Related papers: On Natural Genetic Engineering: Structural Dynamis…
Nested structure, which is non-random, controls cooperation dynamics and biodiversity in plant-animal mutualistic networks. This structural pattern has been explained in a static (non-growth) network models. However, evolutionary processes…
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…
Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
The goal of this tutorial is to promote interest in the study of random Boolean networks (RBNs). These can be very interesting models, since one does not have to assume any functionality or particular connectivity of the networks to study…
Cancer forms a robust system and progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to…
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…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Random Boolean networks (RBNs) have been a popular model of genetic regulatory networks for more than four decades. However, most RBN studies have been made with random topologies, while real regulatory networks have been found to be…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Boolean networks are discrete dynamical systems where each automaton has its own Boolean function for computing its state according to the configuration of the network. The updating mode then determines how the configuration of the network…
Random Boolean Network has been used to find out regulation patterns of genes in organism. his approach is very interesting to use in a game such as N Person PD. Here we assume that action is influenced by input in the form of choices of…
Dynamic gene-regulatory networks are complex since the number of potential components involved in the system is very large. Estimating dynamic networks is an important task because they compromise valuable information about interactions…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Probabilistic Boolean Networks have been proposed for estimating the behaviour of dynamical systems as they combine rule-based modelling with uncertainty principles. Inferring PBNs directly from gene data is challenging however, especially…