Related papers: The Stability of Boolean Networks with Generalized…

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 global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…

The amount of mutual information contained in time series of two elements gives a measure of how well their activities are coordinated. In a large, complex network of interacting elements, such as a genetic regulatory network within a cell,…

Chaotic functions are characterized by sensitivity to initial conditions, transitivity, and regularity. Providing new functions with such properties is a real challenge. This work shows that one can associate with any Boolean network a…

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…

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 study transient sequential dynamics of evolving dynamical networks, i.e., those having active nodes and links and activity-dependent topology. We show that such networks can generate sequences of metastable cluster states where each…

Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…

We study a network model that couples the dynamics of link states with the evolution of the network topology. The state of each link, either A or B, is updated according to the majority rule or zero-temperature Glauber dynamics, in which…

Logical models have been successfully used to describe regulatory and signaling networks without requiring quantitative data. However, existing data is insufficient to adequately define a unique model, rendering the parametrization of a…

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer…

Observabililty is an important topic of Boolean control networks (BCNs). In this paper, we propose a new type of observability named online observability to present the sufficient and necessary condition of determining the initial states of…

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…

Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical…

This work examines the problem of topology inference over discrete-time nonlinear stochastic networked dynamical systems. The goal is to recover the underlying digraph linking the network agents, from observations of their state-evolution.…

The problem of controllability of the dynamical state of a network is central in network theory and has wide applications ranging from network medicine to financial markets. The driver nodes of the network are the nodes that can bring the…

In this paper we study the controllability of networked systems with static network topologies using tools from algebraic graph theory. Each agent in the network acts in a decentralized fashion by updating its state in accordance with a…

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…

The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables,…

Controllability of complex networks arises in many technological problems involving social, financial, road, communication, and smart grid networks. In many practical situations, the underlying topology might change randomly with time, due…