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Xiaoning Qian, Edward R. Dougherty, "Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on LongRun Behavior," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 1, pp. 123136, January/February, 2012.  
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@article{ 10.1109/TCBB.2011.107, author = {Xiaoning Qian and Edward R. Dougherty}, title = {Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on LongRun Behavior}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {9}, number = {1}, issn = {15455963}, year = {2012}, pages = {123136}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.107}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on LongRun Behavior IS  1 SN  15455963 SP123 EP136 EPD  123136 A1  Xiaoning Qian, A1  Edward R. Dougherty, PY  2012 KW  Gene regulatory networks KW  probabilistic Boolean networks KW  network intervention KW  Markov chain KW  stationary control policy KW  melanoma. VL  9 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A. Datta, A. Choudhary, M.L. Bittner, and E.R. Dougherty, “External Control in Markovian Genetic Regulatory Networks,” Machine Learning, vol. 52, nos. 12, pp. 169181, 2003.
[2] A. Datta, R. Pal, A. Choudhary, and E.R. Dougherty, “Control Approaches for Probabilistic Gene Regulatory Networks,” IEEE Signal Processing Magazine, vol. 24, no. 1, pp. 5463, Jan. 2007.
[3] R. Pal, A. Datta, and E.R. Dougherty, “Optimal Infinite Horizon Control for Probabilistic Boolean Networks,” IEEE Trans. Signal Processing, vol. 54, no. 6, pp. 23752387, June 2006.
[4] R. Pal, A. Datta, M.L. Bittner, and E.R. Dougherty, “Intervention in ContextSensitive Probabilistic Boolean Networks,” Bioinformatics, vol. 21, no. 7, pp. 12111218, 2005.
[5] T. Akutsu, M. Hayashida, W.K. Ching, and M.K. Ng, “Control of Boolean Networks: Hardness Results and Algorithms for the Tree Structured Networks,” J. Theoretical Biology, vol. 244, no. 4, pp. 670677, 2007.
[6] W. Ching, S. Zhang, Y. Jiao, T. Akutsu, N. Tsing, and A. Wong, “Optimal Control Policy for Probabilistic Boolean Networks with Hard Constraints,” IET Systems Biology, vol. 3, no. 2, pp. 9099, Mar. 2009.
[7] Y. Cong, W. Ching, N. Tsing, and H. Leung, “On FiniteHorizon Control of Genetic Regulatory Networks with Multiple HardConstraints,” BMC Systems Biology vol. 4(Suppl 2), article S14, 2010.
[8] G. Vahedi, B. Faryabi, J.F. Chamberland, A. Datta, and E.R. Dougherty, “Intervention in Gene Regulatory Networks via a Stationary MeanFirstPassageTime Control Policy,” IEEE Trans. Biomedical Eng., vol. 55, no. 10, pp. 23192331, Oct. 2008.
[9] X. Qian, I. Ivanov, N. Ghaffari, and E.R. Dougherty, “Intervention in Gene Regulatory Networks via Greedy Control Policies Based on LongRun Behavior,” BMC Systems Biology, vol. 3, article 61, 2009.
[10] D.P. Bertsekas, Dynamic Programming and Optimal Control. Athena Scientific, 2005.
[11] M.K. Ng, S.Q. Zhang, W. Ching, and T. Akutsu, “A Control Model for Markovian Genetic Regulatory Networks,” Trans. Computational Systems Biology, vol. 4070, pp. 3648, 2006.
[12] B. Faryabi, G. Vahedi, J.F. Chamberland, A. Datta, and E.R. Dougherty, “Optimal Constrained Stationary Intervention in Gene Regulatory Networks,” EURASIP J. Bioinformatics and Systems Biology, vol. 2008, article 620767, 2008.
[13] G. Vahedi, B. Faryabi, J.F. Chamberland, A. Datta, and E.R. Dougherty, “Optimal Intervention Strategies for Cyclic Therapeutic Methods,” IEEE Trans. Biomedical Eng., vol. 56, no. 2, pp. 281291, Feb. 2009.
[14] X. Qian and E.R. Dougherty, “Effect of Function Perturbation on the SteadyState Distribution of Genetic Regulatory Networks: Optimal Structural Intervention,” IEEE Trans. Signal Processing, vol. 56, no. 10, pp. 49664976, Oct. 2008.
