Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction

Fixed points in Boolean networks (BNs) represent cell types or states of cells and are important to decide characteristics of cells. As the control problem on fixed points, it is important to consider the problem of changing fixed points by using external stimuli (i.e., control inputs). In this pape...

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Bibliographic Details
Published inComplexity (New York, N.Y.) Vol. 2019; no. 2019; pp. 1 - 9
Main Author Kobayashi, Koichi
Format Journal Article
LanguageEnglish
Published Cairo, Egypt Hindawi Publishing Corporation 01.01.2019
Hindawi
John Wiley & Sons, Inc
Hindawi Limited
Hindawi-Wiley
Subjects
Algorithms
Apoptosis
Bioinformatics
Biology
Boolean algebra
Boolean functions
Control theory
Dynamical systems
Feedback
Gene expression
Graph theory
Graphs
Integer programming
Linear programming
Mathematical models
Methods
Model reduction
Tumor necrosis factor-TNF
Vertex sets
Cuba
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Summary:Fixed points in Boolean networks (BNs) represent cell types or states of cells and are important to decide characteristics of cells. As the control problem on fixed points, it is important to consider the problem of changing fixed points by using external stimuli (i.e., control inputs). In this paper, we propose two methods for designing fixed points. First, a design method using model reduction is proposed. Using the reduced model, the problem of placing fixed points can be rewritten as an integer linear programming problem. Next, we consider the design problem using only the graph structure of a given BN and derive some results. In both methods, a feedback vertex set of a directed graph plays an important role. Finally, a biological example is presented.
ISSN:1076-2787
1099-0526
DOI:10.1155/2019/9261793