Encoding threshold Boolean networks into reaction systems for the analysis of gene regulatory networks

DOI10.3233/FI-2021-2021MaRDI QIDQ5164854zbMATH OpenOpenAlexFDO

Authors Roberto Barbuti, Pasquale Bove, Roberta Gori, Damas Gruska, Francesca Levi, Paolo Milazzo

Publication date 15 November 2021

Published in Fundamenta Informaticae (Search for Journal in Brave)

Full work available at URL https://doi.org/10.3233/fi-2021-2021

Mathematics Subject Classification ID

Computer science (68-XX)

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Cites work

• A static analysis for brane calculi providing global occurrence counting information
• A tour of reaction systems
• Abstract interpretation based verification of temporal properties for BioAmbients
• An analysis for causal properties of membrane interactions
• Ancestors, descendants, and gardens of Eden in reaction systems
• Causal static analysis for brane calculi
• Causality in Membrane Systems
• Computing preimages and ancestors in 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
• Modelling opacity using Petri nets
• Multiset patterns and their application to dynamic causalities in membrane systems
• Predictors for flat membrane systems
• Reaction systems
• Specialized predictor for reaction systems with context properties
• Studying opacity of reaction systems through formula based predictors

Cited in

(5)

• Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation
• A new method of determining threshold of gene network based on phenotypes
• Computing preimages and ancestors in reaction systems
• Fixed points and attractors of reactantless and inhibitorless reaction systems
• Cycles and global attractors of reactantless and inhibitorless reaction systems

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