相关论文: Positive and negative cycles in Boolean networks

Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…

Despite their apparent simplicity, random Boolean networks display a rich variety of dynamical behaviors. Much work has been focused on the properties and abundance of attractors. The topologies of random Boolean networks with one input per…

Standard Random Boolean Networks display an order-disorder phase transition. We add to the standard Random Boolean Networks a disconnection rule which couples the control and order parameters. By this way, the system is driven to the…

To simplify the analysis of Boolean networks, a reduction in the number of components is often considered. A popular reduction method consists in eliminating components that are not autoregulated, using variable substitution. In this work,…

Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…

Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean…

Many natural, complex systems are remarkably stable thanks to an absence of feedback acting on their elements. When described as networks, these exhibit few or no cycles, and associated matrices have small leading eigenvalues. It has been…

Many natural and artificial networks evolve in time. Nodes and connections appear and disappear at various timescales, and their dynamics has profound consequences for any processes in which they are involved. The first empirical analysis…

Continuous-time systems with switch-like behaviour occur in chemical kinetics, gene regulatory networks and neural networks. Networks with hard switching, as a limiting case of smooth sigmoidal switching, retain the richest possible range…

The relationship between the properties of a dynamical system and the structure of its defining equations has long been studied in many contexts. Here we study this problem for the class of conjunctive (resp. disjunctive) Boolean networks,…

Relationships between individuals in a social network, genes in biological systems, and spins in magnetic systems often reflect a mixture of positive (friendly) and negative (antagonistic) interactions. However, most studies of complex…

In a complex system, the interactions between individual agents often lead to emergent collective behavior like spontaneous synchronization, swarming, and pattern formation. The topology of the network of interactions can have a dramatic…

Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…

In this paper we try to end the debate concerning the suitability of different updating schemes in random Boolean networks (RBNs). We quantify for the first time loose attractors in asyncrhonous RBNs, which allows us to analyze the…

In this paper we study the phase transitions of different types of Random Boolean networks. These differ in their updating scheme: synchronous, semi-synchronous, or asynchronous, and deterministic or non-deterministic. It has been shown…

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…

Link prediction models are increasingly used to recommend interactions in evolving networks, yet their impact on network structure is typically assessed from static snapshots. In particular, observed homophily conflates intrinsic…

Complex diseases can be modeled as damage to intracellular networks that results in abnormal cell behaviors. Network-based dynamic models such as Boolean models have been employed to model a variety of biological systems including those…

The mathematical theory of quantum feedback networks has recently been developed for general open quantum dynamical systems interacting with bosonic input fields. In this article we show, for the special case of linear dynamical systems…

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…