Related papers: About block-parallel Boolean networks: a position …
The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…
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…
Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a…
Among the fundamental questions in computer science is that of the impact of synchronism/asynchronism on computations, which has been addressed in various fields of the discipline: in programming, in networking, in concurrence theory, in…
Boolean networks at the critical point have been a matter of debate for many years as, e.g., scaling of number of attractor with system size. Recently it was found that this number scales superpolynomially with system size, contrary to a…
There is an obvious need for improving the performance and accuracy of a Bayesian network as new data is observed. Because of errors in model construction and changes in the dynamics of the domains, we cannot afford to ignore the…
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 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,…
In this paper we study the dynamical behavior of Boolean networks with firing memory, namely Boolean networks whose vertices are updated synchronously depending on their proper Boolean local transition functions so that each vertex remains…
We state an algorithm that, given an automata network and a block-sequential update schedule, produces an automata network of the same size or smaller with the same limit dynamics under the parallel update schedule. Then, we focus on the…
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…
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…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
A Boolean network is a finite dynamical system, whose variables take values from a binary set. The value update rule for each variable is a Boolean function, depending on a selected subset of variables. Boolean networks have been widely…
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…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…
We realize autonomous Boolean networks by using logic gates in their autonomous mode-of-operation on a field-programmable gate array. This allows us to implement time-continuous systems with complex dynamical behaviors that can be…
Boolean networks model finite discrete dynamical systems with complex behaviours. The state of each component is determined by a Boolean function of the state of (a subset of) the components of the network. This paper addresses the…
Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more…
The problem of reliability of the dynamics in biological regulatory networks is studied in the framework of a generalized Boolean network model with continuous timing and noise. Using well-known artificial genetic networks such as the…