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Modeling, analysis, and simulation of genetic regulatory networks: From differential equations to logical models |
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In: D. Chatenay, S. Cocco, R. Monasson, D. Thieffry, J. Dalibard (eds.), Multiple Aspects of DNA and RNA: From Biophysics to Bioinformatics, Ecole d'été de Physique des Houches, Session LXXXII, Elsevier, Amsterdam, 2005, 325-351. |
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| H. de Jong, D. Thieffry |
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| Genetic regulatory networks, consisting of genes, proteins, small molecules, and their mutual interactions, control the functioning and differentiation of cells. Given the large number of components of most networks of biological interest, connected by positive and negative feedback loops, an intuitive comprehension of the dynamics of the system is often difficult, if not impossible to obtain. As a consequence, mathematical and computational approaches are indispensable for gaining a comprehension of the functioning of complex networks. In this chapter, we review three approaches towards the modeling, analysis, and simulation of genetic regulatory networks, based on ordinary differential equations, piecewise-linear differential equations, and logical models, respectively. We discuss the strengths and weaknesses of these formalisms, and illustrate their application to the study of a variety of prokaryotic and eukaryotic model systems. |
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