ArticleEcoSal Plus2021
The E. coli Whole-Cell Modeling Project.
Article in EcoSal Plus, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- A novel ψ-χ fusion protein for unravelling the contributions of χ to DNA replication and repair.Nucleic acids research · 2026Article
- Comparative analysis of gene importance inmSystems · 2026Article
- Virtual cell: Current perspectives and future prospects.The Journal of international medical research · 2026Review
- A NovelbioRxiv : the preprint server for biology · 2026Article
- Resolving emergent transient oscillations in gene circuits with a growth-coupled model.Science advances · 2026Article
- The EcoCyc database (2025).EcoSal Plus · 2025Review
- An empirical model of aminoacylation kinetics for E. coli class I and II aminoacyl tRNA synthetases.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
- Challenges and opportunities for digital twins in precision medicine from a complex systems perspective.NPJ digital medicine · 2025Review
- Challenging a decades-old paradigm: ProB and ProA do not channel the unstable intermediate in proline synthesis after all.Proceedings of the National Academy of Sciences of the United States of America · 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
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- 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
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology.Microbial biotechnology · 2022Article
- Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges.Frontiers in bioengineering and biotechnology · 2022Article
- A forecast for large-scale, predictive biology: Lessons from meteorology.Cell systems · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The Escherichia coli whole-cell modeling project seeks to create the most detailed computational model of an E. coli cell in order to better understand and predict the behavior of this model organism. Details about the approach, framework, and current version of the model are discussed. Currently, the model includes the functions of 43% of characterized genes, with ongoing efforts to include additional data and mechanisms. As additional information is incorporated in the model, its utility and predictive power will continue to increase, which means that discovery efforts can be accelerated by community involvement in the generation and inclusion of data. This project will be an invaluable resource to the E. coli community that could be used to verify expected physiological behavior, to predict new outcomes and testable hypotheses for more efficient experimental design iterations, and to evaluate heterogeneous data sets in the context of each other through deep curation.
Indexed as
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What OpenQuestion holds
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.