[15] A. Law and C. Wong, “Stanniocalcin2 Is a Hif1 Target gene that Promotes Cell Proliferation in Hypoxia,” Experimental Cell Research, vol. 316, no. 3, pp. 466476, 2010.
[16] A. Law and C. Wong, “Stanniocalcin2 Promotes Epithelialmesenchymal Transition and Invasiveness in Hypoxic Human Ovarian Cancer Cells,” Experimental Cell Research, vol. 316, no. 20, pp. 34253434, 2010.
[17] S.A. Kauffman, “Homeostasis and Differentiation in Random Genetic Control Networks,” Nature, vol. 224, pp. 177178, 1969.
[18] I. Shmulevich, E.R. Dougherty, S. Kim, and W. Zhang, “Probabilistic Boolean Networks: A RuleBased Uncertainty Model for Gene Regulatory Networks,” Bioinformatics, vol. 18, pp. 261274, 2002.
[19] I. Shmulevich and E.R. Dougherty, Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks. SIAM Press, 2010.
[20] M. Brun, E.R. Dougherty, and I. Shmulevich, “SteadyState Probabilities for Attractors in Probabilistic Boolean Networks,” Signal Processing, vol. 85, no. 10, pp. 19932013, 2005.
[21] S.A. Kauffman, The Origins of Order: SelfOrganization and Selection in Evolution. Oxford Univ. Press, 1993.
[22] F. Li, T. Long, Y. Lu, Q. Ouyang, and C. Tang, “The Yeast CellCycle Network Is Robustly Designed,” Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 47814786, 2004.
[23] P.J. Schweitzer, “Perturbation Theory and Finite Markov Chains,” J. Applied Probability, vol. 5, pp. 401413, 1968.
[24] J.J. Hunter, “Stationary Distributions and Mean First Passage Times of Perturbed Markov Chains,” Linear Algebra and Its Applications, vol. 410, pp. 217243, 2005.
[25] S.A. Kauffman, C. Peterson, B. Samuelsson, and C. Troein, “Genetic Networks with Canalyzing Boolean Rules are Always Stable,” Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 1710217107, 2004.
[26] I. Shmulevich and E.R. Dougherty, Genomic Signal Processing. Princeton Univ. Press, 2007.
[27] I. Shmulevich, H. Lahdesmaki, E.R. Dougherty, J. Astola, and W. Zhang, “The Role of Certain Post Classes in Boolean Network Models of Genetic Networks,” Proc. Nat'l Academy of Sciences USA, vol. 100, pp. 1073410739, 2003.
[28] X. Qian and E.R. Dougherty, “On the LongRun Sensitivity of Probabilistic Boolean Networks,” J. Theoretical Biology, vol. 257, no. 4, pp. 560577, 2009.
[29] M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M. Radmacher, R. Simon, Z. Yakhini, and A. BenDor, “Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling,” Nature, vol. 406, pp. 536540, 2000.
[30] A.T. Weeraratna, Y. Jiang, G. Hostetter, K. Rosenblatt, P. Duray, M. Bittner, and J. Trent, “Wnt5a Signaling Directly Affects Cell Motility and Invasion of Metastatic Melanoma,” Cancer Cell, vol. 1, pp. 279288, 2002.
[31] S.K. Dissanayake, P.B. Olkhanud, M.P. O'Connell, A. Carter, A.D. French, T.C. Camilli, C.D. Emeche, K.J. Hewitt, D.T. Rosenthal, P.D. Leotlela, M.S. Wade, S.W. Yang, L. Brant, B.J. Nickoloff, J.L. Messina, A. Biragyn, K.S. Hoek, D.D. Taub, D.L. Longo, V.K. Sondak, S.M. Hewitt, and A.T. Weeraratna, “Wnt5a Regulates Expression of TumorAssociated Antigens in Melanoma via Changes in Signal Transducers and Activators of Transcription 3 Phosphorylation,” Cancer Research, vol. 68, no. 24, pp. 1020510214, 2008.
[32] S. Kim, H. Li, E.R. Dougherty, N.W. Cao, Y.D. Chen, M. Bittner, and E.B. Suh, “Can Markov Chain Models Mimic Biological Regulation?,” J. Biology Systems, vol. 10, no. 4, pp. 337357, 2002.
[33] I. Miyazaki, S. Simizu, H. Okumura, S. Takagi, and H. Osada, “A SmallMolecule Inhibitor Shows that Pirin Regulates Migration of Melanoma Cells,” Nature Chemical Biology, vol. 6, pp. 667673, 2010.