ArticleCell2022
Fundamental behaviors emerge from simulations of a living minimal cell.
Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
What it found
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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
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
83 citing papers in PubMed, 1 synthesis or guideline pooled it, 154 citations in OpenAlex.
- Principles for Rigorous Design and Application of Synthetic Microbial Communities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Pooled it
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
- Review
- The physicochemical design, structure and permeability of the JCVI-syn3A minimal cell membrane.Nature communications · 2026Article
- Artificial "zombie" cells: An emerging platform for targeted drug delivery and disease treatment.Acta pharmaceutica Sinica. B · 2026Review
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Predicting human mRNA isoform levels from site-specific splicing kineticsbioRxiv : the preprint server for biology · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
- Chromosome segregation in a minimal bacterial cell driven by SMC protein complexes.Protein science : a publication of the Protein Society · 2026Article
- Efficiency, accuracy and robustness of probability generating function based parameter inference method for stochastic biochemical reactions.PLoS computational biology · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities.Briefings in bioinformatics · 2026Review
- Discreteness, Computation, and Rules of Life for Self-Organization Dynamics Beyond Equilibrium.Newton ((New York, N.Y.) · 2026Article
- 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
- Synthetic rewriting technologies in mammalian cells.Nature communications · 2026Review
- Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.The journal of physical chemistry. B · 2026Article
- From Atoms to Cells: AI-Based Structure Prediction Fueling Molecular Dynamics Simulations in Computational Structural Biology.Advances in experimental medicine and biology · 2026Review
- The Beckman legacy and the future of interdisciplinary research.Journal of the Royal Society, Interface · 2025Article
- Construction of complex bacteriogenic protocells from living material assembly.Nature protocols · 2025Review
- Metabolism-dependent succinylation governs resource allocation for antibiotic resistance.Science advances · 2025Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
Abstract
We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.
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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.