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

TitleOn the impact of discreteness and abstractions on modelling noise in gene regulatory networks
Publication TypeJournal Article
Year of Publication2015
AuthorsBodei C, Bortolussi L, Chiarugi D, Guerriero MLuisa, Policriti A, Romanel A
JournalComputational biology and chemistry
Volume56
Pages98–108
KeywordsDiscrete modeling, Gene regulatory networks, Hybrid system, Quasi-steady state approximation, Stochastic Noise
Abstract

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.

DOI10.1016/j.compbiolchem.2015.04.004
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