Related papers: Coevolving Boolean and Multi-Valued Regulatory Net…

Boolean networks have been widely used to explore aspects of gene regulation, traditionally with a single network. A modified form of the model to explore the effects of increasing the number of gene states has also recently been…

Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…

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…

Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…

Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…

The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…

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…

Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may,…

This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…

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}.…

The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…

Boolean networks are a valuable class of discrete dynamical systems models, but they remain fundamentally limited by their inability to capture multi-way interactions in their components. To remedy this limitation, we propose a model of…

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…

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…

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…

To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…

One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…

We study the stability of orbits in large Boolean networks with given complex topology. We impose no restrictions on the form of the update rules, which may be correlated with local topological properties of the network. While recent past…

The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semi-annealed approximation to study the stability properties of Random Boolean Networks…

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…