A Boolean network control algorithm guided by forward dynamic programming

• Published in: PloS one Vol. 14; no. 5; p. e0215449
• Main Authors: Moradi, Mohammad, Goliaei, Sama, Foroughmand-Araabi, Mohammad-Hadi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02.05.2019; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Animals; Bioinformatics; Biology; Biology and Life Sciences; Boolean algebra; Boolean functions; Cancer; Cell cycle; Computer and Information Sciences; Control algorithms; Control theory; Drosophila; Drosophila melanogaster - genetics; Dynamic programming; Fruit flies; Gene expression; Gene Regulatory Networks; Genes; Genetic regulation; Integer programming; Intervention; Lymphocytes T; Mathematical models; Medicine and Health Sciences; Methods; Models, Theoretical; Network control; Networks; Physical Sciences; Receptors, Antigen, T-Cell - genetics; Receptors, Antigen, T-Cell - metabolism; Research and Analysis Methods; Source code; T cell receptors; T cells; T-cell receptor; Web services; Iran
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0215449

Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This paper provides an algorithm to solve the control problem in Boolean networks. The proposed algorithm is implemented and applied on two biological systems: T-cell receptor network and Drosophila melanogaster network. Results show that the proposed algorithm works faster in solving the control problem over these networks, while having similar accuracy, in comparison to previous exact methods. Source code and a simple web service of the proposed algorithm is available at http://goliaei.ir/net-control/www/.