ArticleCell2012
A whole-cell computational model predicts phenotype from genotype.
Article in Cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 570 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
570 citing papers in PubMed.
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
- Protein-Ratio Rheostats: Integrating Stoichiometry, Abundance, and Binding Affinity in Cellular Function.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
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- Multiscale modeling primer: Focus on chromatin and epigenetics.The Journal of biological chemistry · 2026Review
- Artificial intelligence virtual bone organoids (AIVBOs).Journal of orthopaedic translation · 2026Review
- Virtual cells: progress and challenges from mechanistic modeling to data-driven integration.Briefings in bioinformatics · 2026Review
- Towards predictive virtual embryos with genomics and AI.Nature methods · 2026Article
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Article
- Synthesizing Mechanistic Hypotheses from Single-Cell Omics via Discretized Feature Attribution and Empirical Language Model Grounding.bioRxiv : the preprint server for biology · 2026Article
- Artificial intelligence virtual extracellular vesicles (AIVEVs).Bioactive materials · 2026Review
- Towards the construction of a virtual yeast.Nature · 2026Review
- Elucidating the Bell-Shaped Dependence of Protein Translation Activity on EF-Tu Concentration in a Reconstituted Cell-Free System Using a Mechanistic Model.ACS synthetic biology · 2026Article
- Patient-specific modeling of G2/M cell cycle dynamics reveals prognostic dynamical regimes driven by copy number alterations.NPJ systems biology and applications · 2026Article
- Generative machine learning unlocks the first proteome-wide image of human cells.bioRxiv : the preprint server for biology · 2026Article
- Bacterial gene regulatory neural network as a biocomputing library of mathematical solvers.NPJ systems biology and applications · 2026Article
- Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research.Nature communications · 2026Review
- Artificial Intelligence Virtual Organoids (AIVOs).Bioactive materials · 2026Review
- Revisiting the blueprint for an interpretable virtual cell.Nature reviews. Genetics · 2026Article
510 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
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- Commented on byLife, simulated.2012
Authors and funding
9 authors.
Funding
Abstract
Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.
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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.