An efficient approach towards the source-target control of Boolean networks

in IEEE/ACM Transactions on Computational Biology and Bioinformatics (2020), 17(6), 1932-1945

We study the problem of computing a minimal subset of nodes of a given asynchronous Boolean network that need to be perturbed in a single-step to drive its dynamics from an initial state to a target ... [more ▼]

We study the problem of computing a minimal subset of nodes of a given asynchronous Boolean network that need to be perturbed in a single-step to drive its dynamics from an initial state to a target steady state (or attractor), which we call the source-target control of Boolean networks. Due to the phenomenon of state-space explosion, a simple global approach that performs computations on the entire network, may not scale well for large networks. We believe that efficient algorithms for such networks must exploit the structure of the networks together with their dynamics. Taking this view, we derive a decomposition-based solution to the minimal source-target control problem which can be significantly faster than the existing approaches on large networks. We then show that the solution can be further optimised if we take into account appropriate information about the source state. We apply our solutions to both real-life biological networks and randomly generated networks, demonstrating the efficiency and efficacy of our approach. [less ▲]

Controlling large Boolean networks with single-step perturbations

in Bioinformatics (2019), 35(14), 558-567

Controlling large Boolean networks with temporary and permanent perturbations

in Proceedings of the 23rd International Symposium on Formal Methods (FM'19) (2019)

On the Full Control of Boolean Networks

in Proceedings of the 16th International Conference on Computational Methods in Systems Biology (2018)

A Decomposition-based Approach towards the Control of Boolean Networks

in Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (2018)