Dynamics of unperturbed and noisy generalized Boolean networks

DOI10.1016/J.JTBI.2009.06.027MaRDI QIDQ1625932zbMATH OpenOpenAlexWikidataFDO

Authors Ch. Darabos, Marco Tomassini, Mario Giacobini

Publication date 26 November 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0909.5297

zbMATH Keywords

Boolean dynamicscomplex networksgenetic regulatory networksperturbationsrandom Boolean networksscale-free networks

Mathematics Subject Classification ID

Systems biology, networks (92C42) Genetics and epigenetics (92D10)

Abstract: For years, we have been building models of gene regulatory networks, where recent advances in molecular biology shed some light on new structural and dynamical properties of such highly complex systems. In this work, we propose a novel timing of updates in Random and Scale-Free Boolean Networks, inspired by recent findings in molecular biology. This update sequence is neither fully synchronous nor asynchronous, but rather takes into account the sequence in which genes affect each other. We have used both Kauffman's original model and Aldana's extension, which takes into account the structural properties about known parts of actual GRNs, where the degree distribution is right-skewed and long-tailed. The computer simulations of the dynamics of the new model compare favorably to the original ones and show biologically plausible results both in terms of attractors number and length. We have complemented this study with a complete analysis of our systems' stability under transient perturbations, which is one of biological networks defining attribute. Results are encouraging, as our model shows comparable and usually even better behavior than preceding ones without loosing Boolean networks attractive simplicity.

Recommendations

• Boolean networks: beyond generalized asynchronicity
• Attractor analysis of asynchronous Boolean models of signal transduction networks
• Dynamical regimes in non-ergodic random Boolean networks
• Dynamic information handling in continuous time Boolean network model of gene interactions
• An adjustable aperiodic model class of genomic interactions using continuous time Boolean networks (Boolean delay equations)

Cites work

• Boolean dynamics of Kauffman models with a scale-free network
• Boolean dynamics of networks with scale-free topology
• Boolean dynamics with random couplings
• Critical market crashes
• Effects of alternative connectivity on behavior of randomly constructed Boolean networks
• scientific article; zbMATH DE number 1866312 (Why is no real title available?)
• scientific article; zbMATH DE number 795573 (Why is no real title available?)
• Noisy attractors and ergodic sets in models of gene regulatory networks
• Robustness and evolvability in genetic regulatory networks
• Statistical mechanics of complex networks
• The Structure and Function of Complex Networks
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}
• Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data

Cited in

(7)

• Boolean networks: beyond generalized asynchronicity
• The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks
• Unfolding of parametric Boolean networks
• The stability of Boolean network with transmission sensitivity
• On the sparse percolation of damage in finite non-synchronous random Boolean networks
• The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth
• Fitting Boolean networks from steady state perturbation data

This page was built for publication: Dynamics of unperturbed and noisy generalized Boolean networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1625932)