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On the impact of discreteness and abstractions on modelling noise in gene regulatory networks

Paper ID Volume ID Publish Year Pages File Format Full-Text
15061 1370 2015 11 PDF Available
Title
On the impact of discreteness and abstractions on modelling noise in gene regulatory networks
Abstract

•In living cells gene expression is thoroughly regulated.•Computational models help in understanding the mechanisms underlying gene regulation.•Hybrid approaches balance model accuracy and computational efficiency.•We identify the key sources of stochastic noise in a simple gene expression pathway.•We propose a wise method for building hybrid models without ignoring key parameters.

In this paper, we explore the impact of different forms of model abstraction and the role of discreteness on the dynamical behaviour of a simple model of gene regulation where a transcriptional repressor negatively regulates its own expression. We first investigate the relation between a minimal set of parameters and the system dynamics in a purely discrete stochastic framework, with the twofold purpose of providing an intuitive explanation of the different behavioural patterns exhibited and of identifying the main sources of noise. Then, we explore the effect of combining hybrid approaches and quasi-steady state approximations on model behaviour (and simulation time), to understand to what extent dynamics and quantitative features such as noise intensity can be preserved.

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Keywords
Gene regulatory networks; Discrete modelling; Hybrid system; Quasi-steady state approximation; Stochastic noise
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On the impact of discreteness and abstractions on modelling noise in gene regulatory networks
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 56, June 2015, Pages 98–108
Authors
, , , , , ,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
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Any Questions? feel free to contact us