Bilkent University
Department of Computer Engineering


Sequencing and Assembling the White Spruce Genome


Dr. nan Birol
University of British Columbia

Spruces are the most widely planted trees for reforestation in Canada, with ~0.4 billion spruce seedlings planted annually. Conventional spruce breeding to select for favourable traits involves long breeding cycles over 30 years for many traits. Genomics resources to support the development of marker systems for applications in spruce breeding programs would substantially reduce this time. However, at 20 Gb in size, assembling and annotating the spruce genome is a nontrivial task, and requires scalable bioinformatics technologies. In this talk, I will give an overview of the white spruce sequencing project, and discuss the enabling technologies we developed to meet this challenge.

Bio: Birol received his BSc and MSc degrees in Electrical Engineering and PhD in Physics from Bogazici University. Currently, he is a Senior Scientist at British Columbia Cancer Agency, Genome Sciences Centre (GSC), an Associate Professor of Medical Genetics and Computer Science at University of British Columbia, and an Adjunct Professor of Computing Science at Simon Fraser University. He heads the Bioinformatics Technology Lab at the GSC, developing innovative computational solutions and analysis pipelines, and their routine application in genomics studies. Among the technologies he developed is a scalable de novo assembly tool, ABySS, which uses data from next generation sequencing platforms to assemble genomes. Using ABySS, his team was the first to assemble a human genome using short reads. Today, it is an award winning software, its download site returning a first page hit in a Google search for the English word abyss.


DATE: 23 December 2015, Wednesday @ 13:40