Control Strategy Identification via Trap Spaces in Boolean Networks

Cifuentes Fontanals, Laura; Tonello, Elisa; Siebert, Heike

doi:10.1007/978-3-030-60327-4_9

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Control Strategy Identification via Trap Spaces in Boolean Networks

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Cifuentes Fontanals, Laura
IMPRS for Biology and Computation (Anne-Dominique Gindrat), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Cifuentes Fontanals, L., Tonello, E., & Siebert, H. (2020). Control Strategy Identification via Trap Spaces in Boolean Networks. In A. Abate, T. Petrov, & V. Wolf (Eds.), CMSB 2020, part of Lecture Notes in Computer Science 12314 (pp. 159-175). Cham, Switzerland: Springer Nature Switzerland AG. doi:10.1007/978-3-030-60327-4_9.

Cite as: https://hdl.handle.net/21.11116/0000-000E-5B36-0

Abstract

The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables, force the system to evolve to a desired state. This work presents a new approach for finding control strategies in biological systems modeled by Boolean networks. In this context, we explore the properties of trap spaces, subspaces of the state space which the dynamics cannot leave. Trap spaces for biological networks can often be efficiently computed, and provide useful approximations of attraction basins. Our approach provides control strategies for a target phenotype that are based on interventions that allow the control to be eventually released. Moreover, our method can incorporate information about the attractors to find new control strategies that would escape usual percolation-based methods. We show the applicability of our approach to two cell fate decision models.