Graph-theoretic topological control of biological genetic networks

Proceedings of the American Control Conference

Volumn , Issue , 2009, Pages 1700-1705

  Aswani, Anil ^a   Boyd, Nicholas ^a   Tomlin, Claire ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTROL OBJECTIVES; GENE THERAPY; GENETIC NETWORKS; GRAPH PROBLEMS; GRAPH-THEORETIC; NEGATIVE FEEDBACK; NP-HARD; STABLE OSCILLATIONS;

ABSTRACTING; COMPUTATIONAL COMPLEXITY; DRUG THERAPY; FEEDBACK; GENETIC ENGINEERING; HEURISTIC ALGORITHMS; HEURISTIC METHODS; TOPOLOGY;

GRAPH THEORY;

EID: 70449638287     PISSN: 07431619     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ACC.2009.5160714     Document Type: Conference Paper

References (27)

1. A. Aswani and C. Tomlin, "Topology based control of biological genetic networks," in Proceedings of 47th IEEE CDC, Cancun, Dec. 2008, to appear.
2. A. Motter, N. Gulbahce, E. Almaas, and A.-L. Barabási, "Predicting synthetic rescues in metabolic networks," Molecular Systems Biology, vol. 4, 2008.
3. H. L. Smith, Monotone dynamical systems: an introduction to the theory of competitive and cooperative systems. American Mathematical Society, 1995.
4. E. D. Sontag, "Monotone and near-monotone biochemical networks," Systems and Synthetic Biology, vol. 1, no. 2, pp. 59-87, April 2007.
5. H. Kunze and D. Siegel, "A graph theoretical approach to monotonicity with respect to initial conditions," in Comparison Methods and Stability Theory, X. Liu and D. Siegal, Eds. CRC, 1994.
6. T. Kobayashi, L. Chen, and K. Aihara, "Modeling genetic switches with positive feedback loops," Journal of Theoretical Biology, vol. 221, pp. 379-399, 2003.
7. E. Plahte, T. Mestl, and S. Omholt, "Feedback loops, stability, and multistationarity in dynamical systems," Journal of Biological Systems, vol. 3, pp. 409-413, 1995.
8. J.-L. Gouzé, "Positive and negative circuits in dynamical systems," Journal of Biological Systems, vol. 6, pp. 11-15, 1998.
9. O. Cinquin and J. Demongeot, "Positive and negative feedback: striking a balance between necessary antagonists," Journal of Theoretical Biology, vol. 216, pp. 229-241, 2002.
10. C. Soulé, "Graphic requirements for multistationarity," Complexus, vol. 1, pp. 123-133, 2003.
11. A. Aswani and C. Tomlin, "Reachability algorithm for biological piecewise-affine hybrid systems," in HSCC, 2007, pp. 633-636.
12. A. Aswani, "Reachability algorithm for a class of biologically inspired piecewise-affine hybrid systems," Master's thesis, University of California at Berkeley, 2007.
13. F. Hüffner, N. Betzler, and R. Niedermeier, "Optimal edge deletions for signed graph balancing," in Experimental Algorithms, 2007, pp. 297-310.
14. B. DasGupta, G. Enciso, E. Sontag, and Y. Zhang, "Algorithmic and complexity results for decompositions of biological networks into monotone subsystems," Biosystems, vol. 90, no. 1, pp. 161-178, 2007.
15. E. Sontag, A. Veliz-Cuba, R. Laubenbacher, and A. S. Jarrah, "The effect of negative feedback loops on the dynamics of boolean networks," Biophysical Journal, vol. 95, pp. 518-526, 2008.
16. J. Lewis and M. Yannakakis, "The node-deletion problem for hereditary properties is NP-complete," Journal Of Computer and System Sciences, vol. 20, no. 2, pp. 219-230, 1980.
17. J. Cheriyan, H. Karloff, and Y. Rabani, "Approximating directed multicuts," in 42nd IEEE Symposium on Foundatiosn of Computer Science, 2001.
18. A. Gupta, "Improved results for directed multicut," in 14th Annual ACM-SIAM symposium on Discrete algorithms, 2003.
19. S. L. Harris and A. J. Levine, "The p53 pathway: positive and negative feedback loops," Oncogene, vol. 24, pp. 2899-2908, 2005.
20. S. Ries, C. Biederer, D. Woods, O. Shifman, S. Shirasawa, T. Sasazuki, M. McMahon, M. Oren, and F. McCormick, "Opposing effects of Ras on p53: Transcriptional activation of MDM2 and induction of p19 ARF," Cell, vol. 103, pp. 321-330, 2000.
21. M. Takagi, M. J. Absalon, K. G. McLure, and M. B. Kastan, "Regulation of p53 translation and induction after DNA damage by ribosomal protein L26 and Nucleolin," Cell, vol. 123, pp. 49-63, 2005.
22. T. Léveillard and B. Wasylyk, "The MDM2 C-terminal region binds to TAFii250 and is required for MDM2 regulation of the Cyclin A promoter," The Journal of Biological Chemistry, vol. 272, no. 49, pp. 30 651-30 661, 1997.
23. J. Chuzhoy and S. Khanna, "Hardness of cut problems in directed graphs," in STOC '06: Proceedings of the thirty-eighth annual ACM symposium on Theory of computing. New York, NY, USA: ACM, 2006, pp. 527-536.
24. R. Lougee-Heimer, "The Common Optimization INterface for operations research," IBM Journal of Research and Development, vol. 47, no. 1, pp. 57-66, 2003.
25. G. Ganguli and B. Wasylyk, "p53-independent functions of MDM2," Molecular Cancer Research, vol. 1, pp. 1027-1035, 2003.
26. M. Ashcroft and K. H. Vousden, "Regulation of p53 stability," Oncogene, vol. 18, pp. 7637-7643, 1999.
27. L. T. Vassilev, B. T. Vu, B. Graves, D. Carvajal, F. Podlaski, Z. Filipovic, N. Kong, U. Kammlott, C. Lukacs, C. Klein, N. Fotouhi, and E. A. Liu, "In vivo activation of the p53 pathway by small-molecule antagonists of MDM2," Science, vol. 303, no. 5659, pp. 844-848, 2004.