Related papers: About block-parallel Boolean networks: a position …
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
This is the second paper of a series of two about the structural properties that influence the asymptotic dynamics of Random Boolean Networks. Here we study the functionally independent clusters in which the relevant elements, introduced…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
An automata network (AN) is a finite graph where each node holds a state from a finite alphabet and is equipped with a local map defining the evolution of the state of the node depending on its neighbors. The global dynamics of the network…
Biological systems rely on robust internal information processing: Survival depends on highly reproducible dynamics of regulatory processes. Biological information processing elements, however, are intrinsically noisy (genetic switches,…
In this work we study the Boolean Networks of different geometric shape and lattice organization. It was revealed that no only a spatial shape but also type of lattice are very important for definition of the structure-dynamics relation.…
Computer networks have become a critical infrastructure. In fact, networks should not only meet strict requirements in terms of correctness, availability, and performance, but they should also be very flexible and support fast updates,…
This paper studies synchronization in coupled nonlinear dynamic networks with unknown parameters. Adaptation can be added to one or several elements in the network, while preserving the global synchronization conditions derived in…
Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…
Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be…
Boolean networks constitute relevant mathematical models to study the behaviours of genetic and signalling networks. These networks define regulatory influences between molecular nodes, each being associated to a Boolean variable and a…
The dynamical organization in the presence of noise of a Boolean neural network with random connections is analyzed. For low levels of noise, the system reaches a stationary state in which the majority of its elements acquire the same…
We provide the first classification of different types of Random Boolean Networks (RBNs). We study the differences of RBNs depending on the degree of synchronicity and determinism of their updating scheme. For doing so, we first define…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
In this paper, we address the formal characterization of targets triggering cellular trans-differentiation in the scope of Boolean networks with asynchronous dynamics. Given two fixed points of a Boolean network, we are interested in all…
Random boolean cellular automata are investigated, where each gate has two randomly chosen inputs and is randomly assigned a boolean function of its inputs. The effect of non-uniform distributions on the choice of the boolean functions is…
This paper details a method for optimising the size of Boolean automata networks in order to compute their attractors under the parallel update schedule. This method relies on the formalism of modules introduced recently that allows for…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of…