Stochastic hybrid models of gene regulatory networks -- a PDE approach
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Publication:669087
Abstract: A widely used approach to describe the dynamics of gene regulatory networks is based on the chemical master equation, which considers probability distributions over all possible combinations of molecular counts. The analysis of such models is extremely challenging due to their large discrete state space. We therefore propose a hybrid approximation approach based on a system of partial differential equations, where we assume a continuous-deterministic evolution for the protein counts. We discuss efficient analysis methods for both modeling approaches and compare their performance. We show that the hybrid approach yields accurate results for sufficiently large molecule counts, while reducing the computational effort from one ordinary differential equation for each state to one partial differential equation for each mode of the system. Furthermore, we give an analytical steady-state solution of the hybrid model for the case of a self-regulatory gene.
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Cites work
- scientific article; zbMATH DE number 3901778 (Why is no real title available?)
- Analytic solutions for stochastic hybrid models of gene regulatory networks
- Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
- Decomposition and tunability of expression noise in the presence of coupled feedbacks
- Fluid stochastic Petri nets: Theory, applications, and solution techniques
- HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
- Hybrid representation and simulation of stiff biochemical networks
- Inexact Uniformization Method for Computing Transient Distributions of Markov Chains
- On the solution of nonlinear hyperbolic differential equations by finite differences
- Solving the chemical master equation for monomolecular reaction systems analytically
- Stochastic hybrid systems for studying biochemical processes
- Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting
Cited in
(27)- scientific article; zbMATH DE number 5872239 (Why is no real title available?)
- Path integral approach to generating functions for multistep post-transcription and post-translation processes and arbitrary initial conditions
- A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks
- Abstraction-guided truncations for stationary distributions of Markov population models
- Convergence of stochastic gene networks to hybrid piecewise deterministic processes
- Uniform convergence of solutions to stochastic hybrid models of gene regulatory networks
- Exact and WKB-approximate distributions in a gene expression model with feedback in burst frequency, burst size, and protein stability
- Analytic solutions for stochastic hybrid models of gene regulatory networks
- Push-forward method for piecewise deterministic biochemical simulations
- Effective computational methods for hybrid stochastic gene networks
- Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting
- Switching and diffusion models for gene regulation networks
- Dimensionality reduction via path integration for computing mRNA distributions
- Modeling stochasticity in gene regulation: Characterization in the terms of the underlying distribution function
- Stochastic modelling of gene regulatory networks
- Comparing different ODE modelling approaches for gene regulatory networks
- Parameter inference with analytical propagators for stochastic models of autoregulated gene expression
- A kinetic finite volume discretization of the multidimensional PIDE model for gene regulatory networks
- Application of the Goodwin model to autoregulatory feedback for stochastic gene expression
- Conformal Quantitative Predictive Monitoring of STL Requirements for Stochastic Processes
- Steady-state fluctuations of a genetic feedback loop with fluctuating rate parameters using the unified colored noise approximation
- Postponing production exponentially enhances the molecular memory of a stochastic switch
- Multiscale stochastic modelling of gene expression
- Hybrid simulation of autoregulation within transcription and translation
- Time-dependent propagators for stochastic models of gene expression: an analytical method
- Stochastic models and numerical algorithms for a class of regulatory gene networks
- A solver for the stochastic master equation applied to gene regulatory networks
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