ArticleNucleic acids research2016
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers, 1 of them a synthesis that pooled it.
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Who cites it
244 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of Boolean network models reveals design principles of gene regulatory networks.Science advances · 2024Pooled it
- Gut bacteria and their metabolites may influence our decisions, intelligence, cognition, and consciousness.Gut microbes · 2026Review
- Bacterial Sentience Is Determined by the Stochastic, Chaotic, and Deterministic Behavior of Cytoplasmic Particles.Current issues in molecular biology · 2026Review
- Programmable, multiplexed and orthogonal gene control in bacteria with attenuated Cas13d systems.Nature biotechnology · 2026Article
- HSTXGB: a hyperparameter self-tuning XGBoost method integrating pre- and post-processing for gene regulatory network inference.Frontiers in genetics · 2026Article
- The EcoCyc database (2025).EcoSal Plus · 2025Review
- Article
- DNA methylation affects gene expression but not global chromatin structure inJournal of bacteriology · 2025Article
- High-resolution mapping of sigma factor DNA-binding sequences using artificial promoters, RNA aptamers, and deep sequencing.Nucleic acids research · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Symmetries in metabolic networks ofPNAS nexus · 2025Article
- ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0.Database : the journal of biological databases and curation · 2025Article
- Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE.PloS one · 2025Article
- The emergence and evolution of gene expression in genome regions replete with regulatory motifs.eLife · 2024Article
- k- Strong Inference Algorithm: A Hybrid Information Theory Based Gene Network Inference Algorithm.Molecular biotechnology · 2024Article
- Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate ofmSphere · 2024Article
- iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model.BMC bioinformatics · 2024Article
- msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths.BMC biology · 2024Article
- CRISPR-Cas tools for simultaneous transcription & translation control in bacteria.Nucleic acids research · 2024Article
- iPro2L-DG: Hybrid network based on improved densenet and global attention mechanism for identifying promoter sequences.Heliyon · 2024Article
184 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors.
Funding
Abstract
RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates the scattered scientific knowledge of the best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts of data. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Here, we summarize our progress with RegulonDB since our last Nucleic Acids Research publication describing RegulonDB, in 2013. In addition to maintaining curation up-to-date, we report a collection of 232 interactions with small RNAs affecting 192 genes, and the complete repertoire of 189 Elementary Genetic Sensory-Response units (GENSOR units), integrating the signal, regulatory interactions, and metabolic pathways they govern. These additions represent major progress to a higher level of understanding of regulated processes. We have updated the computationally predicted transcription factors, which total 304 (184 with experimental evidence and 120 from computational predictions); we updated our position-weight matrices and have included tools for clustering them in evolutionary families. We describe our semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for 'neighborhood' genes to known operons and regulons, and computational developments.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.