Massively parallel (MP) sequencing technologies are on their way to reduce the cost of whole shotgun sequencing of an individual donor genome to USD 1000. Coupled with algorithms to accurately detect structural (in particular expressed) differences among many individual genomes, MP sequencing technologies are soon to change the way diseases of genomic origin are diagnosed and treated. In this talk we will briefly go through some of the algorithm development efforts at the Lab for Computational Biology in SFU for simultaneously analyzing large collections of MP sequenced genomes and transcriptomes, and in particular for identifying and differentiating common and rare, expressed and unexpressed large scale variants with high accuracy. Our algorithms, which we collectively call CommonLAW (Common Loci structural Alteration detection Widgets) move away from the current model of detecting genomic variants in single MP sequenced donors independently, and checking whether two or more donor genomes indeed agree or disagree on the variations. Instead, we propose a new model in which structural variants are detected among multiple genomes and transcriptomes simultaneously. One of our methods, Comrad, for example, enables integrated analysis of transcriptome (i.e. RNA) and genome (i.e. DNA) sequence data for discovering expressed rearrangements in multiple, possibly related, individuals.
S. Cenk Sahinalp is a Professor of Computing Science at Simon Fraser University, Canada. He received his B.Sc. degree in Electrical Engineering from Bilkent University and his Ph.D. in Computer Science from the University of Maryland at College Park.
Sahinalp is an NSF Career Awardee, a Canada Research Chair and a Michael Smith Scholar for Health Research. He was/is the conference general chair of RECOMB'11, PC chair of APBC'13, sequence analysis area chair for ISMB, and CSHL Genome Informatics Conferences and has co-founded the RECOMB-Seq conference series on Massively Parallel Sequencing. He co-directs the SFU undergraduate program in Bioinformatics and the SFU Bioinformatics for Combating Infectious Diseases Research Program. His research interests include computational genomics, in particular algorithms for high throughput sequence data, network biology, RNA structure and interaction prediction and chemoinformatics algorithms.