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A Compositional Approach to the Stochastic Dynamics of Gene Networks

Ralf Blossey, Luca Cardelli, and Andrew Phillips

Abstract

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 Combinatorial Synthesis of Genetic Networks [1]. 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.

Details

Publication typeArticle
Published inTransactions in Computational Systems Biology
URLhttp://dx.doi.org/10.1007/11539452_3
Pages99–122
Volume3939
Number3939
SeriesLNCS
PublisherSpringer
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