TITLE:
Attractor-Based Simultaneous Design of the Minimum Set of Control Nodes and Controllers in Boolean Networks
AUTHORS:
Koichi Kobayashi
KEYWORDS:
Boolean Networks, Integer Linear Programming, Minimum Set of Control Nodes, Singleton Attractors
JOURNAL NAME:
Applied Mathematics,
Vol.7 No.14,
August
18,
2016
ABSTRACT: Design of control strategies for gene
regulatory networks is a challenging and important topic in systems biology. In
this paper, the problem of finding both a minimum set of control nodes (control
inputs) and a controller is studied. A control node corresponds to a gene that
expression can be controlled. Here, a Boolean network is used as a model of
gene regulatory networks, and control specifications on attractors, which
represent cell types or states of cells, are imposed. It is important to design
a gene regulatory network that has desired attractors and has no undesired
attractors. Using a matrix-based representation of BNs, this problem can be
rewritten as an integer linear programming problem. Finally, the proposed
method is demonstrated by a numerical example on a WNT5A network, which is
related to melanoma.