiotic plasmids or in chromosomal symbiotic islands. The complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a...
With the finished human genome in hand, what next?
Collado-Vides, Julio, Medrano-Soto, Arturo, Tusié-Luna, Maria Teresa
A report on the eighth annual meeting of the Human Genome Organization (HGM2003), Cancun, Mexico, 27-30 April 2003.
Conservation of DNA curvature signals in regulatory regions of prokaryotic genes
Jáuregui, Ruy, Abreu-Goodger, Cei, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Merino, Enrique
DNA curvature plays a well-characterized role in many transcriptional regulation mechanisms. We present evidence for the conservation of curvature signals in putative regulatory regions of several...
Salgado, Heladia, Gama-Castro, Socorro, Martínez-Antonio, Agustino, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Peralta-Gil, Martín, ...
RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of...
A Comparative Genomics Approach to Prediction of New Members of Regulons
Tan, Kai, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Stormo, Gary D.
Identifying the complete transcriptional regulatory network for an organism is a major challenge. For each regulatory protein, we want to know all the genes it regulates, that is, its regulon....
Gutiérrez-Ríos, Rosa María, Rosenblueth, David A., Loza, José Antonio, Huerta, Araceli M., Glasner, Jeremy D., Blattner, Fred R., ...
The transcriptional network of Escherichia coli may well be the most complete experimentally characterized network of a single cell. A rule-based approach was built to assess the degree of...
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes
González, Abel D., Espinosa, Vladimir, Vasconcelos, Ana T., Pérez-Rueda, Ernesto, Collado-Vides, Julio
Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (TFs), TFs' binding...
EcoCyc: a comprehensive database resource for Escherichia coli
Keseler, Ingrid M., Collado-Vides, Julio, Gama-Castro, Socorro, Ingraham, John, Paley, Suzanne, Paulsen, Ian T., ...
The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both...
Janga, Sarath Chandra, Collado-Vides, Julio, Moreno-Hagelsieb, Gabriel
Since operons are unstable across Prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. Thus, genes belonging to a given operon in one genome might re-associate in...
Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli
Flores, Margarita, Morales, Lucia, Avila, Agustín, González, Víctor, Bustos, Patricia, García, Delfino, ...
Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually...
Salgado, Heladia, Gama-Castro, Socorro, Peralta-Gil, Martín, Díaz-Peredo, Edgar, Sánchez-Solano, Fabiola, Santos-Zavaleta, Alberto, ...
RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest...
The comprehensive updated regulatory network of Escherichia coli K-12
Salgado, Heladia, Santos-Zavaleta, Alberto, Gama-Castro, Socorro, Peralta-Gil, Martín, Peñaloza-Spínola, Mónica I, Martínez-Antonio, Agustino, ...
González, Víctor, Santamaría, Rosa I., Bustos, Patricia, Hernández-González, Ismael, Medrano-Soto, Arturo, Moreno-Hagelsieb, Gabriel, ...
We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium Rhizobium etli. Six large plasmids comprise one-third of the total genome size. The chromosome encodes...
Bacterial regulatory networks are extremely flexible in evolution
Lozada-Chávez, Irma, Janga, Sarath Chandra, Collado-Vides, Julio
Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche...
Huerta, Araceli M, Francino, M. Pilar, Morett, Enrique, Collado-Vides, Julio
The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that...
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes
Pérez, Abel González, Angarica, Vladimir Espinosa, Vasconcelos, Ana Tereza R., Collado-Vides, Julio
The version 2.0 of Tractor_DB is now accessible at its three international mirrors: , and . This database contains a collection of computationally predicted Transcription Factors' binding sites in...
Gutierrez-Ríos, Rosa María, Freyre-Gonzalez, Julio A, Resendis, Osbaldo, Collado-Vides, Julio, Saier, Milton, Gosset, Guillermo
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
Rodríguez-Penagos, Carlos, Salgado, Heladia, Martínez-Flores, Irma, Collado-Vides, Julio
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli
Resendis-Antonio, Osbaldo, Reed, Jennifer L, Encarnación, Sergio, Collado-Vides, Julio, Palsson, Bernhard Ø
Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific...
Janga, Sarath Chandra, Salgado, Heladia, Martínez-Antonio, Agustino, Collado-Vides, Julio
The active and inactive state of transcription factors in growing cells is usually directed by allosteric physicochemical signals or metabolites, which are in turn either produced in the cell or...
Multidimensional annotation of the Escherichia coli K-12 genome
Karp, Peter D., Keseler, Ingrid M., Shearer, Alexander, Latendresse, Mario, Krummenacker, Markus, Paley, Suzanne M., ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...
Gama-Castro, Socorro, Jiménez-Jacinto, Verónica, Peralta-Gil, Martín, Santos-Zavaleta, Alberto, Peñaloza-Spinola, Mónica I., Contreras-Moreira, Bruno, ...
RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known...
González Pérez, Abel D, González González, Evelyn, Espinosa Angarica, Vladimir, Vasconcelos, Ana Tereza R, Collado-Vides, Julio
Arturo Medrano-Soto, J.Andres Christen, Julio Collado-vides
Based on mixture models, we present a Bayesian method (called BClass) to classify biological entities (e.g. genes) when variables of quite heterogeneous nature are analyzed. Various statistical...
Prediction of TF target sites based on atomistic models of protein-DNA complexes
Angarica, Vladimir Espinosa, Pérez, Abel González, Vasconcelos, Ana T, Collado-Vides, Julio, Contreras-Moreira, Bruno
Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes
Janga, Sarath Chandra, Collado-Vides, Julio, Babu, M. Madan
Genetic material in eukaryotes is tightly packaged in a hierarchical manner into multiple linear chromosomes within the nucleus. Although it is known that eukaryotic transcriptional regulation is...
Lemmens, Karen, De Bie, Tijl, Dhollander, Thomas, De Keersmaecker, Sigrid C, Thijs, Inge M, Schoofs, Geert, ...
DISTILLER, a data integration framework for the inference of transcriptional module networks, is presented and used to investigate the condition dependency and modularity in Escherichia coli networks.
EcoCyc: A comprehensive view of Escherichia coli biology
Keseler, Ingrid M., Bonavides-Martínez, César, Collado-Vides, Julio, Gama-Castro, Socorro, Gunsalus, Robert P., Johnson, D. Aaron, ...
EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the...
Bioinformatics Resources for the Study of Gene Regulation in Bacteria▿
Collado-Vides, Julio, Salgado, Heladia, Morett, Enrique, Gama-Castro, Socorro, Jiménez-Jacinto, Verónica, Martínez-Flores, Irma, ...
Regulation by transcription factors in bacteria: beyond description
Balleza, Enrique, López-Bojorquez, Lucia N, Martínez-Antonio, Agustino, Resendis-Antonio, Osbaldo, Lozada-Chávez, Irma, Balderas-Martínez, Yalbi I, ...
Transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. By precisely tuning gene expression, transcriptional...
González Pérez, Abel, Espinosa Angarica, Vladimir, Collado-Vides, Julio, Vasconcelos, Ana Tereza Ribeiro
Mendoza-Vargas, Alfredo, Olvera, Leticia, Olvera, Maricela, Grande, Ricardo, Vega-Alvarado, Leticia, Taboada, Blanca, ...
Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding of the...
Freyre-González, Julio A, Alonso-Pavón, José A, Treviño-Quintanilla, Luis G, Collado-Vides, Julio
The E. coli transcriptional regulatory network is shown to have a nonpyramidal architecture of independent modules governed by transcription factors, whose responses are integrated by intermodular...