ArticleBiophysical journal1997
A general computational framework for modeling cellular structure and function.
Article in Biophysical journal, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers.
What it found
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Who cites it
121 citing papers in PubMed.
- Mechanistic machine learning for prediction of prime editing outcomes.Nature biotechnology · 2026Article
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- Practical quantification of immunohistochemistry antigen concentrations and reaction-diffusion parameters.bioRxiv : the preprint server for biology · 2026Article
- Mechanistic machine learning enables interpretable and generalizable prediction of prime editing outcomes.bioRxiv : the preprint server for biology · 2026Article
- Systems-level consequences of low RAF abundance for EGFR-ERK signaling.Biophysical journal · 2026Article
- GBA Solver: a user-friendly web server for growth balance analysis.Bioinformatics (Oxford, England) · 2025Article
- Resistance and germination of spores ofJournal of bacteriology · 2025Article
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.bioRxiv : the preprint server for biology · 2025Article
- Article
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- Protein interactions, calcium, phosphorylation, and cholesterol modulate CFTR cluster formation on membranes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SYK negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy.Journal of immunology (Baltimore, Md. : 1950) · 2025Article
- Article
- Leveraging public AI tools to explore systems biology resources in mathematical modeling.NPJ systems biology and applications · 2025Article
- Dynamics of homeostats: the basis of electrical, chemical, hydraulic, pH and calcium signaling in plants.Quantitative plant biology · 2025Review
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- Role of intercellular interactions on single cell and population level responses: considerations for multicellular bioreporter design.Frontiers in molecular biosciences · 2025Article
- A noncanonical GTPase signaling mechanism controls exit from mitosis in budding yeast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Reaction-diffusion modeling provides insights into biophysical carbon-concentrating mechanisms in land plants.Plant physiology · 2024Article
61 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The "Virtual Cell" provides a general system for testing cell biological mechanisms and creates a framework for encapsulating the burgeoning knowledge base comprising the distribution and dynamics of intracellular biochemical processes. It approaches the problem by associating biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular localizations. Individual processes are collected within a physical and computational infrastructure that accommodates any molecular mechanism expressible as rate equations or membrane fluxes. An illustration of the method is provided by a dynamic simulation of IP3-mediated Ca2+ release from endoplasmic reticulum in a neuronal cell. The results can be directly compared to experimental observations and provide insight into the role of experimentally inaccessible components of the overall mechanism.
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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.