Bifurcations in Boolean Networks [PDF]
Discrete Mathematics & Theoretical Computer Science, 2011 This paper characterizes the attractor structure of synchronous and asynchronous Boolean networks induced by bi-threshold functions. Bi-threshold functions are generalizations of standard threshold functions and have separate threshold values for the transitions $0 \rightarrow $1 (up-threshold) and $1 \rightarrow 0$ (down-threshold).
Chris Kuhlman +3 more
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Analysis and practical guideline of constraint-based boolean method in genetic network inference. [PDF]
PLoS ONE, 2012 Boolean-based method, despite of its simplicity, would be a more attractive approach for inferring a network from high-throughput expression data if its effectiveness has not been limited by high false positive prediction.
Treenut Saithong +3 more
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An attractor-based complexity measurement for Boolean recurrent neural networks. [PDF]
PLoS ONE, 2014 We provide a novel refined attractor-based complexity measurement for Boolean recurrent neural networks that represents an assessment of their computational power in terms of the significance of their attractor dynamics.
Jérémie Cabessa, Alessandro E P Villa
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Quantum annealing algorithms for Boolean tensor networks
Scientific Reports, 2022 Quantum annealers manufactured by D-Wave Systems, Inc., are computational devices capable of finding high-quality heuristic solutions of NP-hard problems.
Elijah Pelofske +4 more
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Asynchronous Simulation of Boolean Networks by Monotone Boolean Networks [PDF]
, 2016 To appear in the proceedings of ACA 2016 (fourth International Workshop on Asynchronous Cellular Automata and Asynchronous Discrete Models)
Melliti, Tarek +3 more
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Concurrency in Boolean networks [PDF]
Natural Computing, 2019 Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component updates can have a dramatic impact on the predicted behaviours.
Chatain, Thomas +4 more
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A Boolean Network Approach to Study the Mechanism Associated with Inflammatory Response Induced by Porphyromonas gingivalis [PDF]
Archives of Razi Institute, 2023 Anaerobic Porphyromonas gingivalis is a rod-shaped bacterium and is a primary agent of periodontal inflammation and thus periodontitis. This bacterium disturbs the normal flora of the oral cavity and causes dysbiosis.
A Gasmi Benahmed +3 more
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A parallel attractor-finding algorithm based on Boolean satisfiability for genetic regulatory networks. [PDF]
PLoS ONE, 2014 In biological systems, the dynamic analysis method has gained increasing attention in the past decade. The Boolean network is the most common model of a genetic regulatory network.
Wensheng Guo +4 more
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An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. [PDF]
PLoS ONE, 2013 Regulatory networks play a central role in cellular behavior and decision making. Learning these regulatory networks is a major task in biology, and devising computational methods and mathematical models for this task is a major endeavor in ...
Natalie Berestovsky, Luay Nakhleh
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Review and assessment of Boolean approaches for inference of gene regulatory networks
Heliyon, 2022 Boolean descriptions of gene regulatory networks can provide an insight into interactions between genes. Boolean networks hold predictive power, are easy to understand, and can be used to simulate the observed networks in different scenarios.We review ...
Žiga Pušnik +3 more
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