ArticlemSystems2025
Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase.
Article in mSystems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients.Molecular systems biology · 2026Article
- FTIR-ATR monitoring of growth-phase-dependent spectral responses ofRSC advances · 2026Article
- Revealing transcriptomic responses inmSystems · 2026Article
- The biophysical properties of the bacterial nucleoid are dynamic, heterogeneous, and responsive to perturbations of cellular processes.bioRxiv : the preprint server for biology · 2026Article
- The transcriptional regulatory network of the Escherichia coli MG1655 reference strain.Nucleic acids research · 2026Article
- Termination of DNA replication drives genomic instability via multiple mechanisms.Nucleic acids research · 2026Article
- Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies.PloS one · 2026Article
- Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.World journal of microbiology & biotechnology · 2025Review
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With IMPORTANCE: Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.
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Registered trials
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