Temporal and structural analysis of biological networks in combination with microarray data

2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08

Volumn , Issue , 2008, Pages 62-69

  You, Chang Hun ^a   Holder, Lawrence B ^a   Cook, Diane J ^a  

^a Washington State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL ACTIVITIES; BIOLOGICAL NETWORKS; BIOLOGICAL PROCESS; DYNAMIC FEATURES; DYNAMIC GRAPH; DYNAMIC PROPERTY; GRAPH REWRITING RULES; GRAPH-BASED; MICROARRAY DATA; RELATIONAL LEARNING; RELATIONSHIPS BETWEEN ENTITIES; SYSTEM LEVELS;

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; BIOLOGY; DATA MINING; DYNAMIC ANALYSIS; STRUCTURAL ANALYSIS;

STRUCTURAL PROPERTIES;

EID: 77950955955     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBCB.2008.4675760     Document Type: Conference Paper

References (18)

1. K. Nielsen, P. Sørensen, and F. H. H.-G. Busse, "Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations," Biophysical Chemistry, vol. 7, pp. 49-62, 1998.
2. H. C. Causton, J. Quackenbush, and A. Brazma, A Beginner's Guide Microarray Gene Expression Data Analysis. Blackwell, 2003.
3. D. J. Lockhart and E. A. Winzeler, "Genomics, gene expression and dna arrays," Nature, vol. 405, pp. 827-836, 2000.
4. J. Kukluk, C. You, L. Holder, and D. Cook, "Learning node replacement graph grammars in metabolic pathways," in Proceedings of BIOCOMP, 2007.
5. C. You, L. Holder, and D. Cook, "Application of graph-based data mining to metabolic pathways," in Proceedings of IEEE ICDM Workshop on Data Mining in Bioinformatics, 2006.
6. J. F. Roddick and M. Spiliopoulou, "A survey of temporal knowledge discovery paradigms and methods," IEEE Transactions on Knowledge and Data Engineering, vol. 14, no. 4, pp. 750-767, 2002.
7. T. Ho, C. Nguyen, S. S. Kawasaki, S. Le, and K. Takabayashi, "Exploiting temporal relations in mining hepatitis data," Journal of New Generation Computing, vol. 25, pp. 247-262, 2007.
8. M. Farach-Colton, Y. Huang, and J. L. L. Woolford, "Discovering temporal relations in molecular pathways using protein-protein interactions," in Proceedings of RECOMBx, 2004, pp. 150-156.
9. H. Dörr, Efficient Graph Rewriting and Its Implementation. Springer, 1995.
10. G. Rozenberg, Handbook of Graph Grammars and Computing by Graph Transformation. World Scientific, 1997.
11. K. Nupponen, "The design and implementation of a graph rewrite engine for model transformations," Master's thesis, Helsinki University of Technology, Dept. of Comp. Sci. and Eng., May 2005.
12. "KEGG website," http://www.genome.jp/kegg/pathway.
13. D. Cook and L. Holder, "Substructure discovery using minimum description length and background knowledge," Journal of Artificial Intelligence Research, vol. 1, pp. 231-255, 1994.
14. -, "Graph-based data mining," IEEE Intelligent Systems, vol. 15, no. 2, pp. 32-41, 2000.
15. M. R. Garey and D. S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman & Co., 1979.
16. B. P. Tu, A. Kudlicki, M. Rowicka, and S. McKnight, "Logic of the yeas metabolic cycle: Temporal compartmentalization of cellular processes," Science, vol. 310, pp. 1152-1158, 2005.
17. D. L. Nelson and M. M. Cox, Lehniger Principle of Biochemistry, 4th ed. New York: Freeman, 2005.
18. M. Qi and E. A. Elion, "Map kinase pathways," Journal of Cell Science, vol. 118, pp. 3569-3572, 2005.