- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 246761, 11 pages
Optimal Control of Gene Regulatory Networks with Effectiveness of Multiple Drugs: A Boolean Network Approach
School of Information Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
Received 30 April 2013; Revised 25 June 2013; Accepted 12 July 2013
Academic Editor: Lei Chen
Copyright © 2013 Koichi Kobayashi and Kunihiko Hiraishi. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- H. Santos-Rosa and C. Caldas, “Chromatin modifier enzymes, the histone code and cancer,” European Journal of Cancer, vol. 41, no. 16, pp. 2381–2402, 2005.
- A. Milias-Argeitis, S. Summers, J. Stewart-Ornstein et al., “In silico feedback for in vivo regulation of a gene expression circuit,” Nature Biotechnology, vol. 29, no. 12, pp. 1114–1116, 2011.
- S. A. Kauffman, “Metabolic stability and epigenesis in randomly constructed genetic nets,” Journal of Theoretical Biology, vol. 22, no. 3, pp. 437–467, 1969.
- H. D. Jong, “Modeling and simulation of genetic regulatory systems: a literature review,” Journal of Computational Biology, vol. 9, no. 1, pp. 67–103, 2002.
- T. Akutsu, M. Hayashida, W. Ching, and M. K. Ng, “Control of Boolean networks: hardness results and algorithms for tree structured networks,” Journal of Theoretical Biology, vol. 244, no. 4, pp. 670–679, 2007.
- S. Azuma, E. Yanagisawa, and J. Imura, “Controllability analysis of biosystems based on piecewise-affine systems approach,” IEEE Transactions on Automatic Control, vol. 53, pp. 139–152, 2008.
- 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.
- C. J. Langmead and S. K. Jha, “Symbolic approaches for finding control strategies in boolean networks,” Journal of Bioinformatics and Computational Biology, vol. 7, no. 2, pp. 323–338, 2009.
- A. Mochizuki, “An analytical study of the number of steady states in gene regulatory networks,” Journal of Theoretical Biology, vol. 236, no. 3, pp. 291–310, 2005.
- 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, no. 2, pp. 261–274, 2002.
- 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, 13 pages, 2009.
- R. Pal, A. Datta, M. L. Bittner, and E. R. Dougherty, “Intervention in context-sensitive probabilistic Boolean networks,” Bioinformatics, vol. 21, no. 7, pp. 1211–1218, 2005.
- I. Shmulevich, E. R. Dougherty, and W. Zhang, “Control of stationary behavior in probabilistic Boolean networks by means of structural intervention,” Journal of Biological Systems, vol. 10, no. 4, pp. 431–445, 2002.
- Y. Xiao and E. R. Dougherty, “The impact of function perturbations in Boolean networks,” Bioinformatics, vol. 23, no. 10, pp. 1265–1273, 2007.
- M. R. Yousefi, A. Datta, and E. R. Dougherty, “Optimal intervention strategies for therapeutic methods with fixed-length duration of drug effectiveness,” IEEE Transactions on Signal Processing, vol. 60, no. 9, pp. 4930–4944, 2012.
- X. Chen, T. Akutsu, T. Tamura, and W. K. Ching, “Finding optimal control policy in probabilistic Boolean networks with hard constraints by using integer programming and dynamic programming,” International Journal of Data Mining and Bioinformatics, vol. 7, no. 3, pp. 321–343, 2013.
- 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.
- A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, “External control in Markovian genetic regulatory networks,” Machine Learning, vol. 52, no. 1-2, pp. 169–191, 2003.
- A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, “External control in Markovian genetic regulatory networks: the imperfect information case,” Bioinformatics, vol. 20, no. 6, pp. 924–930, 2004.
- S. Z. Denic, B. Vasic, C. D. Charalambous, and R. Palanivelu, “Robust control of uncertain context-sensitive probabilistic Boolean networks,” IET Systems Biology, vol. 3, no. 4, pp. 279–295, 2009.
- R. Pal, A. Datta, and E. R. Dougherty, “Optimal infinite-horizon control for probabilistic Boolean networks,” IEEE Transactions on Signal Processing, vol. 54, no. 6, pp. 2375–2387, 2006.
- 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.
- K. Kobayashi and K. Hiraishi, “Probabilistic control of Boolean networks with multiple dynamics: Towards control of gene regulatory,” in Proceedings of the 50th IEEE Conference on Decision and Control and European Control Conference (CDC-ECC), pp. 4371–4376, Orlando, Fla, USA, 2011.
- S. Marshall, L. Yu, Y. Xiao, and E. R. Dougherty, “Inference of a probabilistic boolean network from a single observed temporal sequence,” Eurasip Journal on Bioinformatics and Systems Biology, vol. 2007, Article ID 32454, 15 pages, 2007.
- M. Chaves, “Methods for qualitative analysis of genetic networks,” in Proceedings of the European Control Conference, pp. 671–676, 2009.
- L. Tournier and M. Chaves, “Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics,” Journal of Theoretical Biology, vol. 260, no. 2, pp. 196–209, 2009.
- A. T. Weeraratna, Y. Jiang, G. Hostetter et al., “Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma,” Cancer Cell, vol. 1, no. 3, pp. 279–288, 2002.
- F. Adamek, M. Sobotka, and O. Stursberg, “Stochastic optimal control for hybrid systems with uncertain discrete dynamics,” in Proceedings of the 4th IEEE Conference on Automation Science and Engineering (CASE '08), pp. 23–28, Arlington, Va, USA, August 2008.
- A. Bemporad and S. Di Cairano, “Optimal control of discrete hybrid stochastic automata,” in Hybrid Systems: Computation and Control, vol. 3414 of Lecture Notes in Computer Science, pp. 417–432, 2005.
- K. Kobayashi, K. Matou, and K. Hiraishi, “Probabilistic-constrained optimal control of a class of stochastic hybrid systems,” International Journal of Control, Automation and Systems, vol. 10, no. 5, pp. 897–904, 2012.
- H. P. Williams, Model Building in Mathematical Programming, John Wiley & Sons, New York, NY, USA, 4th edition, 1999.
- T. M. Cavalier, P. M. Pardalos, and A. L. Soyster, “Modeling and integer programming techniques applied to propositional calculus,” Computers and Operations Research, vol. 17, no. 6, pp. 561–570, 1990.
- IBM ILOG CPLEX Optimizer, http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/index.html.
- MathWorks MATLAB, http://www.mathworks.com/.
- J. Liang and J. Han, “Stochastic Boolean networks: an efficient approach to modeling gene regulatory networks,” BMC Systems Biology, vol. 6, article 113, 20 pages, 2012.
- K. Kobayashi and K. Hiraishi, “Optimal control of probabilistic Boolean networks using polynomial optimization,” IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, vol. 95, no. 9, pp. 1512–1517, 2012.
- R. K. Layek, A. Datta, and E. R. Dougherty, “From biological pathways to regulatory networks,” Molecular BioSystems, vol. 7, no. 3, pp. 843–851, 2011.