Boolean networks
Fixed Points of Boolean Networks, Guessing Graphs, and Coding Theory
... that networks whose interaction graphs do not have a positive cycle ...of Boolean networks: a network has at most 2 k + fixed points, where k + is the minimum size of a positive feedback vertex set ...
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Sequential Reprogramming of Boolean Networks Made Practical
... regulatory networks modelled as Boolean ...for networks of more than 60 nodes. Keywords: Cell reprogramming · Boolean networks · ...
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Topological fixed points in Boolean networks
... of Boolean networks. On one side, the dynamics of a Boolean network with n components is usually described by the successive iterations of a map F from {0, 1} n to ...
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Most Permissive Semantics of Boolean Networks
... Bibliography [1] Lo¨ıc Paulev´ e, Juraj Kolˇ c´ ak, Thomas Chatain, and Stefan Haar. Reconciling qualitative, abstract, and scalable modeling of biological networks. bioRxiv, 2020. doi:10.1101/2020.03.22.998377 . ...
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Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision
... Boolean Networks (BNs), and logical models in general, are widely adopted for the modelling of signalling pathways and gene and transcription factors net- works ...
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A fixed point theorem for Boolean networks expressed in terms of forbidden subnetworks
... in Boolean networks, ...sub- networks of f as the restrictions of f to the hypercubes contained in {0, 1} n , and we exhibit a class F of Boolean networks, called even or odd self-dual ...
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Isomorphic Boolean networks and dense interaction graphs
... (x)). Boolean networks have many applications; in particular, they are omnipresent in the modeling of neural and gene networks (see [4] for a ...
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Boolean Networks: Beyond Generalized Asynchronicity
... expecting Boolean networks to produce an over-approximation of reachable configurations due to the abstraction of parameters related to speed and activity threshold of components, as it is usually assumed ...
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From kernels in directed graphs to fixed points and negative cycles in Boolean networks
... of Boolean networks called and-nets, and we address the question of whether the absence of negative cycle in local interaction graphs implies the existence of a fixed ...
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Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data
... signaling networks are not static in nature since proteins go through many biochemical modifications such as ubiquitination and phosphorylation to propagate signals that act as feed-back to the ...protein-protein ...
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Static Analysis of Boolean Networks Based on Interaction Graphs: A Survey
... Abstract Boolean networks are discrete dynamical systems extensively used to model biological regulatory ...these networks suffers from the combinatorial explosion of the state space, which grows ...
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Analysis Tools for Interconnected Boolean Networks With Biological Applications
... France Boolean networks with asynchronous updates are a class of logical models particularly well adapted to describe the dynamics of biological networks with uncertain ...large networks, ...
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A reduction method for noisy Boolean networks
... geneti Boolean networks to study their stability to what he alled minimal perturba- ...probabilisti Boolean networks (a lass of Boolean networks that en
losed the lass of syn
...
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Temporal Reprogramming of Boolean Networks
... the Boolean network and a perturbation counter. A transition of the Boolean network is necessarily between two states with the same counter; a perturbation transition is necessarily between a state with ...
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Concurrency in Boolean networks
... Received: date / Accepted: date Abstract Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolu- tion of each ...
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Reduction and Fixed Points of Boolean Networks and Linear Network Coding Solvability
... over a finite alphabet A (usually referred to as Boolean networks if A = {0, 1}) with a given interaction graph, that describes which local functions depend on which variables. In this paper, we generalise ...
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Fixed point theorems for Boolean networks expressed in terms of forbidden subnetworks
... Theorem 10. 1. f is positive-circular if and only if f is 2-critical and non-expansive. 2. f is negative-circular if and only if f is 0-critical and non-expansive. Even if the two points of this theorem seem similar ...
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Number of Fixed Points and Disjoint Cycles in Monotone Boolean Networks
... gene networks, arcs come from experimental data and are thus usually not ignored: results concerning φ m (G) are then more relevant than those concerning φ 0 m ...
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A semiquantitative framework for gene regulatory networks: increasing the time and quantitative resolution of Boolean networks
... biological networks is impeded by a scarcity in ki- netic information on the biochemical reactions that form them, a focus in systems biology, pio- neered by the work of Kauffman [ 2 ] and Thomas [ 3 ], lies on ...
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Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming
... of Boolean functions and an update ...of Boolean functions composing the candidate BNs is typically delimited by a given influence graph (often called Prior Knowledge Network), which specifies for each node ...
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