ArticlePloS one2013
The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
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- Mutation and Selection in Bacteria: Modelling and Calibration.Bulletin of mathematical biology · 2019Article
- Influence of parameter perturbations on the reachability of therapeutic target in systems with switchings.Biomedical engineering online · 2017Article
- A Paradoxical Evolutionary Mechanism in Stochastically Switching Environments.Scientific reports · 2016Article
- Stochastic modeling suggests that noise reduces differentiation efficiency by inducing a heterogeneous drug response in glioma differentiation therapy.BMC systems biology · 2016Article
- The limiting dynamics of a bistable molecular switch with and without noise.Journal of mathematical biology · 2016Article
- The role of stochastic gene switching in determining the pharmacodynamics of certain drugs: basic mechanisms.Journal of pharmacokinetics and pharmacodynamics · 2016Article
- Gene switching rate determines response to extrinsic perturbations in the self-activation transcriptional network motif.Scientific reports · 2016Article
- Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks.PLoS computational biology · 2015Article
- Mean field analysis of a spatial stochastic model of a gene regulatory network.Journal of mathematical biology · 2015Article
- Automatising the analysis of stochastic biochemical time-series.BMC bioinformatics · 2015Article
- The pharmacodynamics of the p53-Mdm2 targeting drug Nutlin: the role of gene-switching noise.PLoS computational biology · 2014Article
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3 authors.
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Abstract
After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.
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