ArticleMethods in cell biology2012
Spatial modeling of cell signaling networks.
Article in Methods in cell biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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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.
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Who cites it
88 citing papers in PubMed.
- Review
- Active transport by cytoplasmic dynein sustains dendritic MAP2 localization in developing neurons.The Journal of biological chemistry · 2026Article
- Interplay between store-operated calcium entry and mitochondrial phosphate handling modulates force and fatigue during exercise.bioRxiv : the preprint server for biology · 2026Article
- Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling.Biophysical journal · 2026Article
- A rule-based simulation model illuminates the role of asymmetric mitochondrial fission on beta-cell health.NPJ systems biology and applications · 2026Article
- Practical quantification of immunohistochemistry antigen concentrations and reaction-diffusion parameters.bioRxiv : the preprint server for biology · 2026Article
- A predictive mechanochemical modeling framework for the deformation and remodeling of the nuclear lamina.bioRxiv : the preprint server for biology · 2026Article
- Systems-level consequences of low RAF abundance for EGFR-ERK signaling.Biophysical journal · 2026Article
- Coupling Molecular and Cellular Dynamics in a Large-Scale Monte Carlo Simulation.International journal of molecular sciences · 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
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- Logic-based modeling of biological networks with Netflux.PLoS computational biology · 2025Article
- 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
- Article
- A continuum model of mechanosensation based on contractility kit assembly.Biophysical journal · 2025Article
- Role of intercellular interactions on single cell and population level responses: considerations for multicellular bioreporter design.Frontiers in molecular biosciences · 2025Article
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 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
28 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 shape of a cell, the sizes of subcellular compartments, and the spatial distribution of molecules within the cytoplasm can all control how molecules interact to produce a cellular behavior. This chapter describes how these spatial features can be included in mechanistic mathematical models of cell signaling. The Virtual Cell computational modeling and simulation software is used to illustrate the considerations required to build a spatial model. An explanation of how to appropriately choose between physical formulations that implicitly or explicitly account for cell geometry and between deterministic versus stochastic formulations for molecular dynamics is provided, along with a discussion of their respective strengths and weaknesses. As a first step toward constructing a spatial model, the geometry needs to be specified and associated with the molecules, reactions, and membrane flux processes of the network. Initial conditions, diffusion coefficients, velocities, and boundary conditions complete the specifications required to define the mathematics of the model. The numerical methods used to solve reaction-diffusion problems both deterministically and stochastically are then described and some guidance is provided in how to set up and run simulations. A study of cAMP signaling in neurons ends the chapter, providing an example of the insights that can be gained in interpreting experimental results through the application of spatial modeling.
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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.