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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| Format: | Article |
| Language: | English |
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Wiley
2019-01-01
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| Series: | Complexity |
| Online Access: | http://dx.doi.org/10.1155/2019/9261793 |
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| _version_ | 1850176491187339264 |
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| author | Koichi Kobayashi |
| author_facet | Koichi Kobayashi |
| author_sort | Koichi Kobayashi |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-c1747f8fe8b146a4a0f0a8d21c14bb1d |
| institution | OA Journals |
| issn | 1076-2787 1099-0526 |
| language | English |
| publishDate | 2019-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Complexity |
| spelling | doaj-art-c1747f8fe8b146a4a0f0a8d21c14bb1d2025-08-20T02:19:15ZengWileyComplexity1076-27871099-05262019-01-01201910.1155/2019/92617939261793Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model ReductionKoichi Kobayashi0Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, JapanFixed 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.http://dx.doi.org/10.1155/2019/9261793 |
| spellingShingle | Koichi Kobayashi Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction Complexity |
| title | Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction |
| title_full | Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction |
| title_fullStr | Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction |
| title_full_unstemmed | Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction |
| title_short | Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction |
| title_sort | design of fixed points in boolean networks using feedback vertex sets and model reduction |
| url | http://dx.doi.org/10.1155/2019/9261793 |
| work_keys_str_mv | AT koichikobayashi designoffixedpointsinbooleannetworksusingfeedbackvertexsetsandmodelreduction |