Related papers: Synthesis of Boolean Networks from Biological Dyna…
In the context of discrete dynamical systems and their applications, fixed points often have a clear interpretation. This is indeed a central topic of gene regulatory mechanisms modeled by Boolean automata networks (BANs), where a…
Boolean networks can be viewed as functions on the set of binary strings of a given length, described via logical rules. They were introduced as dynamic models into biology, in particular as logical models of intracellular regulatory…
The effects of the finite size of the network on the evolutionary dynamics of a Boolean network are analyzed. In the model considered, Boolean networks evolve via a competition between nodes that punishes those in the majority. It is found…
The determination and classification of fixed points of large Boolean networks is addressed in terms of constraint satisfaction problem. We develop a general simplification scheme that, removing all those variables and functions belonging…
Dynamic processes of interacting units on a network are out of equilibrium in general. In the case of a directed tree, the dynamic cavity method provides an efficient tool that characterises the dynamic trajectory of the process for the…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
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…
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…
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…
Boolean networks, inspired by gene regulatory networks, were developed to understand the complex behaviors observed in biological systems, with network attractors corresponding to biological phenotypes or cell types. In this article, we…
We study the target control problem of asynchronous Boolean networks, to identify a set of nodes, the perturbation of which can drive the dynamics of the network from any initial state to the desired steady state (or attractor). We are…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
The network inference problem arises in biological research when one needs to quantitatively choose the best protein-interaction model for explaining a phenotype. The diverse nature of the data and nonlinear dynamics pose significant…
Probabilistic Boolean Networks have been proposed for estimating the behaviour of dynamical systems as they combine rule-based modelling with uncertainty principles. Inferring PBNs directly from gene data is challenging however, especially…
Boolean networks are a general model of interacting entities, with applications to biological phenomena such as gene regulation. Attractors play a central role, and the schedule of entities update is a priori unknown. This article presents…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
We consider the problem of studying the simulation capabilities of the dynamics of arbitrary networks of finite states machines. In these models, each node of the network takes two states 0 (passive) and 1 (active). The states of the nodes…
The ability to achieve coordinated behavior --engineered or emergent-- on networked systems has attracted widespread interest over several fields. This has led to remarkable advances on the development of a theoretical understanding of the…
Boolean functional synthesis is the process of constructing a Boolean function from a Boolean specification that relates input and output variables. Despite significant recent developments in synthesis algorithms, Boolean functional…
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…