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

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  • Koichi Kobayashi

Abstract

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.

Suggested Citation

  • Koichi Kobayashi, 2019. "Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction," Complexity, Hindawi, vol. 2019, pages 1-9, March.
  • Handle: RePEc:hin:complx:9261793
    DOI: 10.1155/2019/9261793
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    1. Filippo Menolascina & Gianfranco Fiore & Emanuele Orabona & Luca De Stefano & Mike Ferry & Jeff Hasty & Mario di Bernardo & Diego di Bernardo, 2014. "In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-14, May.
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