title: Integer programming-based method for observability of singleton attractors in Boolean networks.
abstract: Boolean network (BN) is a popular mathematical model for revealing the behaviour of a genetic regulatory network. Furthermore, observability, an important network feature, plays a significant role in understanding the underlying network. Several studies have been done on analysis of observability of BNs and complex networks. However, the observability of attractor cycles, which can serve as biomarker detection, has not yet been addressed in the literature. This is an important, interesting and challenging problem that deserves a detailed study. In this study, a novel problem was first proposed on attractor observability in BNs. Identification of the minimum set of consecutive nodes can be used to discriminate different attractors. Furthermore, it can serve as a biomarker for different disease types (represented as different attractor cycles). Then a novel integer programming method was developed to identify the desired set of nodes. The proposed approach is demonstrated and verified by numerical examples. The computational results further illustrates that the proposed model is effective and efficient.
authors.affiliation: School of Mathematics and Statistics, Xian Jiaotong Univeristy, Xian, People's Republic of China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Cheng
authors.affiliation: College of Mathematics and Statistics, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. Yushan.Qiu@bcm.edu.
authors.forename: Yushan
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Advanced Modeling and Applied Computing Laboratory, Department of Mathematics, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Wenpin
authors.initials: W
authors.lastname: Hou
authors.affiliation: Advanced Modeling and Applied Computing Laboratory, Department of Mathematics, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Wai-Ki
authors.initials: WK
authors.lastname: Ching
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020543:Proteome / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D020543:Proteome