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Congratulations to Bogdan for successfully defending his Ph.D. thesis on Scalable Algorithms for Analysis of Genomic Diversity Data! After getting married next month, he will start working as a post-doctoral scholar with the Algorithms group at the International Computer Science Institute (ICSI) in Berkeley, CA beginning in July. |
The poster “Genotype Error Detection and Imputation using Hidden Markov Models of Haplotype Diversity” (ppt, poster abstract) received the best poster award at ISBRA 2008. The poster describes GEDI, a software package for genotype error detection and imputation of genotypes at untyped SNP loci based on reference haplotypes such as those available in HapMap. Detection of genotyping errors and imputation of missing genotypes is based on multi-locus genotype likelihoods efficiently computed using an HMM that captures the linkage disequilibrium in the population under study. With a runtime that scales linearly both in the number of markers and the number of typed individuals, GEDI is able to handle very large datasets while achieving high accuracy rates for both error detection and imputation.
Congratulations to group alumnus Alexander (Sasha) Gusev for receiving a NSF Graduate Research Fellowship! NSF Graduate Research Fellows receive three years of funding at the institution they choose. Sasha is currently pursuing a Ph.D. in Computer Science at Columbia University.