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A compositional approach to the stochastic dynamics of gene networks. (English) Zbl 1179.92021
Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology IV. Berlin: Springer (ISBN 3-540-33245-6/pbk). Lecture Notes in Computer Science 3939. Lecture Notes in Bioinformatics. Journal Subline, 99-122 (2006).
Summary: We propose a compositional approach to the dynamics of gene regulatory networks based on the stochastic \(\pi\)-calculus, and develop a representation of gene network elements which can be used to build complex circuits in a transparent and efficient way. To demonstrate the power of the approach we apply it to several artificial networks, such as the repressilator and combinatorial gene circuits first studied in [C. C. Guet, M. B. Elowitz, W. Hsing and S. Leibler, “Combinatorial synthesis of genetic networks”, Science 296, No. 5572, 1466–1470 (2002)]. For two examples of the latter systems, we point out how the topology of the circuits and the interplay of the stochastic gate interactions influence the circuit behavior. Our approach may be useful for the testing of biological mechanisms proposed to explain the experimentally observed circuit dynamics.
For the entire collection see [Zbl 1103.92300].

MSC:
92C42 Systems biology, networks
92C40 Biochemistry, molecular biology
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