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Finite Buffer Method for Direct Solution of Discrete Chemical Master Equation

By Youfang Cao1, Anna Terebus, John Feser2

1. University of Illinois at Chicago 2. University of Illinois at Urbana-Champaign

Finite Buffer dCME

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Version 1.1b - published on 06 Aug 2014

doi:10.4231/D3154DQ02 cite this

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Steady state probability landscape of phage lambda epigenetic switch

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Abstract

= Finite Buffer dCME = '''Finite Buffer dCME''' (full name: Finite Buffer Method for Optimal State Space Enumeration and Direct Solution of Discrete Chemical Master Equation) provides an efficient and optimal algorithm for enumerating state spaces and directly solving discrete chemical master equations, which is a fundamental method for modeling stochastic gene regulatory networks in systems biology. Instead of running millions of stochastic simulation trajectories using Gillespie's algorithm (Gillespie, 1977), Finite Buffer method can accurately efficiently capture the important rare events in biological networks by directly solving full stochastic probability landscapes for '''both time evolution and steady state''' of reaction networks with arbitrary stoichiometry. Finite Buffer method has been successfully applied to study many critical biological processes, such as the cell fate determination and switching efficiency and stability issues in the epigenetic circuits of phage lambda, a virus to E. coli cell (Cao et al. 2010). Finite Buffer dCME can be applied to study broad issues in systems biology, such as the regulation of stem cell development and differentiation, and cell cancerogenesis. It has also been used to identify key interactions in a complex network (Cao et al. 2010), which can be potentially used to aid in discovering novel drug targets in a complex regulatory network.

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Researchers should cite this work as follows:

  • Cao, Y., & Liang, J. (2008). Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability. BMC Systems Biology, 2(1), 30. Cao, Y., Lu, H. M., & Liang, J. (2010). Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proceedings of the National Academy of Sciences, 107(43), 18445-18450.

  • Youfang Cao; Anna Terebus; John Feser (2014), "Finite Buffer Method for Direct Solution of Discrete Chemical Master Equation," http://nanohub.org/resources/fbsdcme. (DOI: 10.4231/D3154DQ02).

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