ArticleBMC systems biology2008
Exact model reduction of combinatorial reaction networks.
Article in BMC systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 67 citations in OpenAlex.
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- Maximal aggregation of polynomial dynamical systems.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends.Bulletin of mathematical biology · 2017Article
- Modeling for (physical) biologists: an introduction to the rule-based approach.Physical biology · 2015Review
- Analytical reduction of combinatorial complexity arising from multiple protein modification sites.Journal of the Royal Society, Interface · 2015Article
- Markov chain aggregation and its applications to combinatorial reaction networks.Journal of mathematical biology · 2014Article
- Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria.Molecular systems biology · 2014Article
- Exact hybrid particle/population simulation of rule-based models of biochemical systems.PLoS computational biology · 2014Article
- Spatial rule-based modeling: a method and its application to the human mitotic kinetochore.Cells · 2013Article
- The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail.BMC bioinformatics · 2012Article
- A framework for mapping, visualisation and automatic model creation of signal-transduction networks.Molecular systems biology · 2012Article
- Crosstalk and signaling switches in mitogen-activated protein kinase cascades.Frontiers in physiology · 2012Article
- A method for zooming of nonlinear models of biochemical systems.BMC systems biology · 2011Article
- New approaches to modeling complex biochemistry.Nature methods · 2011Article
- RuleMonkey: software for stochastic simulation of rule-based models.BMC bioinformatics · 2010Article
- Mass and information feedbacks through receptor endocytosis govern insulin signaling as revealed using a parameter-free modeling framework.The Journal of biological chemistry · 2010Article
- Zooming of states and parameters using a lumping approach including back-translation.BMC systems biology · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReceptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models.
resultsWe introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs) to a model with 87 ODEs.
conclusionThe methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks.
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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.