Discrete time piecewise affine models of genetic regulatory networks

DOI10.1007/S00285-005-0359-XzbMATH Open1094.92026arXivmath/0505044OpenAlexW2019859797WikidataQ51947490 ScholiaQ51947490MaRDI QIDQ2500115FDOQ2500115

Authors: Yanyan Li 

Publication date: 23 August 2006

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables represent gene expression levels. When compared to other models of regulatory networks, these models have an additional parameter which is identified as quantifying interaction delays. In spite of their simplicity, their dynamics presents a rich variety of behaviours. This phenomenology is not limited to piecewise affine model but extends to smooth nonlinear discrete time models of regulatory networks. In a first step, our analysis concerns general properties of networks on arbitrary graphs (characterisation of the attractor, symbolic dynamics, Lyapunov stability, structural stability, symmetries, etc). In a second step, focus is made on simple circuits for which the attractor and its changes with parameters are described. In the negative circuit of 2 genes, a thorough study is presented which concern stable (quasi-)periodic oscillations governed by rotations on the unit circle -- with a rotation number depending continuously and monotonically on threshold parameters. These regular oscillations exist in negative circuits with arbitrary number of genes where they are most likely to be observed in genetic systems with non-negligible delay effects.

Full work available at URL: https://arxiv.org/abs/math/0505044

Recommendations

• scientific article
• Chaotic dynamics in an electronic model of a genetic network
• Nonlinear perturbations of piecewise-linear systems with delay and applications to gene regulatory networks
• Dynamical complexity of discrete-time regulatory networks
• Piecewise-linear models of genetic regulatory networks: equilibria and their stability

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Dynamical systems in biology (37N25) Symbolic dynamics (37B10)

Cites Work

• Qualitative simulation of genetic regulatory networks using piecewise-linear models
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Weakly connected neural networks
• Title not available (Why is that?)
• Analysis of continuous-time switching networks
• Chaotic Behavior in Piecewise Continuous Difference Equations
• Exotic attractors. From Liapunov stability to riddled basins
• Title not available (Why is that?)
• On the dynamics of quasi-contractions
• Dynamical complexity of discrete-time regulatory networks
• Combinatorial explosion in model gene networks.
• Extended symbolic dynamics in bistable CML: Existence and stability of fronts

Cited In (50)

• Title not available (Why is that?)
• The hidden sensitivity of non-smooth dynamics
• Self-organization in trees and motifs of two-dimensional chaotic maps with time delay
• Qualitative simulation of genetic regulatory networks using piecewise-linear models
• RANDOM SHUFFLING OF SWITCHING PARAMETERS IN A MODEL OF GENE EXPRESSION REGULATORY NETWORK
• Exponential synchronization of switched genetic oscillators with time-varying delays
• Homogeneous polynomials as Lyapunov functions in the stability research of solutions of difference equations
• Dynamical complexity of discrete-time regulatory networks
• An adjustable aperiodic model class of genomic interactions using continuous time Boolean networks (Boolean delay equations)
• Dynamics of large cooperative pulsed-coupled networks
• Bifurcation analysis of a mathematical model for genetic regulatory network with time delays
• MODELING GENETIC REGULATORY NETWORKS: CONTINUOUS OR DISCRETE?
• Modeling gene regulatory networks with piecewise linear differential equations
• Angels' staircases, Sturmian sequences, and trajectories on homothety surfaces
• Polynomial representations of piecewise-linear differential equations arising from gene regulatory networks
• Geometric properties of a class of piecewise affine biological network models
• Dominant vertices in regulatory networks dynamics
• Study of discrete automaton models of gene networks of nonregular structure using symbolic calculations
• Modeling the dynamics of genetic regulatory networks: continuous and discrete approaches
• On the asymptotic properties of piecewise contracting maps
• Time-delayed models of gene regulatory networks
• A simple model of genetic oscillations through regulated degradation
• \(H_{\infty }\) filtering for discrete-time genetic regulatory networks with random delays
• Limit cycles in piecewise-affine gene network models with multiple interaction loops
• Comparing different ODE modelling approaches for gene regulatory networks
• Chaotic dynamics and diffusion in a piecewise linear equation
• Complexity of injective piecewise contracting interval maps
• Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems
• A survey on piecewise-linear models of regulatory dynamical systems
• Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models
• Stability analysis for discrete-time switched GRNs with persistent dwell-time and time delays
• Calculation of bifurcation curves by map replacement
• Synchronizability of coupled PWL maps
• Chaotic dynamics in an electronic model of a genetic network
• Dynamic modularity in discrete-time models of regulatory networks
• Symbolic dynamics of two coupled Lorenz maps: from uncoupled regime to synchronisation
• Periodicity in piecewise-linear switching networks with delay
• Discontinuity-induced bifurcations of piecewise smooth dynamical systems
• Robust state estimation for discrete-time genetic regulatory networks with randomly occurring uncertainties
• Fronts between periodic patterns for bistable recursions on lattices
• Stability of genetic regulatory networks with interval time-varying delays and stochastic perturbation
• Symbolic numeric analysis of attractors in randomly generated piecewise affine models of gene networks
• Stability analysis for genetic regulatory networks with delays: the continuous-time case and the discrete-time case
• Probabilistic approach for predicting periodic orbits in piecewise affine differential models
• Switched server systems whose parameters are normal numbers in base 4
• Local Identification of Piecewise Deterministic Models of Genetic Networks
• A discrete time neural network model with spiking neurons
• A piecewise contractive dynamical system and Phragmèn's election method
• Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors
• Regulatory dynamics of standard two-component systems in bacteria

This page was built for publication: Discrete time piecewise affine models of genetic regulatory networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2500115)