Stochastic neural network models for gene regulatory networks

2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings

Volumn 1, Issue , 2003, Pages 162-169

  Tian, Tianhai ^a   Burrage, Kevin ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

POPULATION STATISTICS; RANDOM PROCESSES; RANDOM VARIABLES; STABILITY; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

GENE EXPRESSION PATTERNS; GENE REGULATORY NETWORKS; NORMAL RANDOM VARIABLE; POISSON RANDOM VARIABLES; STABILITY PROPERTIES; STATISTICAL DISTRIBUTION; STOCHASTIC NEURAL NETWORK; STOCHASTIC SIMULATIONS;

GENE EXPRESSION;

EID: 77950265066     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2003.1299570     Document Type: Conference Paper

References (25)

1. Akutsu. T., Miyano, S. and Kuhara, S. (2000) Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformaiics 16, 727-734.
2. Alon. U., Surette, M. G., Barkai, N. and Leibler, S. (1999) Robustness in bacterial chemotaxis. Nature 397, 168-171.
3. Arkin, A., Ross, J. and McAdams. H. H. (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage A-infected Escherichia coli cells. Genetics 149, 1633-1648.
4. Barkai, N. and Leibler, S. (1999) Biological rhythms - Circadian clocks limited by noise. Nature 403, 267-268.
5. De Jong, H. (2002) Modeling and simulation of genetic regulatory systems: A literature review. J. Comput. Bio. 9. 67-103.
6. D'haeseleer, P., I. Liang, S., and Sorno-gyi, R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics, 16 707-726.
7. Elowitz, M. B., Levine, A. J., Siggia. E. D. and Swain, P. S. (2002) Stochastic gene expression in a single cell. Science 297, 1183-1186.
8. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115, 1716-1733.
9. Gillespie, D. T. (1977) Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361.
10. Hasty, J., Pradines. J., Dolnik, M. and Collins, J. J. (2000) Noise-based switches and amplifiers for gene expression. Proc. Natl. Acad. Sci. 97, 2075-2080.
11. Hasty, J., McMillcn, D., Isaacs, F. and Collins, J. J. (2001) Computational studies of gene regulatory networks: in numero molecular biology. Nat. Rev. Genet. 2, 268-279
12. Hume, D. A. (2000) Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96. 2323-2328.
13. Kepler, T. B, and Elston, T. C. (2001) Stochastic-ity in transcriptional regulation: Origins, consequences, and mathematical representations. Bio-phys. J. 81, 3116-3136'
14. Liang, S. Fuhrman. S. and Somogyi, R. (1998) REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. Pacific Symp. Biocomput 3, 18-29.
15. McAdams, H. H. and Arkin, A. (1997) Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. 94, 814-819.
16. Nadon, R. and Shoemaker, J. (2002) Statistical issues with microarrays: processing and analysis. Trends, Genet 18, 265-271.
17. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. and Van Oudenaarden, A. (2002) Regulation of noise in the expression of a single gene. Nature Genet, 31, 69-73.
18. Shmulevich, I., Dougherty, E. R., Kim, S. and Zhang, W. (2002) Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18, 261-274.
19. Somogyi. R. and Sniegoski, C. A. (1996) Modeling the complexity of genetic networks: understanding muJtigenic and pleiotropic regulation. Complexity 1. 45-63.
20. Thattai, M. and Van Oudenaarden. A. (2001) Intrinsic noise in gene regulatory networks. Proc. Natl, Acad. Sci. 98, 8614-8619.
21. Tian, T, and Burrage, K. (2001) Implicit Taylor methods for stiff stochastic differential equations. Appl. Numer. Math. 38, 167-185.
22. Vohradsky. J. (2001) Neural network model of gene expression. FASEB J. 15, 846-854.
23. Wahde, M and Hertz, J. (2001) Modeling genetic regulatory dynamics in neural development. J. Comput. Bio. 8, 429-442.
24. Wen, X., Fuhrman, S., Michaels. G. S., Carr, D. B., Smith, S., Barker, J. L. and Somogyi, R. (1998) Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. 95, 334-339.
25. Wessels, L. F. A., Van Someren, E. P. and Rein-ders, M. J. T. (2001) A comparison of genetic network models. Pacific Symp. Biocomput. 6, 508-519.