Integer programming-based methods for attractor detection and control of boolean networks

One of the important topics in systems biology is to develop theory and methods for control of biological networks, which might lead to development of novel treatment methods for difficult diseases. On the other hand, the Boolean network (BN) model is known as a mathematical model of genetic networks. Though many studies have been done on analysis of steady states (i.e., attractors) in BNs, only a few studies have been done on control of BNs. In this paper, we consider three problems on BNs: detection of a singleton attractor, finding a control strategy that brings a BN from a given initial state to the desired state, and control of attractors. We propose integer programming-based methods which solve these problems in a unified manner. We also present results of computational experiments, which suggest that the proposed methods are useful for solving moderate size instances of these problems.