Sampling-rate-dependent probabilistic Boolean networks

Journal of Theoretical Biology

Volumn 261, Issue 4, 2009, Pages 540-547

  Vahedi, Golnaz ^a   Faryabi, Babak ^a   Chamberland, Jean Francois ^a   Datta, Aniruddha ^a   Dougherty, Edward R ^a,b  

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

^b TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

Gene regulatory network; Intervention; Optimal control; Probabilistic Boolean network

Indexed keywords

BIOLOGICAL ANALYSIS; GENE; MARKOV CHAIN; OBSERVATIONAL METHOD; PROBABILITY; SAMPLING;

ARTICLE; BIOMEDICINE; GENE REGULATORY NETWORK; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROBABILITY; SAMPLING; STATISTICAL ANALYSIS; STATISTICAL MODEL;

GENE REGULATORY NETWORKS; HUMANS; MARKOV CHAINS; MODELS, STATISTICAL; PROBABILITY; TIME FACTORS;

EID: 70350571734     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.08.026     Document Type: Article

References (19)

1. Bertsekas D.P. Dynamic Programming and Optimal Control (2005), Athena Scientific, Belmont, MA
2. Bouvet M., Bold R.J., Lee J., Evans D.B., Abbruzzese J.L., Chiao P.J., McConkey D.J., Chandra J., Chada S., Fang B., and Roth J.A. Adenovirus-mediated wild-type p53 tumor suppressor gene therapy induces apoptosis and suppresses growth of human pancreatic cancer. Annals of Surgical Oncology 5 8 (1998) 681-688
3. Deng X., Geng H., and Matache M.T. Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes. BioSystems 88 1-2 (2007) 16-34
4. El-Deiry W.S., Tokino T., Velculescu V.E., Levy D.B., Parsons R., Trent J.M., Lin D., Mercer W.E., Kinzler K.W., and Vogelstein B. Waf1, a potential mediator of p53 tumor suppression. Cell 75 4 (1993) 817-825
5. Faryabi B., Chamberland J.F., Vahedi G., Datta A., and Dougherty E.R. Optimal intervention in asynchronous genetic regulatory networks. IEEE Journal of Selected Topics in Signal Processing 2 3 (2008) 412-423
6. Faryabi, B., Chamberland, J.F., Vahedi, G., Datta, A., Dougherty, E.R., 2009. Intervention in context-sensitive probabilistic Boolean networks revisited. EURASIP Journal on Bioinformatics and Systems Biology 2009 (2009), Article ID 360864, 13 pages.
7. Gershenson, C., 2002. Classification of random Boolean networks. In: Proceedings of the Eighth International Conference on Artificial Life (Artificial Life VIII), Sydney, Australia, December 2002, pp. 1-8.
8. Greil F., and Drossel B. The dynamics of critical Kauffman networks under asynchronous stochastic update. Physical Review Letters 95 4 (2005) 048701
9. Harvey, I., Bossomaier, T., 1997. Time out of joint: attractors in asynchronous random Boolean networks. In: Proceedings of the Fourth European Conference on Artificial Life (ECAL97), July 1997. MIT Press, Cambridge, MA, pp. 67-75.
10. Huang S. Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. Journal of Molecular Medicine 77 6 (1999) 469-480
11. Kauffman S. The Origins of Order: Self-Organization and Selection in Evolution (1993), Oxford University Press, New York
12. Miyashita T., and Reed J.C. Tumor suppressor p53 is a direct transcriptional activator of the human Bax gene. Cell 80 2 (1995) 193-199
13. Norris J.R. Markov Chains (1998), Cambridge University Press, Cambridge
14. Oktem H., Pearson R., and Egiazarian K. An adjustable aperiodic model class of genomic interactions using continuous time Boolean networks (Boolean delay equations). Chaos 3 4 (2003) 1167-1174
15. Owen-Schaub L.B., Zhang W., Cusack J.C., Angelo L.S., Santee S.M., Fujiwara T., Roth J.A., Deisseroth A.B., Zhang W.W., Kruzel E., and Radinsky R. Wild-type human p5 and a temperature-sensitive mutant induce Fas/APO-1 expression. Molecular and Cellular Biology 15 6 (1995) 3032-3040
16. Pal R., Datta A., and Dougherty E.R. Optimal infinite-horizon control for probabilistic Boolean networks. IEEE Transactions on Signal Processing 54 6 (2006) 2375-2387
17. Shmulevich I., Dougherty E.R., Kim S., and Zhang W. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18 2 (2002) 261-274
18. Swisher S.G., Roth J.A., et al. Adenovirus-mediated p53 gene transfer in advanced non-small-cell lung cancer. Journal of the National Cancer Institute 91 9 (1999) 763-771
19. Thomas R. Kinetic Logic: A Boolean Approach to the Analysis of Complex Regulatory Systems (1979), Springer, Berlin