ArticleJournal of the Royal Society, Interface2016
Bursting noise in gene expression dynamics: linking microscopic and mesoscopic models.
Article in Journal of the Royal Society, Interface, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Efficient approximations of transcriptional bursting effects on the dynamics of a gene regulatory network.Journal of the Royal Society, Interface · 2025Article
- Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting.Genome biology · 2023Article
- Reduction of a stochastic model of gene expression: Lagrangian dynamics gives access to basins of attraction as cell types and metastabilty.Journal of mathematical biology · 2021Article
- Analytic solutions for stochastic hybrid models of gene regulatory networks.Journal of mathematical biology · 2021Article
- Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics.In silico biology · 2021Article
- Mixture distributions in a stochastic gene expression model with delayed feedback: a WKB approximation approach.Journal of mathematical biology · 2020Article
- Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations.Molecular biology and evolution · 2020Article
- Generalizing Gillespie's Direct Method to Enable Network-Free Simulations.Bulletin of mathematical biology · 2019Article
- Exact and efficient hybrid Monte Carlo algorithm for accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts.The Journal of chemical physics · 2019Article
- Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks.The Journal of chemical physics · 2019Article
- A stochastic and dynamical view of pluripotency in mouse embryonic stem cells.PLoS computational biology · 2018Article
- Analysis of stochastic bifurcations with phase portraits.PloS one · 2018Article
- Characterization of noise in multistable genetic circuits reveals ways to modulate heterogeneity.PloS one · 2018Article
- Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes.Journal of the Royal Society, Interface · 2018Article
- Efficient and flexible implementation of Langevin simulation for gene burst production.Scientific reports · 2017Article
- Inferring gene regulatory networks from single-cell data: a mechanistic approach.BMC systems biology · 2017Article
- Gene expression noise is affected differentially by feedback in burst frequency and burst size.Journal of mathematical biology · 2017Article
- A minimal model of burst-noise induced bistability.PloS one · 2017Article
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2 authors.
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Abstract
The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks. We investigate the propagation of bursting noise between different levels of mathematical modelling and demonstrate that conventional approaches based on diffusion approximations can fail to capture bursting noise. An alternative coarse-grained model, the so-called piecewise deterministic Markov process (PDMP), is seen to outperform the diffusion approximation in biologically relevant parameter regimes. We provide a systematic embedding of the PDMP model into the landscape of existing approaches, and we present analytical methods to calculate its stationary distribution and switching frequencies.
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