Modeling and querying biomolecular interaction networks

DOI10.1016/J.TCS.2004.03.063MaRDI QIDQ1884862zbMATH OpenOpenAlexFDO

Authors Nathalie Chabrier-Rivier, Marc Chiaverini, Vincent Danos, François Fages, Vincent Schächter

Publication date 27 October 2004

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

Full work available at URL https://doi.org/10.1016/j.tcs.2004.03.063

Mathematics Subject Classification ID

Specification and verification (program logics, model checking, etc.) (68Q60) Biochemistry, molecular biology (92C40)

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Cited in

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• Bioinformatics in protein kinases regulatory network and drug discovery
• Reasoning about non-immediate triggers in biological networks
• CTL update of Kripke models through protections
• Abstract interpretation and types for systems biology
• On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity
• Dynamical modeling and analysis of large cellular regulatory networks
• Analyzing oscillatory behavior with formal methods
• scientific article; zbMATH DE number 6488170 (Why is no real title available?)
• Proving stabilization of biological systems
• From Reaction Models to Influence Graphs and Back: A Theorem
• Computation Tree Regular Logic for Genetic Regulatory Networks
• Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods
• Process Algebra Modelling Styles for Biomolecular Processes
• Simulation techniques for the calculus of wrapped compartments
• Typed stochastic semantics for the calculus of looping sequences
• scientific article; zbMATH DE number 1950559 (Why is no real title available?)
• scientific article; zbMATH DE number 1955876 (Why is no real title available?)
• Multiscale Graph-Theoretic Modeling of Biomolecular Structures
• Bio-logics: logical analysis of bioregulatory networks
• Inferring reaction systems from ordinary differential equations
• A framework for modelling molecular interaction maps
• Translating stochastic CLS into Maude
• Temporal logic modeling of biological systems
• Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints
• Approximating probabilistic behaviors of biological systems using abstract interpretation
• A model and analysis of the AKAP scaffold
• Model Revision from Temporal Logic Properties in Computational Systems Biology
• The Calculus of Looping Sequences for Modeling Biological Membranes
• CTRL: extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks
• A formal approach for tuning stochastic oscillators
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• Modular modelling of signalling pathways and their cross-talk
• Bisimulations in calculi modelling membranes
• On temporal logic constraint solving for analyzing numerical data time series
• Abstract interpretation based verification of temporal properties for BioAmbients

Describes a project that uses

Uses Software

• NuSMV

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