Stochastic hybrid models of gene regulatory networks -- a PDE approach
From MaRDI portal
Publication:669087
DOI10.1016/J.MBS.2018.09.009zbMATH Open1412.35344arXiv1803.10958OpenAlexW2810319892WikidataQ91654336 ScholiaQ91654336MaRDI QIDQ669087FDOQ669087
Authors: Pavel Kurasov, Alexander Lück, Delio Mugnolo, Verena Wolf 
Publication date: 20 March 2019
Published in: Mathematical Biosciences (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/1803.10958
Recommendations
- Analytic solutions for stochastic hybrid models of gene regulatory networks
- Stochastic models and numerical algorithms for a class of regulatory gene networks
- Stochastic modelling of gene regulatory networks
- Dynamics of gene regulatory networks with stochastic propensities
- Refining dynamics of gene regulatory networks in a stochastic \(\pi\)-calculus framework
- Stochastic delay differential equations for genetic regulatory networks
- A solver for the stochastic master equation applied to gene regulatory networks
- Convergence of stochastic gene networks to hybrid piecewise deterministic processes
- Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting
Numerical analysis or methods applied to Markov chains (65C40) Genetics and epigenetics (92D10) PDEs in connection with biology, chemistry and other natural sciences (35Q92) Inverse problems for PDEs (35R30)
Cites Work
- HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
- Title not available (Why is that?)
- Fluid stochastic Petri nets: Theory, applications, and solution techniques
- Stochastic hybrid systems for studying biochemical processes
- Solving the chemical master equation for monomolecular reaction systems analytically
- On the solution of nonlinear hyperbolic differential equations by finite differences
- Hybrid representation and simulation of stiff biochemical networks
- Inexact Uniformization Method for Computing Transient Distributions of Markov Chains
- Analytic solutions for stochastic hybrid models of gene regulatory networks
- Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting
- Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
- Decomposition and tunability of expression noise in the presence of coupled feedbacks
Cited In (26)
- Title not available (Why is that?)
- 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
- Switching and diffusion models for gene regulation networks
- Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting
- 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
- 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
Uses Software
This page was built for publication: Stochastic hybrid models of gene regulatory networks -- a PDE approach
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q669087)
