ArticleNPJ systems biology and applications2022
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control.
Article in NPJ systems biology and applications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 45 citations in OpenAlex.
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research.Nature communications · 2026Review
- Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational ModiBications under Light Disturbance.bioRxiv : the preprint server for biology · 2026Article
- The EcoCyc database (2025).EcoSal Plus · 2025Review
- Review
- Mechanistic modeling of cell viability assays with in silico lineage tracing.PLoS computational biology · 2025Article
- A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations.PLoS computational biology · 2025Article
- (p)ppGpp-mediated GTP homeostasis ensures survival and antibiotic tolerance of Staphylococcus aureus.Communications biology · 2025Article
- (p)ppGpp mediates persister formation inFrontiers in microbiology · 2025Article
- Predicting fitness inFrontiers in tuberculosis · 2025Article
- How to build the virtual cell with artificial intelligence: Priorities and opportunities.Cell · 2024Article
- How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.ArXiv · 2024Article
- Engineering is evolution: a perspective on design processes to engineer biology.Nature communications · 2024Article
- Article
- Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons.Cell systems · 2024Article
- The EcoCyc Database (2023).EcoSal Plus · 2023Review
- Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis.Nucleic acids research · 2023Article
- Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses.PLoS computational biology · 2023Article
- Bridging the gap between mechanistic biological models and machine learning surrogates.PLoS computational biology · 2023Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Growth and environmental responses are essential for living organisms to survive and adapt to constantly changing environments. In order to simulate new conditions and capture dynamic responses to environmental shifts in a developing whole-cell model of E. coli, we incorporated additional regulation, including dynamics of the global regulator guanosine tetraphosphate (ppGpp), along with dynamics of amino acid biosynthesis and translation. With the model, we show that under perturbed ppGpp conditions, small molecule feedback inhibition pathways, in addition to regulation of expression, play a role in ppGpp regulation of growth. We also found that simulations with dysregulated amino acid synthesis pathways provide average amino acid concentration predictions that are comparable to experimental results but on the single-cell level, concentrations unexpectedly show regular fluctuations. Additionally, during both an upshift and downshift in nutrient availability, the simulated cell responds similarly with a transient increase in the mRNA:rRNA ratio. This additional simulation functionality should support a variety of new applications and expansions of the E. coli Whole-Cell Modeling Project.
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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.