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

Phenotype control and elimination of variables in Boolean networks

Corresponding author(s): Tonello, Elisa (elisa.tonello@fu-berlin.de); Paulevé, Loïc (loic.pauleve@labri.fr)

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

Conflict of interest of the recommender and peer reviewers:
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.

[1] Akutsu, T.; Zhao, Y.; Hayashida, M.; Tamura, T. Integer programming-based approach to attractor detection and control of boolean networks, IEICE TRANSACTIONS on Information and Systems, Volume 95 (2012) no. 12, pp. 2960-2970 | DOI

[2] Argyris, G. A.; Lluch Lafuente, A.; Tribastone, M.; Tschaikowski, M.; Vandin, A. Reducing Boolean networks with backward equivalence, BMC bioinformatics, Volume 24 (2023) no. Suppl 1, p. 212 (Publisher: Springer) | DOI

[3] Biane, C.; Delaplace, F. Causal reasoning on Boolean control networks based on abduction: theory and application to cancer drug discovery, IEEE/ACM transactions on computational biology and bioinformatics, Volume 16 (2018) no. 5, pp. 1574-1585 (Publisher: IEEE) | DOI

[4] Chaouiya, C. Disclosing effects of Boolean network reduction on dynamical properties and control strategies, Peer Community in Mathematical and Computational Biology (2024) | DOI

[5] Cifuentes Fontanals, L.; Tonello, E.; Siebert, H. Control strategy identification via trap spaces in Boolean networks, Computational Methods in Systems Biology: 18th International Conference, CMSB 2020, Konstanz, Germany, September 23–25, 2020, Proceedings 18, Springer, 2020, pp. 159-175 | DOI

[6] Cifuentes-Fontanals, L.; Tonello, E.; Siebert, H. Control in Boolean networks with model checking, Frontiers in Applied Mathematics and Statistics, Volume 8 (2022), p. 838546 (Publisher: Frontiers Media SA) | DOI

[7] Glass, L.; Kauffman, S. A. The logical analysis of continuous, non-linear biochemical control networks, Journal of Theoretical Biology, Volume 39 (1973) no. 1, pp. 103-129 | DOI

[8] Kadelka, C.; Butrie, T.-M.; Hilton, E.; Kinseth, J.; Schmidt, A.; Serdarevic, H. A meta-analysis of Boolean network models reveals design principles of gene regulatory networks, Science Advances, Volume 10 (2024) no. 2 | DOI

[9] Kaminski, R.; Schaub, T.; Siegel, A.; Videla, S. Minimal intervention strategies in logical signaling networks with ASP, Theory and Practice of Logic Programming, Volume 13 (2013) no. 4-5, pp. 675-690 (Publisher: Cambridge University Press) | DOI

[10] Klarner, H.; Siebert, H. Approximating attractors of Boolean networks by iterative CTL model checking, Frontiers in bioengineering and biotechnology, Volume 3 (2015), p. 130 (Publisher: Frontiers Media SA) | DOI

[11] Moon, K.; Lee, K.; Paulevé, L. Computational Complexity of Minimal Trap Spaces in Boolean Networks, arXiv (2022) | DOI

[12] Naldi, A.; Remy, E.; Thieffry, D.; Chaouiya, C. A reduction of logical regulatory graphs preserving essential dynamical properties, International Conference on Computational Methods in Systems Biology, Springer, 2009, pp. 266-280 | DOI

[13] Naldi, A.; Remy, E.; Thieffry, D.; Chaouiya, C. Dynamically consistent reduction of logical regulatory graphs, Theoretical Computer Science, Volume 412 (2011) no. 21, pp. 2207-2218 (Publisher: Elsevier) | DOI

[14] Naldi, A.; Richard, A.; Tonello, E. Linear cuts in Boolean networks, Natural Computing (2023), pp. 1-21 (Publisher: Springer) | DOI

[15] Paulevé, L. Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis, Peer Community Journal, Volume 3 (2023) (Publisher: Peer Community In) | DOI

[16] Paulevé, L.; Kolčák, J.; Chatain, T.; Haar, S. Reconciling qualitative, abstract, and scalable modeling of biological networks, Nature communications, Volume 11 (2020) no. 1, p. 4256 | DOI

[17] Plaugher, D.; Murrugarra, D. Phenotype control techniques for Boolean gene regulatory networks, Bulletin of mathematical biology, Volume 85 (2023) no. 10, p. 89 (Publisher: Springer) | DOI

[18] Pušnik, Ž.; Mraz, M.; Zimic, N.; Moškon, M. Review and assessment of Boolean approaches for inference of gene regulatory networks, Heliyon, Volume 8 (2022) no. 8 | DOI

[19] Riva, S.; Lagniez, J.-M.; López, G. M.; Paulevé, L. Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks, International Conference on Computational Methods in Systems Biology, Springer, 2023, pp. 157-174 | DOI

[20] Samaga, R.; Kamp, A. V.; Klamt, S. Computing combinatorial intervention strategies and failure modes in signaling networks, Journal of Computational Biology, Volume 17 (2010) no. 1, pp. 39-53 (Publisher: Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA) | DOI

[21] Schwab, J. D.; Kühlwein, S. D.; Ikonomi, N.; Kühl, M.; Kestler, H. A. Concepts in Boolean network modeling: What do they all mean?, Computational and structural biotechnology journal, Volume 18 (2020), pp. 571-582 (Publisher: Elsevier) | DOI

[22] Schwieger, R.; Tonello, E. Reduction for asynchronous Boolean networks: elimination of negatively autoregulated components, Discrete Mathematics & Theoretical Computer Science, Volume 25 (2024) no. Automata, Logic and Semantics (Publisher: Episciences. org) | DOI

[23] Sordo Vieira, L.; Laubenbacher, R. C.; Murrugarra, D. Control of intracellular molecular networks using algebraic methods, Bulletin of mathematical biology, Volume 82 (2020) no. 1, p. 2 (Publisher: Springer) | DOI

[24] Su, C.; Pang, J. A dynamics-based approach for the target control of Boolean networks, Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 2020, pp. 1-8 | DOI

[25] Su, C.; Pang, J. Sequential temporary and permanent control of Boolean networks, International Conference on Computational Methods in Systems Biology, Springer, 2020, pp. 234-251 | DOI

[26] Tonello, E.; Paulevé, L. Attractor identification in asynchronous Boolean dynamics with network reduction, 21st International Conference on Computational Methods in Systems Biology (CMSB 2023), 2023 | DOI

[27] Trinh, V.-G.; Benhamou, B.; Hiraishi, K.; Soliman, S. Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding, Computational Methods in Systems Biology: 20th International Conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022, Proceedings, Springer, 2022, pp. 158-176 | DOI

[28] Veliz-Cuba, A. Reduction of Boolean network models, Journal of Theoretical Biology, Volume 289 (2011), pp. 167-172 | DOI

[29] Veliz-Cuba, A.; Aguilar, B.; Hinkelmann, F.; Laubenbacher, R. Steady state analysis of Boolean molecular network models via model reduction and computational algebra, BMC bioinformatics, Volume 15 (2014), pp. 1-8 (Publisher: Springer) | DOI

[30] Zañudo, J. G. T.; Albert, R. Cell Fate Reprogramming by Control of Intracellular Network Dynamics, PLOS Computational Biology, Edited by Denis Thieffry, Volume 11 (2015) no. 4 | DOI

[31] Zañudo, J. G. T.; Albert, R. An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks, Chaos: An Interdisciplinary Journal of Nonlinear Science, Volume 23 (2013) no. 2 | DOI

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