Controlling large boolean networks with temporary and permanent perturbations

Abstract

A salient objective of studying gene regulatory networks (GRNs) is to identify potential target genes whose perturbations would lead to effective treatment of diseases. In this paper, we develop two control methods for GRNs in the context of asynchronous Boolean networks. Our methods compute a minimal subset of nodes of a given Boolean network, such that temporary or permanent perturbations of these nodes drive the network from an initial state to a target steady state. The main advantages of our methods include: (1) temporary and permanent perturbations can be feasibly conducted with techniques for genetic modifications in biological experiments; and (2) the minimality of the identified control sets can reduce the cost of experiments to a great extent. We apply our methods to several real-life biological networks in silico to show their efficiency in terms of computation time and their efficacy with respect to the number of nodes to be perturbed.