Comparing different ODE modelling approaches for gene regulatory networks
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Publication:1628929
DOI10.1016/j.jtbi.2009.07.040zbMath1403.92095OpenAlexW2054286320WikidataQ51803503 ScholiaQ51803503MaRDI QIDQ1628929
A. Polynikis, Mario di Bernardo, S. John Hogan
Publication date: 11 December 2018
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jtbi.2009.07.040
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Cites Work
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- Qualitative simulation of genetic regulatory networks using piecewise-linear models
- An analytical study of the number of steady states in gene regulatory networks
- Modeling gene regulatory networks with piecewise linear differential equations
- Modeling transcriptional control in gene networks -- methods, recent results, and future directions
- Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation.
- Analysis and generic properties of gene regulatory networks with graded response functions
- The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model
- Dynamic patterns of gene regulation. I: Simple two-gene systems
- Piecewise-linear models of genetic regulatory networks: equilibria and their stability
- Discrete time piecewise affine models of genetic regulatory networks
- A class of piecewise linear differential equations arising in biological models
- Temporal Logic Analysis of Gene Networks Under Parameter Uncertainty
- Stochastic modelling of gene regulatory networks
- Analysis of continuous-time switching networks