Optimal control of probabilistic Boolean networks using polynomial optimization

IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

Volumn E95-A, Issue 9, 2012, Pages 1512-1517

  Kobayashi, Koichi ^a   Hiraishi, Kunihiko ^a  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Optimal control; Polynomial optimization; Probabilistic Boolean networks; Systems biology

Indexed keywords

BOOLEAN ALGEBRA; OPTIMAL CONTROL SYSTEMS; OPTIMIZATION; SOFTWARE RELIABILITY;

GENE REGULATORY NETWORKS; OPTIMAL CONTROL PROBLEM; OPTIMAL CONTROLS; POLYNOMIAL OPTIMIZATION; POLYNOMIAL OPTIMIZATION PROBLEM; PROBABILISTIC BOOLEAN NETWORKS; STATE TRANSITION DIAGRAMS; SYSTEMS BIOLOGY;

POLYNOMIALS;

EID: 84865722519     PISSN: 09168508     EISSN: 17451337     Source Type: Journal    
DOI: 10.1587/transfun.E95.A.1512     Document Type: Article

References (22)

1. T. Akutsu, M. Hayashida, W.-K. Ching, and M. K. Ng, "Control of Boolean networks: Hardness results and algorithms for tree structured networks", J. Theoretical Biology, vol. 244, pp. 670-679, 2007. (Pubitemid 46148979)
2. T. Akutsu, "Discrete models of genetic networks and their control", J. Society of Instrument and Control Engineering, vol. 47, no. 8, pp. 664-669, 2008 (in Japanese).
3. S. Azuma, E. Yanagisawa, and J. Imura, "Controllability analysis of biosystems based on piecewise affine systems approach", IEEE Trans. Autom. Control, vol. 53, no. 1, pp. 139-152, 2008. (Pubitemid 351314545)
4. C. Belta, J. Schug, T. Dang, V. Kumar, G. J. Pappas, H. Rubin, and P. Dunlap, "Stability and reachability analysis of a hybrid model of luminescence in the marine bacterium Vibrio fischeri", Proc. 40th IEEE Conf. on Decision and Control, pp. 869-874, 2001. (Pubitemid 34139031)
5. W.-K. Ching, S.-Q. Zhang, Y. Jiao, T. Akutsu, N.-K. Tsing, and A. S. Wong, "Optimal control policy for probabilistic Boolean networks with hard constraints", IET Systems Biology, vol. 3, no. 2, pp. 90-99, 2009.
6. A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, "External control in Markovian genetic regulatory networks", Mach. Learn., vol. 52, pp. 169-191, 2003.
7. A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, "External control in Markovian genetic regulatory networks: The imperfect information case", Bioinfomatics, vol. 20, pp. 924-930, 2004. (Pubitemid 38559734)
8. B. Faryabi, G. Vahedi, J.-F. Chamberland, A. Datta, and E. R. Dougherty, "Intervention in context-sensitive probabilistic Boolean networks revisited", EURASIP Journal on Bioinformatics and Systems Biology, vol. 2009, article ID 360864, 2009.
9. S. A. Kauffman, "Metabolic stability and epigenesis in randomly constructed genetic nets", J. Theoretical Biology, vol. 22, pp. 437-467, 1969.
10. K. Kobayashi, J. Imura, and K. Hiraishi, "Polynomial-time algorithm for controllability test of a class of Boolean biological networks", EURASIP Journal on Bioinformatics and Systems Biology, vol. 2010, Article ID 210685, p. 12, 2010.
11. K. Kobayashi and K. Hiraishi, "An integer programming approach to optimal control problems in context-sensitive probabilistic Boolean networks", Automatica, vol. 47, no. 6, pp. 1260-1264, 2011.
12. C. J. Langmead and S. K. Jha, "Symbolic approaches to finding control strategies in Boolean networks", J. Bioinformatics and Computational Biology, vol. 7, no. 2, pp. 323-338, 2009.
13. A. Milias-Argeitis, S. Summers, J. Stewart-Ornstein, I. Zuleta, D. Pincus, H. El-Samad, M. Khammash, and J. Lygeros, "In silico feedback for in vivo regulation of a gene expression circuit", Nature Biotechnology, vol. 29, no. 12, pp. 1114-1116, 2011.
14. A. Mochizuki, "An analytical study of the number of steady states in gene regulatory networks", J. Theoretical Biology, vol. 236, pp. 291-310, 2005. (Pubitemid 41008696)
15. R. Pal, A. Datta, M. L. Bittner, and E. R. Dougherty, "Intervention in context-sensitive probabilistic Boolean networks", Bioinformatics, vol. 21, pp. 1211-1218, 2005. (Pubitemid 40467947)
16. R. Pal, A. Datta, M. L. Bittner, and E. R. Dougherty, "Optimal infinite-horizon control for probabilistic Boolean networks", IEEE Trans. Signal Process., vol. 54, no. 6, pp. 2375-2387, 2006. (Pubitemid 43805580)
17. H. Santos-Rosa and C. Caldas, "Chromatin modifier enzymes, the histone code and cancer", European Journal of Cancer, vol. 41, pp. 2381-2402, 2005. (Pubitemid 41540617)
18. I. Shmulevich, E. R. Dougherty, S. Kim, and W. Zhang, "Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks", Bioinformatics, vol. 18, pp. 261-274, 2002. (Pubitemid 34183104)
19. A. T. Weeraratna, Y. Jiang, G. Hostetter, K. Rosenblatt, P. Duray, M. Bittner, and J. M. Trent, "Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma", Cancer Cell, vol. 1, pp. 279-288, 2002. (Pubitemid 41039152)
20. H. P. Williams, Model building in mathematical programming, 4th ed., John Willey & Sons, 1999.
21. Y. Xiao and E. R. Dougherty, "The impact of function perturbations in Boolean networks", Bioinformatics, vol. 23, pp. 1265-1273, 2007. (Pubitemid 47050543)
22. http://www.is.titech.ac.jp/-kojima/SparsePOP/SparsePOP.html