Intervention in gene regulatory networks with maximal phenotype alteration

Bioinformatics

Volumn 29, Issue 14, 2013, Pages 1758-1767

  Yousefi, Mohammadmahdi R ^a   Dougherty, Edward R ^a,b  

^a Department of Electrical and Computer Engineering   (United States)

^b TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CELL CYCLE; GENE REGULATORY NETWORK; GENETICS; HUMAN; MELANOMA; METABOLISM; METASTASIS; PATHOLOGY; PHENOTYPE; PROBABILITY; SYSTEM ANALYSIS; ARTICLE;

ALGORITHMS; CELL CYCLE; GENE REGULATORY NETWORKS; HUMANS; MELANOMA; NEOPLASM METASTASIS; PHENOTYPE; PROBABILITY; PROGRAMMING, LINEAR;

EID: 84880216913     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt242     Document Type: Article

References (38)

1. Altman, E. (1999) Constrained Markov Decision Processes. Chapman & Hall/CRC, Boca Raton, FL, USA.
2. Bittner, M. et al. (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature, 406, 536-540.
3. Brun, M. et al. (2005) Steady-state probabilities for attractors in probabilistic Boolean networks. Signal. Process., 85, 1993-2013.
4. Ching, W.K. et al. (2009) Optimal control policy for probabilistic boolean networks with hard constraints. IET Syst. Biol., 3, 90-99.
5. Cho, G.E. and Meyer, C.D. (2001) Comparison of perturbation bounds for the stationary distribution of a Markov chain. Linear Algebra Appl., 335, 137-150.
6. Datta, A. et al. (2003) External control in Markovian genetic regulatory networks. Mach. Learn., 52, 169-191.
7. Datta, A. and Dougherty, E.R. (2006) Introduction to Genomic Signal Processing with Control. CRC Press.
8. Derman, C. (1970) Finite State Markovian Decision Processes. Academic Press, New York.
9. Dissanayake, S.K. et al. (2008) Wnt5a regulates expression of tumor-associated antigens in melanoma via changes in signal transducers and activators of transcription 3 phosphorylation. Cancer Res., 68, 10205-10214.
10. Dougherty, E.R. and Datta, A. (2005) Genomic signal processing: diagnosis and therapy. IEEE Signal Process. Mag., 22, 107-112.
11. Dougherty, E.R. et al. (2010) Stationary and structural control in gene regulatory networks: basic concepts. Int. J. Syst. Sci., 41, 5-16.
12. Faryabi, B. et al. (2007) On approximate stochastic control in genetic regulatory networks. IET Syst. Biol., 1, 361-368.
13. Faryabi, B. et al. (2009) Intervention in context-sensitive probabilistic Boolean networks revisited. EURASIP J. Bioinform. Syst. Biol., 2009, Aritcle ID 360864.
14. Faure, A. et al. (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics, 22, e124-e131.
15. Ghaffari, N. et al. (2010) A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. Bioinformatics, 26, 1556-1563.
16. Ivanov, I. et al. (2007) Dynamics preserving size reduction mappings for probabilistic Boolean networks. IEEE Trans. Signal Process., 55, 2310-2322.
17. Ivanov, I. et al. (2010) Selection policy-induced reduction mappings for Boolean networks. IEEE Trans. Signal Process., 58, 4871-4882.
18. Kallenberg, L.C.M. (1983) Linear Programming and Finite Markovian Control Problems. Mathematisch Centrum, Amsterdam.
19. Kauffman, S.A. (1993) The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, New York, NY, USA.
20. Law, A. and Wong, C. (2010a) Stanniocalcin-2 is a Hif-1 target gene that promotes cell proliferation in hypoxia. Exp. Cell Res., 316, 466-476.
21. Law, A. and Wong, C. (2010b) Stanniocalcin-2 promotes epithelialmesenchymal transition and invasiveness in hypoxic human ovarian cancer cells. Exp. Cell Res., 316, 3425-3434.
22. Megiddo, N. (1987) On the complexity of linear programming. In: Advances in Economic Theory: Fifth World Congress. Cambridge University Press, New York, NY, USA, pp. 225-268.
23. Pal, R. et al. (2006) Optimal infinite-horizon control for probabilistic Boolean networks. IEEE Trans. Signal Process., 54, 2375-2387.
24. Pal, R. et al. (2008) Robust intervention in probabilistic Boolean networks. IEEE Trans. Signal Process., 56, 1280-1294.
25. Pal, R. et al. (2009) Bayesian robustness in the control of gene regulatory networks. IEEE Trans. Signal Process., 57, 3667-3678.
26. Qian, X. and Dougherty, E.R. (2008) Effect of function perturbation on the steady-state distribution of genetic regulatory networks: optimal structural intervention. IEEE Trans. Signal Process., 56, 4966-4976.
27. Qian, X. and Dougherty, E.R. (2012) Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior. IEEE ACM Trans. Comput. Biol., 9, 123-136.
28. Qian, X. et al. (2009) Intervention in gene regulatory networks via greedy control policies based on long-run behavior. BMC Syst. Biol., 3, 61.
29. Qian, X. et al. (2010) State reduction for network intervention with probabilistic Boolean networks. Bioinformatics, 26, 3098-3194.
30. Ross, K.W. (1989) Randomized and past-dependent policies for Markov decision processes with multiple constraints. Oper. Res., 37, 474-477.
31. Seneta, E. (1988) Perturbation of the stationary distribution measured by ergodicity coefficients. Adv. Appl. Probab., 20, 228-230.
32. Shmulevich, I. et al. (2002a) Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics, 18, 261-274.
33. Shmulevich, I. et al. (2002b) Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics, 18, 1319-1331.
34. Shmulevich, I. et al. (2002c) Control of stationary behavior in probabilistic Boolean networks by means of structural intervention. J. Biol. Syst., 10, 431-445.
35. Vahedi, G. et al. (2008) Intervention in gene regulatory networks via a stationary mean-first-passage-time control policy. IEEE Trans. Biomed. Eng., 55, 2319-2331.
36. Weeraratna, A.T. et al. (2002) Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma. Cancer Cell, 1, 279-288.
37. Xiao, Y. and Dougherty, E.R. (2007) The impact of function perturbations in Boolean networks. Bioinformatics, 23, 1265-1273.
38. Yousefi, M.R. et al. (2012) Optimal intervention strategies for therapeutic methods with fixed-length duration of drug effectiveness. IEEE Trans. Signal Process., 60, 4930-4944.