Journal
JOURNAL OF THEORETICAL BIOLOGY
Volume 462, Issue -, Pages 514-527Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jtbi.2018.11.034
Keywords
Molecular regulatory networks; Signaling motifs; Logical models; Dynamic models; Stochastic models; Piecewise-linear odes; Bifurcation theory
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Funding
- NIH [5R01GM078989-12]
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Strategies for modeling the complex dynamical behavior of gene/protein regulatory networks have evolved over the last 50 years as both the knowledge of these molecular control systems and the power of computing resources have increased. Here, we review a number of common modeling approaches, including Boolean (logical) models, systems of piecewise-linear or fully non-linear ordinary differential equations, and stochastic models (including hybrid deterministic/stochastic approaches). We discuss the pro's and con's of each approach, to help novice modelers choose a modeling strategy suitable to their problem, based on the type and bounty of available experimental information. We illustrate different modeling strategies in terms of some abstract network motifs, and in the specific context of cell cycle regulation. (C) 2018 Elsevier Ltd. All rights reserved.
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