ArticleMolecular systems biology2015
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.
Article in Molecular systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed.
- The phenotypic landscape of the model firmicuteProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Large-scale, interpretable gene regulatory network inference through biologically informed matrix factorization.bioRxiv : the preprint server for biology · 2026Article
- Article
- Gene regulatory network determinants of rapid recall in human memory CD4Cell reports · 2026Article
- Resistance and germination of spores ofJournal of bacteriology · 2025Article
- Real-time nanoscale investigation of spore coat assembly in Bacillus subtilis.Communications biology · 2025Article
- MdfA is a novel ClpC adaptor protein that functions in the developingGenes & development · 2025Article
- Augusta: From RNA-Seq to gene regulatory networks and Boolean models.Computational and structural biotechnology journal · 2024Article
- Transcriptome data are insufficient to control false discoveries in regulatory network inference.Cell systems · 2024Article
- Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana.Bioinformatics (Oxford, England) · 2024Article
- PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization.Genome biology · 2024Article
- SpoVAF and FigP assemble into oligomeric ion channels that enhance spore germination.Genes & development · 2024Article
- Spore germination: Two ion channels are better than one.Genes & development · 2024Article
- Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.Genome biology · 2024Article
- Bacillus subtilis NrnB is expressed during sporulation and acts as a unique 3'-5' exonuclease.Nucleic acids research · 2023Article
- Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression.bioRxiv : the preprint server for biology · 2023Article
- Extensive cellular multi-tasking withinmSystems · 2023Article
- New Thoughts on an Old Topic: Secrets of Bacterial Spore Resistance Slowly Being Revealed.Microbiology and molecular biology reviews : MMBR · 2023Review
- EnsInfer: a simple ensemble approach to network inference outperforms any single method.BMC bioinformatics · 2023Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
Abstract
Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism-environment interactions, and difficulty of estimating the activity of regulatory factors. Taking advantage of the large number of known regulatory interactions in Bacillus subtilis and two transcriptomics datasets (including one with 38 separate experiments collected specifically for this study), we use a new combination of network component analysis and model selection to simultaneously estimate transcription factor activities and learn a substantially expanded transcriptional regulatory network for this bacterium. In total, we predict 2,258 novel regulatory interactions and recall 74% of the previously known interactions. We obtained experimental support for 391 (out of 635 evaluated) novel regulatory edges (62% accuracy), thus significantly increasing our understanding of various cell processes, such as spore formation.
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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.