A5091338305- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Biomedical Text Mining and Ontologies
- Salmonella and Campylobacter epidemiology
- Genomics and Chromatin Dynamics
- Vibrio bacteria research studies
- Evolution and Genetic Dynamics
- Gene expression and cancer classification
- Advanced Data Storage Technologies
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- Semantic Web and Ontologies
- Escherichia coli research studies
- Legume Nitrogen Fixing Symbiosis
- Protist diversity and phylogeny
- Diffusion and Search Dynamics
- DNA and Biological Computing
- Cell Image Analysis Techniques
- Enzyme Structure and Function
- Scientific Computing and Data Management
Universidad Nacional Autónoma de México
2013-2024
Center for Genomic Science
2005-2020
Universidad Autónoma del Estado de Morelos
2008-2013
Max Planck Institute for Molecular Genetics
2010
Université Libre de Bruxelles
2010
European Bioinformatics Institute
2010
Wellcome Trust
2010
SRI International
2006
RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates scattered scientific knowledge best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts data. Its electronic format enables researchers to compare their results with legacy previous supports bioinformatics tools model building. Here, we summarize our progress since last Nucleic Acids Research publication describing...
RegulonDB ( http://regulondb.ccg.unam.mx/ ) is the primary reference database offering curated knowledge of transcriptional regulatory network Escherichia coli K12, currently best-known electronically encoded genetic any free-living organism. This paper summarizes improvements, new biology and features available in version 6.0. Curation original literature is, from now on, up to date for every release. All objects are supported by their corresponding evidences, classified as strong or weak....
This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date knowledge from published literature regarding transcriptional regulation in Escherichia coli K-12. maintained and expanded curation efforts to improve breadth quality of encoded experimental knowledge, we implemented criteria for computational predictions. Regulatory phrases now provide high-level descriptions regulatory regions. assignment various sources...
RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge regulatory network and operon organization. It currently largest electronically-encoded any free-living organism. We present here recently launched version 5.0 radically different in content, interface design capabilities. Continuous curation original scientific literature provides evidence behind every single object feature. This complemented with comprehensive computational...
RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation Escherichia coli K-12 with decades knowledge from classic molecular biology experiments, and recently also high-throughput genomic methodologies. We curated the literature to keep RegulonDB up date, initiated curation ChIP gSELEX experiments. estimate that current describes between 10% 30% expected total number factor- gene regulatory interactions in E. coli. provides...
RegulonDB ( http://regulondb.ccg.unam.mx/ ) is the primary reference database of best-known regulatory network any free-living organism, that Escherichia coli K-12. The major conceptual change since 3 years ago an expanded biological context so transcriptional regulation now part a unit initiates with signal and continues transduction to core regulation, modifying expression affected target genes responsible for response. We call these genetic sensory response units, or Gensor Units. have...
Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding the regulatory circuits that control gene expression this model organism. RegulonDB (http://regulondb.ccg.unam.mx/) is aimed at integrating genetic network E. K12 as an entirely bioinformatic project up till now. In work, we extended aims by generating experimental data genome scale on TSSs, promoters and...
Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying different players define gene regulation, particularly regulation transcription initiation and operon organization. These are available in public repositories, such as Gene Expression Omnibus, or ArrayExpress. However, accessing navigating wealth data is not straightforward. No resource currently exists offers all high low-throughput on transcriptional
The rich knowledge of operon organization in Escherichia coli , together with the completed chromosomal sequence this bacterium, enabled us to perform an analysis distances between genes and functional relationships adjacent same operon, as opposed different transcription units. We measured demonstrated expected tendencies within operons have much shorter intergenic than at borders A clear peak short contrasts a flat frequency distribution Also, tend physiological class. results these...
RegulonDB is the primary database of major international maintained curation original literature with experimental knowledge about elements and interactions network transcriptional regulation in Escherichia coli K‐12. This includes mechanistic information operon organization their decomposition into transcription units (TUs), promoters σ type, binding sites specific regulators (TRs), 'regulatory phrases', active inactive conformations TRs, as well terminators ribosome sites. The complemented...
RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers regulatory elements such as promoters, binding sites terminators. complete repertoire known predicted DNA-binding transcriptional regulators can be considered to included this version. now distinguishes different allosteric conformations proteins indicating the one active regulating promoters. A new set predictions been...
RegulonDB is a database that contains the most comprehensive corpus of knowledge regulation transcription initiation Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper 2019. We explain changes to satisfy FAIR requirements. also present full reconstruction computational infrastructure, which has significantly improved storage, retrieval accessibility thus supports more...
LeuO is a LysR-type transcriptional regulator that has been implicated in the bacterial stringent response and virulence of Salmonella. A genomic analysis with Salmonella enterica serovar Typhi revealed positive OmpS1, OmpS2, AssT, STY3070. In contrast, down-regulated expression OmpX, Tpx, STY1978. Transcriptional fusions supported negative regulation. Expression ompS1, assT, STY3070 was induced an hns mutant, consistent notion H-NS represses these genes; activity lower for tpx STY1978...
Position-specific scoring matrices (PSSMs) are routinely used to predict transcription factor (TF)-binding sites in genome sequences. However, their reliability novel binding can be far from optimum, due the use of a small number training or inappropriate choice parameters when building matrix scanning sequences with it. Measures quality such as E -value and information content rely on theoretical models, may fail context full We propose method, implemented program 'matrix-quality', that...
The evolution of bacterial pathogenicity, heavily influenced by horizontal gene transfer, provides new virulence factors and regulatory connections that alter phenotypes. Salmonella pathogenicity islands 1 2 (SPI-1 SPI-2) are chromosomal regions were acquired at different evolutionary times essential for virulence. In the intestine mammalian hosts, expresses SPI-1 genes mediate its invasion to gut epithelium. Once inside cells, down-regulates induces expression SPI-2 genes, which favor...
Abstract MOTIVATION: As one of the best-characterized free-living organisms, Escherichia coli and its recently completed genomic sequence offer a special opportunity to exploit systematically variety regulatory data available in literature order make comprehensive set predictions whole genome. RESULTS: The complete genome E.coli was analyzed for binding transcriptional regulators upstream coding sequences. biological information contained RegulonDB (Huerta, A.M. et al., Nucleic Acids...
Transcription factors (TFs) are the key elements responsible for controlling expression of genes in bacterial genomes and when visualized on a genomic scale form dense network transcriptional interactions among themselves with other protein coding genes. Although structure regulatory networks (TRNs) is well understood, it not clear what constrains govern them. Here, we explore this question using TRNs model prokaryotes provide link between hierarchy regulons their genome organization. We...
Our understanding of the regulation gene expression has benefited from availability high-throughput technologies that interrogate whole genome for binding specific transcription factors and profiles. In case widely used model organisms, such as Escherichia coli K-12, new knowledge gained these approaches needs to be integrated with legacy accumulated genetic molecular biology experiments conducted in pre-genomic era order attain deepest level possible based on available data.In this paper,...
RegulonDB is a database on transcription regulation and operon organization in Escherichia coli. The current version describes regulatory signals of initiation, promoters, binding sites specific regulators, ribosome terminators, as well information genes clustered operons. These annotations have been gathered from constant search the literature, based computational sequence predictions. genomic coordinates all these objects E.coli K-12 chromosome are clearly indicated. Every known object has...
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 a state-of-the-art Natural Language Processing system that creates computer-readable networks regulatory interactions directly from different collections abstracts full-text papers. Our major aim to understand how automatic annotation using Text-Mining techniques can complement manual databases. We implemented rule-based...
Post-genomic implementations have expanded the experimental strategies to identify elements involved in regulation of transcription initiation. Here, we present for first time a detailed analysis sources knowledge supporting collection transcriptional regulatory interactions (RIs)
The small RNAs CsrB and CsrC of Salmonella indirectly control the expression numerous genes encoding widespread cellular functions, including virulence. csrB csrC genes, which are located in different chromosomal regions, is coordinated by positive transcriptional mediated two-component regulatory system BarA/SirA. Here, we identified computational analysis an 18-bp inverted repeat (IR) sequence far upstream from promoter enterica serovar Typhimurium genes. Deletion site-directed mutagenesis...