Related papers: Coevolving Boolean and Multi-Valued Regulatory Net…
Different Boolean networks may reveal similar dynamics although their definition differs, then preventing their distinction from the observations. This raises the question about the sufficiency of a particular Boolean network for properly…
Boolean networks have been the object of much attention, especially since S. Kauffman proposed them in the 1960's as models for gene regulatory networks. These systems are characterized by being defined on a Boolean state space and by…
Discrete modelling frameworks of Biological networks can be divided in two distinct categories: Boolean and Multi-valued. Although Multi-valued networks are more expressive for qualifying the regulatory behaviours modelled by more than two…
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…
The effects of the finite size of the network on the evolutionary dynamics of a Boolean network are analyzed. In the model considered, Boolean networks evolve via a competition between nodes that punishes those in the majority. It is found…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
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…
Boolean networks can be viewed as functions on the set of binary strings of a given length, described via logical rules. They were introduced as dynamic models into biology, in particular as logical models of intracellular regulatory…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Distinct channels of interaction in a complex networked system define network layers, which co-exist and co-operate for the system's function. Towards realistic modeling and understanding such multiplex systems, we introduce and study a…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
Results and tools on discrete interaction networks are often concerned with Boolean variables, whereas considering more than two levels is sometimes useful. Multivalued networks can be converted to partial Boolean maps, in a way that…
Boolean networks constitute relevant mathematical models to study the behaviours of genetic and signalling networks. These networks define regulatory influences between molecular nodes, each being associated to a Boolean variable and a…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
The generating functional method is employed to investigate the synchronous dynamics of Boolean networks, providing an exact result for the system dynamics via a set of macroscopic order parameters. The topology of the networks studied and…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…