Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic
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Publication:2189295
DOI10.1016/j.jtbi.2004.04.003zbMath1440.92036OpenAlexW2121149194WikidataQ80282566 ScholiaQ80282566MaRDI QIDQ2189295
Janine Guespin, Adrien Richard, Gilles Bernot, Jean-Paul Comet
Publication date: 15 June 2020
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jtbi.2004.04.003
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Cites Work
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- Identification of all steady states in large networks by logical analysis
- Logical identification of all steady states: The concept of feedback loop characteristic states
- Dynamical behaviour of biological regulatory networks. I: Biological role of feedback loops and practical use of the concept of the loop- characteristic state
- Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits
- Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior
- Qualitative dynamics of piecewise-linear differential equations: a discrete mapping approach
- Interpolants and Symbolic Model Checking
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