Modeling and control in cancer genomics

Modeling and Control of Complex Systems

Volumn , Issue , 2007, Pages 339-366

  Datta, Aniruddha ^a   Choudhary, Ashish ^a   Bittner, Michael L ^b   Dougherty, Edward R ^a,b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79551624721     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (28)

1. DeRisi, J., Penland, L., Brown, P. O., Bittner, M. L., Meltzer, P. S., Ray, M., Chen, Y., Su, Y. A., &Trent, J. M. (1996). Use of a cDNA Microarray to Analyze Gene Expression Patterns in Human Cancer. Nature Genetics, 14, 457-460.
2. DeRisi, J. L., Iyer, V. R., &Brown, P. O. (1997). Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science, 278, 680-686.
3. Schena, M., Shalon, D., Davis, R. W., &Brown, P. O. (1995). Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray. Science, 270, 467-470.
4. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O., &Davis, R. W. (1996). Parallel Human Genome Analysis: Microarray-Based Expression Monitoring of 1000 Genes. Proceedings of the National Academy of Sciences USA, 93,10614-10619.
5. Wodicka, L., Dong, H., Mittmann, M., Ho, M. H., &Lockhart, D. J. (1997). Genome-wide Expression Monitoring inSaccharomyces cerevisiae. Nature Biotechnology, 15, 1359-1367.
6. Dougherty, E. R., Kim, S., &Chen, Y. (2000). Coefficient of Determination in Nonlinear Signal Processing. Signal Processing, 80(10), 2219-2235.
7. Kim, S., Dougherty, E. R., Bittner, M. L., Chen, Y., Sivakumar, K., Meltzer, P., &Trent, J. M. (2000). A General Framework for the Analysis of Multivariate Gene Interaction via Expression Arrays. Biomedical Optics, 4(4), 411-424.
8. Kim, S., Dougherty, E. R., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J. M., &Bittner, M. (2000). Multivariate Measurement of Gene-Expression Relationships. Genomics, 67, 201-209.
9. Kemeny, J. G. &Snell, J. L. (1976). Finite Markov Chains. Springer-Verlag, Berlin, 1976.
10. Shmulevich, I., Dougherty, E. R., Kim, S., &Zhang, W. (2002). Probabilistic Boolean Networks: A Rule-Based Uncertainty Model for Gene Regulatory Networks. Bioinformatics, 18, 261-274.
11. Shmulevich, I., Dougherty, E. R., &Zhang, W. (2002). From Boolean to Probabilistic Boolean Networks as Models of Genetic Regulatory Networks. Proceedings of the IEEE, 90(11), 1778-1792.
12. Shmulevich, I., Dougherty, E. R., &Zhang, W. (2002). Gene Perturbation and Intervention in Probabilistic Boolean Networks. Bioinformatics, 18,1319-1331.
13. Shmulevich, I., Dougherty, E. R., &Zhang, W. (2002). Control of Stationary Behavior in Probabilistic Boolean Networks by Means of Structural Intervention. Biological Systems, 10(4), 431-446.
14. Kauffman, S. A. (1969). Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets. Theoretical Biology, 22, 437-467.
15. Kauffman, S. A. &Levin, S. (1987). Towards a General Theory of Adaptive Walks on Rugged Landscapes. Theoretical Biology, 128, 11-45.
16. Kauffman, S. A. (1993). The Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press, New York.
17. Bertsekas, D. P. (2000). Dynamic Programming and Optimal Control, Athena Scientific, Nashua, NH.
18. Bellman, R. (1957). Dynamic Programming, Princeton University Press, Princeton, NJ.
19. Bittner, M., Meltzer, P., Chen, Y., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben-Dor, A., Sampas, N., Dougherty, E., Wang, E., Marincola, F., Gooden, C., Lueders, J., Glatfelter, A., Pollock, P., Carpten, J., Gillanders, E., Leja, D., Dietrich, K., Beaudry, C., Berens, M., Alberts, D., &Sondak, V. (2000). Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling. Nature, 406 (6795), 536-540.
20. Weeraratna, A. T., Jiang, Y., Hostetter, G., Rosenblatt, K., Duray, P., Bittner, M., &Trent, J. M. (2002). Wnt5a Signalling Directly Affects Cell Motility and Invasion of Metastatic Melanoma. Cancer Cell, 1, 279-288.
21. Kim, S., Li, H., Dougherty, E. R., Cao, N., Chen, Y., Bittner, M., &Suh, E. (2002). Can Markov Chain Models Mimic Biological Regulation?Journal of Biological Systems, 10(4), 337-357.
22. Datta, A., Choudhary, A., Bittner, M. L., &Dougherty, E. R. (2004). External Control in Markovian Genetic Regulatory Networks: The Imperfect Information Case. Bioinformatics, 20(6), 924-930.
23. Pal, R., Datta, A., Bittner, M. L., &Dougherty, E. R. (2005). Intervention in Context-Sensitive Probabilistic Boolean Networks. Bioinformatics, 21,1211-1218.
24. Choudhary, A., Datta, A., Bittner, M. L., &Dougherty, E. R. (2005). Assignment of Terminal Penalties in Controlling Genetic Regulatory Networks. Proceedings of the American Control Conference, 417-422.
25. Kalman, R. E. (1962). Canonical Structure of Linear Dynamical Systems. Proc. Natl. Acad. Sci., 596-600.
26. Pal, R., Datta, A., &Dougherty, E. R. (2006). Optimal Infinite Horizon Control for Probabilistic Boolean Networks. IEEE Transactions on Signal Processing, 54, 2375-2387.
27. Pal, R., Ivanov, I., Datta, A., &Dougherty, E. R. (2005). Generating Boolean Networks with a Prescribed Attractor Structure. Bioinformatics, 21, 4021-4025.
28. Zhou, X., Wang, X., Pal, R., Ivanov, I., &Dougherty, E. R. (2004). A Bayesian Connectivity-Based Approach to Constructing Probabilistic Gene Regulatory Networks. Bioinformatics, 20, 2918-2927.