Related papers: Evolution of Activity-Dependent Adaptive Boolean N…

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…

Estimating the influence that individual nodes have on one another in a Boolean network is essential to predict and control the system's dynamical behavior, for example, detecting key therapeutic targets to control pathways in models of…

In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or…

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are…

The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…

We present and discuss the results of an experimental analysis in the design of Boolean networks by means of genetic algorithms. A population of networks is evolved with the aim of finding a network such that the attractor it reaches is of…

Random Boolean networks, originally invented as models of genetic regulatory networks, are simple models for a broad class of complex systems that show rich dynamical structures. From a biological perspective, the most interesting networks…

Boolean automata networks (aka Boolean networks) are space-time discrete dynamical systems, studied as a model of computation and as a representative model of natural phenomena. A collection of simple entities (the automata) update their…

Boolean network models of molecular regulatory networks have been used successfully in computational systems biology. The Boolean functions that appear in published models tend to have special properties, in particular the property of being…

As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…

This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate…

Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…

Disease awareness in infection dynamics can be modeled with adaptive contact networks whose rewiring rules reflect the attempt by susceptibles to avoid infectious contacts. Simulations of this type of models show an active phase with…

Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component…

We present a rigorous mathematical framework for analyzing dynamics of a broad class of Boolean network models. We use this framework to provide the first formal proof of many of the standard critical transition results in Boolean network…

We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…

Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be…

The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…

Boolean networks serve as discrete models of regulation and signaling in biological cells. Identifying the key controllers of such processes is important for understanding the dynamical systems and planning further analysis. Here we…