Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation

DOI10.1016/J.TCS.2020.07.031MaRDI QIDQ2044945zbMATH OpenOpenAlexWikidataFDO

Authors Roberto Barbuti, Roberta Gori, Paolo Milazzo

Publication date 11 August 2021

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2020.07.031

zbMATH Keywords

Boolean networksdynamic causalitiesgene regulatory networksreaction systems

Mathematics Subject Classification ID

Theory of computing (68Qxx)

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Cites work

• A tour of reaction systems
• Ancestors, descendants, and gardens of Eden in reaction systems
• Controllability of reaction systems
• Criticality in random threshold networks: annealed approximation and beyond
• Generalized contexts for reaction systems: definition and study of dynamic causalities
• Investigating dynamic causalities in reaction systems
• Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation.
• Multiset patterns and their application to dynamic causalities in membrane systems
• Predictors for flat membrane systems
• Reaction systems
• Robustness and fragility of Boolean models for genetic regulatory networks
• Specialized predictor for reaction systems with context properties
• Studying opacity of reaction systems through formula based predictors
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}

Cited in

(9)

• Formalizing and enriching phenotype signatures using Boolean networks
• A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
• Automated inference of gene regulatory networks using explicit regulatory modules
• Evolvability of reaction systems and the invisibility theorem
• Boolean modeling of genetic regulatory networks
• Encoding threshold Boolean networks into reaction systems for the analysis of gene regulatory networks
• Exploiting Modularity of SOS Semantics to Define Quantitative Extensions of Reaction Systems
• Robust set stability of implicit Boolean networks with time delay and function perturbation
• Cycles and global attractors of reactantless and inhibitorless reaction systems

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