COMPUTATIONAL MODELS OF SNPS AND HAPLOTYPES
Research themes:
- HapMap analysis tools design for SNP selection
- Haplotype Phasing
- and Genome-wide Disease Associations
People: Fumei Lam, Lian Garton
Collaborators:
- Andy Clark (Cornell University)
- Bjarni Halldorsson (deCode Genomics)
- Eran Halperin (Berkeley University)
- Roded Sharan (Tel Aviv University)
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Publications:
- Sharan, R., Halldorsson, B. V., Istrail, S., Islands of Tractability for Parsimony
Haplotyping, IEEE/ACM Transactions on Computational Biology and Bioinformatics,
vol. 3, No. 3, pp. 303-311 (2006)
- Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V.
Halldrsson, Xiaoping Su, Ross A. Lippert, Francis Kalush, Stephen J. O'Brian, Andrew
Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier, and Dennis Gilbert,
The linkage disequilibrium maps of three human chromosomes across four populations
reflect their demographic history and a common underlying recombination pattern.
Genome Research, March 21 (2005)
- Bjarni Halldorsson, Roded Sharan, and Sorin Istrail, Islands of Tractability
for Parsimony Haplotyping, Proceedings of the Stanford Computational Systems
Biology 2005, pp. 65-72 (IEEE/ACM Transactions on Computational Biology and Bioinformatics,
in press) (2005)
- Bjarni V. Halld\'orsson, Vineet Bafna,
Ross Lippert, Russell S. Schwartz, Francisco M. De La Vega, Andrew G. Clark, Sorin
Istrail, Optimal haplotype block free selection of tagging
SNPs for genome-wide association studies, Genome Research,
August, 2004
- Russell S. Schwartz, Bjarni V. Halld\'{o}rsson,
Vineet Bafna, Andrew G. Clark, Sorin Istrail Robustness of
Inference of Haplotype Block Structure. Journal of Computational
Biology, 10:13-19, 2003
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R. Lippert, R. Schwartz, G. Lancia, S. Istrail, Algorithmic Strategies for the SNP Haplotype Assembly Problem,
Briefings in Bioinformatics, Vol 3. No 1, p. 1-9,
March 2002
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Vineet Bafna, Bjarni V. Halld\'orsson, Russell
S. Schwartz, Andrew G. Clark, Sorin Istrail, Haplotypes and
Informative SNP Selection Algorithms: Don't Block Out Information, ,
Proceedings of the 7th Annual International Conference on Computational
Molecular Biology (RECOMB03) , ACM Press, pp. 19-27, 2003
- R. Schwartz, A. Clark, S. Istrail, Inferring piecewise
ancestral sequences from haploid sequences, Proceedings
of the First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference,
(RECOMB SNP\&HAP03), Springer Lecture Notes in Bioinformatics, LNBI
2983, 2003
- Bjarni V. Halld\'{o}rsson, Vineet Bafna, Nathan
Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail, Combinatorial
problems arising in SNP and haplotype analysis, Proceedings
of the Fourth International Conference on Discrete Mathematics and Theoretical Computer
Science, (CDMTCS03), Springer Lecture Notes in Computer Science,
pp. 26-47, 2003
- Rizzi, R., V. Bafna, S. Istrail, G. Lancia, Practical Algorithms and Fixed-Parameter Tractability for the
Single Individual SNP Haplotyping Problem, Proceeding
of the 2nd Workshop on Algorithms in Bioinformatics, (WABI02), Springer
Lecture Notes in Computer Science, 29-43, 2002
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Schwartz, R., A. Clark, S. Istrail,
Methods for inferring block-wise ancestral history from haploid sequences: The haplotype
coloring problem, Proceedings of the 2nd Workshop on
Algorithms in Bioinformatics, (WABI02), Springer Lecture Notes in Computer
Science, 44-59, 2002
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G. Lancia, V. Bafna, S. Istrail, R. Lippert, R. Schwartz,
SNPs Problems: Complexity and Algorithms, Proceedings of the 3rd European Symposium on Algorithms, (EAS01)
Springer Lecture Notes in Computer Science, 2161, p. 182-193, 2001
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