ArticleNucleic acids research2021
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
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Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing.ACS synthetic biology · 2024Pooled it
- Profiling large-scale protein occupancy on bacterial genomes using IPOD-HR.Nature protocols · 2026Review
- Regulatory cascade of NdpR and NdpR2 in controlling nicotine degradation operons inApplied and environmental microbiology · 2026Article
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- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Regulatory and metabolic control of microbial biosynthetic gene clusters.Communications biology · 2026Review
- Metab8D: a metabolic regulome network from multiomics and machine learning.Communications biology · 2026Article
- Article
- Transcript-Capture sequencing enriches mRNA ofNAR molecular medicine · 2026Article
- Staphylococcus aureus fatty acid metabolism governs saeRS-mediated aggregation in joint infections.Nature communications · 2025Article
- Integrated genomic-transcriptomic analysis of clavulanic acid production in differentially productive Streptomyces clavuligerus strains.Scientific reports · 2025Article
- Differences in GenBank and RefSeq annotations may affect genomics data interpretation formSphere · 2025Article
- Transcript-Capture sequencing enriches mRNA ofbioRxiv : the preprint server for biology · 2025Article
- Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning.Nucleic acids research · 2025Article
- Predicting input signals of transcription factors in Escherichia coli.Molecular systems biology · 2025Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- A transcriptional plasticity-aware framework for RNA-seq differential expression analysis.Briefings in bioinformatics · 2025Article
- Congruence between noise and plasticity in protein expression.Scientific reports · 2025Article
- Thermally adapted Escherichia coli keeps transcriptomic response during temperature upshift exposure.Applied microbiology and biotechnology · 2025Article
- Genetic properties underlying transcriptional variability across different perturbations.Nature communications · 2025Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their association to known genetic regulators. By grouping and analyzing genes based on observations from big data alone, iModulons can provide a novel perspective into how the composition of the transcriptome adapts to environmental conditions. Here, we present iModulonDB (imodulondb.org), a knowledgebase of prokaryotic transcriptional regulation computed from high-quality transcriptomic datasets using ICA. Users select an organism from the home page and then search or browse the curated iModulons that make up its transcriptome. Each iModulon and gene has its own interactive dashboard, featuring plots and tables with clickable, hoverable, and downloadable features. This site enhances research by presenting scientists of all backgrounds with co-expressed gene sets and their activity levels, which lead to improved understanding of regulator-gene relationships, discovery of transcription factors, and the elucidation of unexpected relationships between conditions and genetic regulatory activity. The current release of iModulonDB covers three organisms (Escherichia coli, Staphylococcus aureus and Bacillus subtilis) with 204 iModulons, and can be expanded to cover many additional organisms.
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