Related papers: Harmonic Analysis of Boolean Networks: Determinati…
Canalization is a classic concept in Developmental Biology that is thought to be an important feature of evolving systems. In a Boolean network it is a form of network robustness in which a subset of the input signals control the behavior…
We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
We consider the problem of selecting a minimum size subset of nodes in a network, that allows to activate all the nodes of the network. We present a fast and simple algorithm that, in real-life networks, produces solutions that outperform…
Inhibition is considered to shape neural activity, and broaden its pattern repertoire. In the sensory organs, where the anatomy of neural circuits is highly structured, lateral inhibition sharpens contrast among stimulus properties. The…
We study the relationship between dynamical properties and interaction patterns in complex oscillator networks in the presence of noise. A striking finding is that noise leads to a general, one-to-one correspondence between the dynamical…
This paper proposes and investigates a Boolean gossip model as a simplified but non-trivial probabilistic Boolean network. With positive node interactions, in view of standard theories from Markov chains, we prove that the node states…
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…
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of…
The collective behavior of cortical neurons is strongly affected by the presence of noise at the level of individual cells. In order to study these phenomena in large-scale assemblies of neurons, we consider networks of firing-rate neurons…
When using Bayesian networks for modelling the behavior of man-made machinery, it usually happens that a large part of the model is deterministic. For such Bayesian networks deterministic part of the model can be represented as a Boolean…
We study experimentally the synchronization patterns in time-delayed directed Boolean networks of excitable systems. We observe a transition in the network dynamics when the refractory time of the individual systems is adjusted. When the…
This paper aims at the study of controllability properties and induced controllability metrics on complex networks governed by a class of (discrete time) linear decision processes with mul-tiplicative noise. The dynamics are given by a…
We examined the effects of inhomogeneity on the dynamics and structural properties using Boolean networks. Two different power-law rank outdegree distributions were embedded to determine the role of hubs. The degree of randomness and…
Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…
A Boolean network is a mapping $f :\{0,1\}^n \to \{0,1\}^n$, which can be used to model networks of $n$ interacting entities, each having a local Boolean state that evolves over time according to a deterministic function of the current…
We present and discuss the results of an experimental analysis in the design of Boolean networks by means of genetic algorithms. A population of networks is evolved with the aim of finding a network such that the attractor it reaches is of…
We consider the problem of identifying the most influential nodes for a spreading process on a network when prior knowledge about structure and dynamics of the system is incomplete or erroneous. Specifically, we perform a numerical analysis…
Discrete-time regulatory networks are dynamical systems on directed graphs, with a structure inspired on natural systems of interacting units. There is a natural notion of determination amongst vertices, which we use to classify the nodes…