Computational Models of SNPs and Haplotypes
This project focuses on three major themes:- HapMap analysis tools design for SNP selection
- Haplotype Phasing
- and Genome-wide Disease Associations
Project status: Active
Project Home Page: http://www.cs.brown.edu/people/sorin/lab/pages/proj_cmsh.html
People
| Sorin Istrail |
Publications
Sharan, R., Halldorsson, B. V., and Istrail, S. Islands of Tractability for Parsimony Haplotyping. IEEE Computer Society Press 3 (Sept. 2006), 303-311. [ pdf ]
Halldorsson, B., Sharan, R., and Istrail, S. Islands of tractability for parsimony haplotyping. In Proceedings of the Stanford Conference on Computational Systems Biology (2005), pp. 65-72. [ pdf ]
Halldorsson, B. V., Bafna, V., Lippert, R., Schwartz, R. S., Vega, F. M. D. L., Clark, A. G., and Istrail, S. Optimal haplotype block free selection of tagging SNPs for genome-wide association studies. Genome Research 14 (2004), 1633-1640. [ pdf ]
Bafna, V., Halldorsson, B. V., Schwartz, R. S., Clark, A. G., and Istrail, S. Haplotypes and informative SNP selection algorithms : don't block out information. In Proceedings of the 7th Annual Conference on Research in Computational Biology (RECOMB03) (2003), ACM Press, pp. 19-27. [ pdf ]
Halldorsson, B. V., Bafna, V., Edwards, N., Lippert, R., Yooseph, S., and Istrail, S. Combinatorial problems arising in SNP and haplotype analysis. In Proceedings of the 4th International Conference on Discrete Mathematics and Theoretical Computer Science (CDMTCS03) (2003), Springer (Lecture Notes in Computer Science), pp. 26-47. [ pdf ]
Schwartz, R. S., Halldorsson, B. V., Bafna, V., Clark, A. G., and Istrail, S. Robustness of inference of haplotype block structure. Journal of Computational Biology 10 (2003), 13-19. [ pdf ]
Lippert, R., Schwartz, R., Lancia, G., and Istrail, S. Algorithmic strategies for the SNP haplotype assembly problem. Briefings in Bioinformatics 3, 1 (Mar. 2002), 1-9. [ pdf ]
Rizzi, R., Bafna, V., Istrail, S., and Lancia, G. Priactical algorithms and fixed-parameter tractability for the single individual SNP haplotyping problem. In Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI02) (2002), Springer (Lecture Notes in Computer Science), pp. 29-43. [ pdf ]
Schwartz, R., Clark, A., and Istrail, S. Methods for inferring block-wise ancestral history from haploid sequences: The haplotype coloring problem. In Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI02) (2002), Springer (Lecture Notes in Computer Science), pp. 44-59. [ pdf ]
Lancia, G., Bafna, V., Istrail, S., Lippert, R., and Schwartz, R. SNPs problems: complexity and algorithms. In Proceedings of the 3rd European Symposium on Algorithms (EAS01) (2001), Springer (Lecture Notes in Computer Science), pp. 182-193. [ pdf ]
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