Haplotype tagging using support vector machines

2006 IEEE International Conference on Granular Computing

Volumn , Issue , 2006, Pages 758-761

  He, Jingwu ^a   Zhang, Jun ^a   Altun, Gulsah ^a   Zelikovsky, Alexander ^a   Zhang, Yanqing ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COST EFFECTIVENESS; COSTS; DISEASES; MAPS;

HAPLOTYPES; POLYMORPHISMS; SUPPORT VECTOR MACHINES (SVM);

PARALLEL PROCESSING SYSTEMS;

EID: 33751098784     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. http://www.hapmap.org
2. Avi-Itzhak, H.I., Su, X., and de la Vega, F.M. Selection of minimum subsets of single nucleotide polymorphism to capture haplotype block diversity. (2003) In Proceedings of Pacific Symposium on Biocomputing, 8:466-477.
3. Bafna, V., Halld?rsson, B.V., Schwartz, R.S., Clark, A.G., and Istrail, S. (2003) 'Haplotypes and informative SNP selection algorithms: don't block out information', Proceedings of the Seventh International Conference on Research in Computational Molecular Biology, 19-27.
4. Carlson C.S., Eberle M. A., Rieder M. J., Yi Q., Kruglyak L., and Nickerson D. A. (2004) 'Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium', American Journal of Human Genetics, 74(1):106-120.
5. Clark, A., Weiss, K., Nickerson, D., Taylor, S., Buchanan, A., Stengard, J., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E., et al. (1998) 'Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase', Am. J. Hum. Genet., 63:595-612.
6. Daly M., Rioux J., Schaffner S., Hudson T., and Lander E. (2001) 'High resolution haplotype structure in the human genome.', Nature Genetics, 29:229-232.
7. Halldorsson B.V., Bafna V., Lippert R., Schwartz R., De La Vega F.M., Clark A.G., Istrail S. (2004) 'Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies.', Genome Res., 14(8):1633-1640.
8. Halperin, E., Kimmel, G. and Shamir, R. (2005) 'Tag SNP Selection in Genotype Data for Maximizing SNP Prediciton Accuracy', Bioinformatics 21:195-203.
9. He J. and Zelikovsky A. (2004) 'Linear Reduction Methods for Tag SNP Selection', Proc. International Conf. of the IEEE Engineering in Medicine and Biology (EMBC'04), 840-2843.
10. He J. and Zelikovsky A. (2004) 'Linear Reduction for Haplotype Inference.', Proc. Workshop on Algorithms in Bioinformatics (WABI'04), Lecture Notes in Bioinformatics (LNBI) 3240:242-253.
11. He, J. and Zelikovsky, A. (2005) 'Linear Reduction Method for Predictive and Informative Tag SNP Selection', International Journal Bioinformtics Research and Applications, 3:249-260.
12. He, J. and Zelikovsky, A. 'Tag SNP Selection Based on Multivariate Linear Regression', International Workshop on Bioinformatics Research and Applications (IWBRA 2006), to appear.
13. Kimmel, G and Shamir R. (2004) 'GERBIL: Genotype resolution and block identification using likelihood', PNAS 102:158-162.
14. Sebastiani, P., Lazarus, R., Weiss, S., Kunkel, L., Kohane, I., and Ramoni, M. (2003) 'Minimal haplotype tagging', Proc. Natl Acad. Sci., 100:9900-9905.
15. Joachims J., SVMlight Support Vector Machine, Department of Computer Science.
16. V. Vapnik and C. Cortes, (1995) 'Support vector networks', Machine Learning, 20:273-293.
17. Zhang, K., Qin, Z., Liu, J., Chen, T., Waterman, M., and Sun, F. (2004) 'Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies', Genome Res., 14:908-916.