[Colloquium] TTIC Colloquium: Cenk Sahinalp, Simon Fraser University

[Liv Leader]

*REMINDER:*

When:     Friday, May 6 @ 11 a.m.

Where:    TTIC Conference Room #526, 6045 S. Kenwood Avenue, 5th Floor

Who:      Cenk Sahinalp, Simon Fraser University

Title:      *Population scale detection of common and rare genomic
rearrangements and transcriptomic aberrations*

High throughput sequencing (HTS) technologies have been decreasing the cost
and increasing the world-wide capacity for sequence production at an
unprecedented rate, making the initiation of large scale projects aiming to
sequence more than 1000s of human genomes possible. The ability to detect
structural alterations as well as single nucleotide variants on HTS personal
genomes will 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
analyzing large collections of HTS genomes and transcriptomes, for the
purposes of identifying common and rare structural variants with high
accuracy. Our algorithms, which we collectively call CommonLAW (Common Loci
structural Alteration detection Widgets) move away from the current model of
(1) detecting genomic variants in single HTS donor genomes independently,
and (2) checking whether two or more donor genomes indeed agree or disagree
on the variations, to 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 RNA-Seq and
Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering
genomic rearrangements and aberrant transcripts in one or more individuals
simultaneously. Comrad leverages the advantages of both RNA-Seq and WGSS
data providing accurate classification of rearrangements as
expressed/not-expressed and classification of transcripts as of
genomic/non-genomic origin. Comrad only requires low coverage WGSS data,
significantly reducing the cost of sequencing for detecting expressed
structural alterations on the donor genomes in question.

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, his Ph.D. in Computer Science from the University
of Maryland at College Park and did his postdoctoral work at Bell Labs,
Murray Hill. Previously he was on the Faculty of the Division of Computer
Science at Case Western Reserve University.  Sahinalp is an NSF Career
Awardee, a Canada Research Chair and a Michael Smith Scholar for Health
Research. He was the conference general chair of RECOMB'11, an area chair in
computational genomics, sequence analysis etc. for ISMB, PSB and CSHL Genome
Informatics Conferences and serves on the editorial boards of several
journals. His research interests include computational genomics, in
particular algorithms for high throughput sequence data, network biology,
RNA structure and interaction prediction and algorithms for chemoinformatics
applications.http://www.cs.sfu.ca/~cenk/

Host: Jinbo Xu, j3xu at ttic.edu

-- 
Liv Leader
Faculty Services

Toyota Technological Institute
6045 S Kenwood Ave, #504
Chicago, IL 60637
Phone- (773) 834-2567
Fax-     (773) 834-9881
Email-  lleader at ttic.edu <jam at ttic.edu>
Web-   www.ttic.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.cs.uchicago.edu/pipermail/colloquium/attachments/20110505/099ad0ad/attachment.htm