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Journal of Computational and Applied Mathematics
Article
License: Elsevier Non-Commercial
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Journal of Computational and Applied Mathematics
Article . 2007
License: Elsevier Non-Commercial
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Article . 2007 . Peer-reviewed
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A solver for the stochastic master equation applied to gene regulatory networks

Authors: Hegland, Markus; Burden, Conrad; Santoso, Lucia; MacNamara, Shevarl; Booth, Hilary;

A solver for the stochastic master equation applied to gene regulatory networks

Abstract

AbstractAn important driver of gene regulatory networks is noise arising from the stochastic nature of interactions of genes, their products and regulators. Thus, such systems are stochastic and can be modelled by the chemical master equations. A major challenge is the curse of dimensionality which occurs when one attempts to integrate these equations. While stochastic simulation techniques effectively address the curse, many repeated simulations are required to provide precise information about stationary points, bifurcation phenomena and other properties of the stochastic processes. An alternative way to address the curse of dimensionality is provided by sparse grid approximations. The sparse grid methodology is applied and the application demonstrated to work efficiently for up to 10 proteins. As sparse grid methods have been developed for the approximation of smooth functions, a variant for infinite sequences had to be developed together with a multiresolution analysis similar to Haar wavelets. Error bounds are provided which confirm the effectiveness of sparse grid approximations for smooth high-dimensional probability distributions.

Keywords

sparse grids, Cells, master equations systems biology, Bacteriophage-lambda, Escherichia-coli, Gene regulatory networks, Aggregation, C1, 518, gene regulatory networks, Keywords: Approximation theory, Problem solving, Applied Mathematics, Systems, Random processes, Sparse grids, Computer simulation, Computational Mathematics, Bifurcation (mathematics), Genetic engineering Gene regulatory networks, Applied, Systems biology, Multiresolution analysis, Mathematics, Master equations

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    Top 10%
    influence
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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
90
Top 10%
Top 10%
Top 10%
Green
hybrid