ArticleJournal of the Royal Society, Interface2013
Simplifying biochemical models with intermediate species.
Article in Journal of the Royal Society, Interface, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Positive equilibria in mass action networks: geometry and bounds.Journal of mathematical biology · 2026Article
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- The Inheritance of Local Bifurcations in Mass Action Networks.Journal of nonlinear science · 2025Article
- Connectivity of Parameter Regions of Multistationarity for Multisite Phosphorylation Networks.Bulletin of mathematical biology · 2024Article
- Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding.PLoS computational biology · 2023Article
- The unraveling of balanced complexes in metabolic networks.Scientific reports · 2023Article
- Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity.PLoS computational biology · 2023Article
- A structural property for reduction of biochemical networks.Scientific reports · 2021Article
- Stochastic Simulations as a Tool for Assessing Signal Fidelity in Gene Expression in Synthetic Promoter Design.Biology · 2021Article
- Dynamics of ERK regulation in the processive limit.Journal of mathematical biology · 2021Article
- Joining and decomposing reaction networks.Journal of mathematical biology · 2020Article
- Oscillations and bistability in a model of ERK regulation.Journal of mathematical biology · 2019Article
- Regions of multistationarity in cascades of Goldbeter-Koshland loops.Journal of mathematical biology · 2019Article
- Dynamics of Posttranslational Modification Systems: Recent Progress and Future Directions.Biophysical journal · 2018Review
- Memory functions reveal structural properties of gene regulatory networks.PLoS computational biology · 2018Article
- Identifying parameter regions for multistationarity.PLoS computational biology · 2017Article
- Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling.PLoS computational biology · 2017Article
- Intermediates, catalysts, persistence, and boundary steady states.Journal of mathematical biology · 2017Article
- Graphical reduction of reaction networks by linear elimination of species.Journal of mathematical biology · 2017Article
- Core signalling motif displaying multistability through multi-state enzymes.Journal of the Royal Society, Interface · 2016Article
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2 authors.
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Abstract
Mathematical models are increasingly being used to understand complex biochemical systems, to analyse experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to the choice and uncertainties of the model. Using algebraic techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady-state concentrations of the species in the core model, after suitable matching of parameters. Importantly, our results provide guidelines to the modeller in choosing between models and in distinguishing their properties. Further, our work provides a formal way of comparing models that share a common skeleton.
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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.