ArticlePLoS computational biology2024
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
15 citing papers in PubMed.
- Transcriptional regulatory network differences between six industrialMetabolic engineering communications · 2026Article
- Review
- iModulonMiner 2.0: multi-modality modularization of prokaryotic bulk, single-cell, and community omics data.Nucleic acids research · 2026Article
- Article
- Disentangling factors affecting bacterial transcriptional regulatory network inference.iScience · 2026Article
- A systems-level atlas of carbon-response transcriptional states inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Revealing transcriptomic responses inmSystems · 2026Article
- Dissecting host stress responses for predictable heterologous gene expression in E. coli.Nucleic acids research · 2026Article
- The transcriptional regulatory network of the Escherichia coli MG1655 reference strain.Nucleic acids research · 2026Article
- Unraveling proteomic chaos by independent component analysis-ClpX proficiency promotes the iron and oxygen limitation responses ofmSystems · 2025Article
- Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa.NPJ systems biology and applications · 2025Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- Deciphering the proteome ofComputational and structural biotechnology journal · 2025Article
- Predicting fitness inFrontiers in tuberculosis · 2025Article
- Diversity of Transcriptional Regulatory Adaptation in E. coli.Molecular biology and evolution · 2024Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications. As a demonstration, we applied this workflow to generate the iModulon structure of Bacillus subtilis using all high-quality, publicly-available RNA-seq data. Using this structure, we predicted regulatory interactions for multiple transcription factors, identified groups of co-expressed genes that are putatively regulated by undiscovered transcription factors, and predicted properties of a recently discovered single-subunit phage RNA polymerase. We also present a Python package, PyModulon, with functions to characterize, visualize, and explore computed iModulons. The pipeline, available at https://github.com/SBRG/iModulonMiner, can be readily applied to diverse organisms to gain a rapid understanding of their transcriptional regulatory network structure and condition-specific activity.
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Registered trials
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.