ArticleBioinformatics (Oxford, England)2025
Refining Boolean models with the partial most permissive scheme.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Applications of synthetic biology in biomedicine.Molecular biomedicine · 2026Review
- BioLogical: a universal analysis framework for biosystem logical dynamics.Computational and structural biotechnology journal · 2026Article
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4 authors.
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Abstract
motivationIn systems biology, modeling strategies aim to decode how molecular components interact to generate dynamical behavior. Boolean modeling is more and more used, but the description of the dynamics generated by discrete variables with only two values may be too limited to capture certain dynamical properties. Multivalued logical models can overcome this limitation by allowing more than two levels for each component. However, multivaluing a Boolean model is challenging.
resultsWe present MRBM, a method for efficiently identifying the components of a Boolean model to be multivalued in order to capture specific fixed-point reachabilities in the asynchronous dynamics. To this goal, we defined a new updating scheme locating reachability properties in the most permissive dynamics. MRBM is supported by mathematical demonstrations and illustrated on a toy model and on two models of stem cell differentiation. AVAILABILITY AND IMPLEMENTATION: The MRBM method and the BMs used in this article are available on GitHub at: https://github.com/NdnBnBn/MRBM, and archived in Zenodo (doi: 10.5281/ZENODO.14979798).
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