Inference of large-scale topology of gene regulation networks by neural nets

Proceedings of the IEEE International Conference on Systems, Man and Cybernetics

Volumn 4, Issue , 2003, Pages 3969-3975

  Kim, Sohyoung ^a   Weinstein, John N ^b   Grefenstette, John J ^a  

^a GEORGE MASON UNIVERSITY   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Gene regulation networks; Inference; Perturbation analysis; Topology

Indexed keywords

ALGORITHMS; BACKPROPAGATION; COMPUTER SIMULATION; DNA; LEARNING SYSTEMS; PROBABILITY; RANDOM PROCESSES; TOPOLOGY;

GENE REGULATION NETWORKS; INFERENCE; PERTURBATION ANALYSIS;

NEURAL NETWORKS;

EID: 0242468794     PISSN: 08843627     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. R. Albert and A. Barabasi, "Statistical mechanics of complex networks," Review of Modern Physics, vol. 74, pp. 47, 2002.
2. R. Albert, H. Jeong, and A. Barabasi, "Error and attack tolerance of complex networks," Nature, vol. 406, pp. 378-382, 2000.
3. R. Albert and H. G. Othmer, "The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster," J Theor Biol, vol. 223, pp. 1-18, 2003.
4. A. L. Barabasi and R. Albert, "Emergence of scaling in random networks," Science, vol. 286, pp. 509-512, 1999.
5. A. Bhan, D. J. Galas, and T. G. Dewey, "A duplication growth model of gene expression networks," Bioinformatics, vol. 18, pp. 1486-1493, 2002.
6. E. H. Davidson, R. A. Cameron, and A. Ransick, "Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms," Development, vol. 125, pp. 3269-3290, 1998.
7. H. Demuth and M. Beale, "Neural network toolbox for use with MATLAB," The MathWorks Inc., Natick, MA 1998.
8. P. Erdos and A. Renyi, "On random graphs I," Publ. Math. (Debrecen), vol. 6, pp. 290-297, 1959.
9. J. J. Fox and C. C. Hill, "From topology to dynamics in biochemical networks," Chaos, vol. 11, pp. 809-815, 2001
10. C. C. Guet, M. M. Elowitz, H. Hsing, and S. Leibler, "Combinatorial synthesis of genetic networks," Science, vol. 296, pp. 1466-1470, 2002.
11. H. Jeong, S. P. Mason, A. L. Barabasi, and Z. N. Oltvai, "Lethality and centrality in protein networks," Nature, vol. 411, pp. 41-42, 2001.
12. H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A. L. Barabasi, "The large-scale organization of metabolic networks," Nature, vol. 407, pp. 651-654, 2000.
13. S. A. Kaufmann, The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, 1993.
14. J. Khan, J. S. Wei, M. Ringner, L. H. Saal, M. Ladanyi, F. Westermann, F. Berthold, M. Schwab, C. R. Antonescu, C. Peterson, and P. S. Meltzer, "Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks," Nat Med, vol. 7, pp. 673-679, 2001.
15. A. D. Lattener, S. Kim, G. Cervone, and J. Grefenstette, "Experimental Comparison of Symbolic Learning Programs for the Classification of Gene Network Topology Models.," presented at FGML 2003 Workshop, Annual Meeting of the GI Working Group "Machine Learning, Knowledge Discovery, Data Mining" (FGML), Karlsruhe, Germany, 2003 (submitted).
16. T. Michell, Machine Learning. WCB/McGraw-Hill, USA, 1997.
17. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi, "Hierarchical organization of modularity in metabolic networks," Science, vol. 297, pp. 1551-1555, 2002.
18. D. J. Shuey, D. E. McCallus, and T. Giordano, "RNAi: gene-silencing in therapeutic intervention," Drug Discov Today, vol. 7, pp. 1040-1046, 2002.
19. D. J. Watts and S. H. Strogatz, "Collective dynamics of 'small-world' networks," Nature, vol. 393, pp. 440-442, 1998.
20. J. N. Weinstein, K. W. Kohn, M. R. Grever, V. N. Viswanadhan, L. V. Rubinstein, A. P. Monks, D. A. Scudiero, L. Welch, A. D. Koutsoukos, A. J. Chiausa, and et al., "Neural computing in cancer drug development: predicting mechanism of action," Science, vol. 258, pp. 447-451, 1992.
21. M. Wigler and B. Mishra, "Genetics. Wild by nature," Science, vol. 296, pp. 1407-1408, 2002.
22. C. Wu, Neural Networks and Genome Informatics. Elsevier Science, 2000.
23. C. H. Yuh, J. G. Moore, and E. H. Davidson, "Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo 16 gene," Development, vol. 122, pp. 4045-4056, 1996.