Publications by authors named "Pablo Pena-Loredo"
RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of 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 of 2019. We explain the changes to satisfy FAIR requirements.
View Article and Find Full Text PDFGenomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward.
View Article and Find Full Text PDFArticle Synopsis
- RegulonDB is a detailed online resource launched 20 years ago that tracks transcription regulation in E. coli K-12, using historical molecular biology and recent genomic data.
- It curates research literature and includes data from ChIP and gSELEX experiments, estimating that only 10% to 30% of the gene regulatory interactions in E. coli are currently known.
- The platform features a JBrowse for visualizing datasets, a Microbial Conditions Ontology for experiment reproducibility, and analyzes Genetic Sensory-Response Units for transcription factors, enhancing its biocuration with natural language processing techniques.