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Veerman, F.* ; Marr, C. ; Popović, N.*

Time-dependent propagators for stochastic models of gene expression: An analytical method.

J. Math. Biol., 1-52 (2017)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
The inherent stochasticity of gene expression in the context of regulatory networks profoundly influences the dynamics of the involved species. Mathematically speaking, the propagators which describe the evolution of such networks in time are typically defined as solutions of the corresponding chemical master equation (CME). However, it is not possible in general to obtain exact solutions to the CME in closed form, which is due largely to its high dimensionality. In the present article, we propose an analytical method for the efficient approximation of these propagators. We illustrate our method on the basis of two categories of stochastic models for gene expression that have been discussed in the literature. The requisite procedure consists of three steps: a probability-generating function is introduced which transforms the CME into (a system of) partial differential equations (PDEs); application of the method of characteristics then yields (a system of) ordinary differential equations (ODEs) which can be solved using dynamical systems techniques, giving closed-form expressions for the generating function; finally, propagator probabilities can be reconstructed numerically from these expressions via the Cauchy integral formula. The resulting ‘library’ of propagators lends itself naturally to implementation in a Bayesian parameter inference scheme, and can be generalised systematically to related categories of stochastic models beyond the ones considered here.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Asymptotic Analysis ; Dynamical Systems ; Perturbation Techniques ; Probability Generating Function ; Propagator ; Stochastic Gene Expression
ISSN (print) / ISBN 0303-6812
e-ISSN 1432-1416
Journal Journal of Mathematical Biology
Quellenangaben Volume: , Issue: , Pages: 1-52 Article Number: , Supplement: ,
Publisher Springer
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)