ArticlemSystems2022
Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 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
- Revealing transcriptomic responses inmSystems · 2026Article
- How Klebsiella pneumoniae controls its virulence.PLoS pathogens · 2025Review
- Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Improving prediction of bacterial sRNA regulatory targets with expression data.NAR genomics and bioinformatics · 2025Article
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- iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets.Nucleic acids research · 2025Article
- iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.PLoS computational biology · 2024Article
- Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches.PLoS genetics · 2024Article
- Machine learning reveals the transcriptional regulatory network and circadian dynamics ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders.Bioinformatics advances · 2024Article
- Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell reports · 2023Article
- Independent Component Analysis Reveals the Transcriptional Regulatory Modules inInternational journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes. By decomposing a compendia of RNA sequencing (RNA-seq) data with independent component analysis, we obtained 400 independently modulated sets of genes, called iModulons. We (i) performed pan-genome analysis of the phylogroup structure of
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Registered trials
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