Related papers: Boolean networks with veto functions
In network control theory, driving all the nodes in the Feedback Vertex Set (FVS) forces the network into one of its attractors (long-term dynamic behaviors). The FVS is often composed of more nodes than can be realistically manipulated in…
This article is set in the field of regulation networks modeled by discrete dynamical systems. It focuses on Boolean automata networks. In such networks, there are many ways to update the states of every element. When this is done…
The concept of a nested canalizing Boolean function has been studied over the course of the last decade in the context of understanding the regulatory logic of molecular interaction networks, such as gene regulatory networks. Such functions…
The response to a knockout of a node is a characteristic feature of a networked dynamical system. Knockout resilience in the dynamics of the remaining nodes is a sign of robustness. Here we study the effect of knockouts for binary state…
Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…
Boolean networks (BNs) are important models for gene regulatory networks and many other biological systems. In this paper, we study the minimal controllability problem of threshold and XOR BNs with degree constraints. Firstly, we derive…
There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…
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…
This paper focuses on the study of certain classes of Boolean functions that have appeared in several different contexts. Nested canalyzing functions have been studied recently in the context of Boolean network models of gene regulatory…
Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The…
We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We…
We investigate how elimination of variables can affect the asymptotic dynamics and phenotype control of Boolean networks. In particular, we look at the impact on minimal trap spaces, and identify a structural condition that guarantees their…
We propose new activity-dependent adaptive Boolean networks inspired by the cis-regulatory mechanism in gene regulatory networks. We analytically show that our model can be solved for stationary in-degree distribution for a wide class of…
Noise caused by fluctuations at the molecular level is a fundamental part of intracellular processes. While the response of biological systems to noise has been studied extensively, there has been limited understanding of how to exploit it…
In this report, we present a formal approach that addresses the problem of emergence of phase transitions in stochastic and attractive nonlinear threshold Boolean automata networks. Nonlinear networks considered are informally defined on…
A four-node network consisting of a negative loop controlling a positive one is studied. It models some of the features of the p53 gene network. Using piecewise linear dynamics with thresholds, the allowed dynamical classes are fully…
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…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
The canalizing properties of biological functions have been mainly studied in the context of Boolean modelling of gene regulatory networks. An important mathematical consequence of canalization is a low average sensitivity, which ensures in…