Related papers: Complexity of limit-cycle problems in Boolean netw…
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}.…
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…
Boolean networks have been used in a variety of settings, as models for general complex systems as well as models of specific systems in diverse fields, such as biology, engineering, and computer science. Traditionally, their properties as…
A Boolean network is a finite state discrete time dynamical system. At each step, each variable takes a value from a binary set. The value update rule for each variable is a local function which depends only on a selected subset of…
In temporal planning, many different temporal network formalisms are used to model real world situations. Each of these formalisms has different features which affect how easy it is to determine whether the underlying network of temporal…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…
Boolean networks are dynamical models of disease development in which the activation levels of genes are represented by binary variables. Given a Boolean network, controls represent mutations or medical treatments that fix the activation…
Many familial diseases are caused by genetic accidents, which affect both the genome and its epigenetic environment, expressed as an interaction graph between the genes as that involved in one familial disease we shall study, the hereditary…
Boolean Networks (BNs) describe the time evolution of binary states using logic functions on the nodes of a network. They are fundamental models for complex discrete dynamical systems, with applications in various areas of science and…
Our daily social and political life is more and more impacted by social networks. The functioning of our living bodies is deeply dependent on biological regulation networks such as neural, genetic, and protein networks. And the physical…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
The parallel computational complexity or depth of growing network models is investigated. The networks considered are generated by preferential attachment rules where the probability of attaching a new node to an existing node is given by a…
Boolean networks, widely used to model gene regulation, exhibit a phase transition between regimes in which small perturbations either die out or grow exponentially. We show and numerically verify that this phase transition in the dynamics…
Increased biological complexity is generally associated with the addition of new genetic information, which must be integrated into the existing regulatory network that operates within the cell. General arguments on network control, as well…
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…
Hybrid logic with binders is an expressive specification language. Its satisfiability problem is undecidable in general. If frames are restricted to N or general linear orders, then satisfiability is known to be decidable, but of…
This paper addresses the problem of finding cycles in the state transition graphs of synchronous Boolean networks. Synchronous Boolean networks are a class of deterministic finite state machines which are used for the modeling of gene…
We extend classical methods of computational complexity to the realm of distributed computing, where they sometimes prove more effective than in their original context. Our focus is on decision problems in the LOCAL model, a setting in…
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…