ArticleCells2013
Spatial rule-based modeling: a method and its application to the human mitotic kinetochore.
Article in Cells, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Network architecture determines delay robustness in the spindle assembly checkpoint.Scientific reports · 2026Article
- Delayed Signaling in Mitotic Checkpoints: Biological Mechanisms and Modeling Perspectives.Biology · 2026Review
- Artificial intelligence in mitotic checkpoint modeling: transforming our understanding of cellular division through machine learning and predictive biology.Briefings in bioinformatics · 2026Review
- Dynamics of spindle assembly and position checkpoints: Integrating molecular mechanisms with computational models.Computational and structural biotechnology journal · 2025Review
- Cell Cycle Complexity: Exploring the Structure of Persistent Subsystems in 414 Models.Biomedicines · 2024Article
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Computing all persistent subspaces of a reaction-diffusion system.Scientific reports · 2023Article
- Structure and Hierarchy of SARS-CoV-2 Infection Dynamics Models Revealed by Reaction Network Analysis.Viruses · 2020Article
- FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins.Scientific reports · 2020Article
- Trends in mathematical modeling of host-pathogen interactions.Cellular and molecular life sciences : CMLS · 2020Review
- Systems Biology Modeling of Five Pathways for Regulation and Potent Inhibition of the Anaphase-Promoting Complex (APC/C): Pivotal Roles for MCC and BubR1.Omics : a journal of integrative biology · 2015Article
- Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control.Computational and structural biotechnology journal · 2015Article
- Active transport can greatly enhance Cdc20:Mad2 formation.International journal of molecular sciences · 2014Article
- Multi-state modeling of biomolecules.PLoS computational biology · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A common problem in the analysis of biological systems is the combinatorial explosion that emerges from the complexity of multi-protein assemblies. Conventional formalisms, like differential equations, Boolean networks and Bayesian networks, are unsuitable for dealing with the combinatorial explosion, because they are designed for a restricted state space with fixed dimensionality. To overcome this problem, the rule-based modeling language, BioNetGen, and the spatial extension, SRSim, have been developed. Here, we describe how to apply rule-based modeling to integrate experimental data from different sources into a single spatial simulation model and how to analyze the output of that model. The starting point for this approach can be a combination of molecular interaction data, reaction network data, proximities, binding and diffusion kinetics and molecular geometries at different levels of detail. We describe the technique and then use it to construct a model of the human mitotic inner and outer kinetochore, including the spindle assembly checkpoint signaling pathway. This allows us to demonstrate the utility of the procedure, show how a novel perspective for understanding such complex systems becomes accessible and elaborate on challenges that arise in the formulation, simulation and analysis of spatial rule-based models.
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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.