Algorithms for the discovery of normal genomic variants and complex rearrangements in cancer via high throughput sequencing

SCAIM Seminar
November 27, 2012 8:30 pm

Speaker:  Cenk Sahinalp, Department of Computer Science, Simon Fraser University

URL for Speaker:

Location:  ESB 4133

Intended Audience:  Public

In this talk we will focus on some of the genome and transcriptome analysis software developed at the Lab for Computational Biology at SFU. These programs are all based on combinatorial optimization formulations for which exact or provably approximate polynomial time solutions exist – either for the original problem or its dual formulation. Some of the problems can be solved through standard integer linear program solvers while others require specialized (approximate) solutions to known NP-hard problems. The software we will cover include VariationHunter, a program to identify structural differences between a next generation sequenced genome and a reference genome, CommonLAW, a program to compare two or more next generation sequenced genomes through the help of a reference genome, deFuse, Comrad and nFuse, programs to detect gene fusions through the use of genomic or transcriptomic data or both, dissect, a program to associate assembled transcripts to a genome, and CLIIQ, a program to simultaneously identify and quantify novel splice variants.