The poster “Bioinformatics pipeline for detection of immunogenic cancer mutations by high throughput mRNA sequencing” (ppt, poster abstract) received the best poster award at ISBRA 2009. The poster presents a bioinformatics pipeline for detecting immunogenic cancer mutations from high throughput sequencing data. Immunogenic mutations predicted from Illumina mRNA reads generated from a mouse cancer tumor cell line are currently under experimental validation in the Srivastava lab at UCHC.

The 1st Workshop on Computational Issues in Genetic Epidemiology will be held on August 21-22, 2008 at the DIMACS Center of Rutgers University. The workshop brings together computer scientists, geneticists, and statisticians aiming to address current computational challenges in gene mapping, for details see the workshop program is available at http://dimacs.rutgers.edu/Workshops/ComputationalIssues/program.html. Pre-registration deadline is August 14, 2008.

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.