Section: Mathematical & Computational Biology
Topic: Biophysics and computational biology, Applied mathematics

Phenotype control and elimination of variables in Boolean networks

Tonello, Elisa1  ; Paulevé, Loïc2  
1 Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
2 Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France

10.24072/pcjournal.452 - Peer Community Journal, Volume 4 (2024), article no. e79.

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We investigate how elimination of variables can affect the asymptotic dynamics and phenotype control of Boolean networks. In particular, we look at the impact on minimal trap spaces, and identify a structural condition that guarantees their preservation. We examine the possible effects of variable elimination under three of the most popular approaches to control (attractor-based control, value propagation and control of minimal trap spaces), and under different update schemes (synchronous, asynchronous, generalized asynchronous). We provide some insights on the application of reduction, and an ample inventory of examples and counterexamples.

Published online:
DOI: 10.24072/pcjournal.452
Type: Research article
Keywords: Boolean networks, control, reduction, trap spaces

Tonello, Elisa 1; Paulevé, Loïc 2

1 Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
2 Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Tonello, Elisa; Paulevé, Loïc. Phenotype control and elimination of variables in Boolean networks. Peer Community Journal, Volume 4 (2024), article  no. e79. doi : 10.24072/pcjournal.452. https://peercommunityjournal.org/articles/10.24072/pcjournal.452/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100318

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The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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