Optimal control of asynchronous boolean networks modeled by petri nets

CEUR Workshop Proceedings

Volumn 724, Issue , 2011, Pages 7-20

  Kobayashi, Koichi ^a   Hiraishi, Kunihiko ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS AND CONTROLS; ASYNCHRONOUS BEHAVIOR; BOOLEAN NETWORK MODELS; BOOLEAN NETWORKS; DISCRETE-TIME NONLINEAR SYSTEMS; GENE REGULATORY NETWORKS; OPTIMAL CONTROL PROBLEM; OPTIMAL CONTROLS;

GENES; OPTIMAL CONTROL SYSTEMS; PETRI NETS;

BOOLEAN ALGEBRA;

EID: 84890324986     PISSN: 16130073     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (26)

1. T. Akutsu, M. Hayashida, W.-K. Ching, and M. K. Ng, Control of Boolean networks: Hardness results and algorithms for tree structured networks, Journal of Theoretical Biology, vol. 244, pp. 670-679, 2007.
2. M. Andrecut, S. A. Kauffman, and A. M. Madni, Evidence of Scale-Free Topology in Gene Regulatory Network of Human Tissues, Int'l Journal of Modern Physics C, vol. 19, no. 2, pp. 283-290, 2008.
3. S. Azuma, E. Yanagisawa, and J. Imura, Controllability Analysis of Biosystems Based on Piecewise Affine Systems Approach, IEEE Trans. on Automatic Control, vol. 53, no. 1, pp. 139-152, 2008.
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.
5. A. Bemporad and M. Morari, Control of systems integrating logic, dynamics, and constraints. Automatica, Vol. 35, pp. 407-427, 1999.
6. E. F. Camacho, C. Bordons, Model Predictive Control, 2nd Edition, Springer, 2004.
7. T. M. Cavalier, P. M. Pardalos, and A. L. Soyster, Modeling and integer programming techniques applied to propositional calculus, Computer & Operations Research, vol. 17, no. 6, pp. 561-570, 1990.
8. C. Chaouiya, E. Remy, P. Ruet, and D. Thieffry, Qualitative Modelling of Genetic Networks: from Logical Regulatory Graphs to Standard Petri Nets, 25th Int'l Conf. on Application and Theory of Petri Nets, LNCS 3099, pp. 137-156, 2004.
9. M. Chaves, Methods for Qualitative Analysis of Genetic Networks, Proc. European Control Conference 2009, pp. 671-676, 2009.
10. A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, External Control in Markovian Genetic Regulatory Networks, Machine Learning, vol. 52, pp. 169-191, 2003.
11. 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.
12. B. Faryabi, J.-F. Chamberland, G. Vahedi, A. Datta, and E. R. Dougherty, Optimal Intervention in Asynchronous Genetic Regulatory Networks, IEEE Journal of Selected Topics in Signal Processing, Vol. 2, No. 3, pp. 412-423, 2008.
13. A. Ichikawa and K. Hiraishi, Analysis and Control of Discrete Event Systems Represented by Petri Nets, Discrete Event Systems: Models and Applications, LNCIS 103, pp. 115-134, 1988.
14. H. D. Jong, Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal of Computational Biology, vol. 9, pp. 67-103, 2002.
15. S. A. Kauffman, Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, vol. 22, pp. 437-467, 1969.
16. M.-S. Kim et al., DNA demethylation in hormone-induced transcriptional derepression, Nature, vol. 461, pp. 1007-1012, 2009.
17. 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, 12 pages, 2010.
18. C. J. Langmead and S. K. Jha, Symbolic Approaches to Finding Control Strategies in Boolean Networks, Journal of Bioinformatics and Computational Biology, vol. 7, no. 2, pp. 323-338, 2009.
19. H. Santos-Rosa and C. Caldas, Chromatin modifier enzymes, the histone code and cancer, European Journal of Cancer, vol. 41, pp. 2381-2402, 2005.
20. 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.
21. L.J. Steggles, R. Banks, and A. Wipat, Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets, Int'l Conf. on Computational Methods in Systems Biology, LNBI 4210, pp. 127-141, 2006.
22. L. Tournier and M.Chaves, Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics, Journal of Theoretical Biology, vol. 260, pp. 196-209, 2009.
23. T. Ushio, Maximally Permissive Feedback and Modular Control Synthesis in Petri Nets with External Input Places, IEEE Trans on Automatic Control, Vol. 35, No. 7, pp. 844-848, 1990.
24. http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/ .
25. http://www.informatik.uni-hamburg.de/TGI/PetriNets/.
26. http://www.princeton.edu/̃chaff/zchaff.html.