Yu Lin     
Yu Lin
Postdoctoral Fellow
Department of Computer Science and Engineering
University of California, San Diego
"Genome Assembly for Third-Generation Sequencing "

Thursday, March 24, 4:00 PM
Packard Lab room 360

Abstract:  The recent breakthroughs in assembling long error-prone reads (generated by third-generation sequencing) were based on the overlap-layout-consensus approach and did not use the strengths of the alternative de Bruijn graph approach to genome assembly. There is an implicit assumption that the de Bruijn graph approach, which dominated genome assembly in the last decade, is limited to short and accurate reads from second-generation sequencing. In this talk, I will show how to generalize the de Bruijn graphs to assemble long error-prone reads and describe the A-Bruijn graph approach that results in more accurate genome reconstructions than existing state-of-the-art algorithms. The A-Bruijn graph model can also be applied to improving assemblies for second-generation sequencing, bridging the analysis of genome assembly, genome rearrangements and segmental duplications in the human genome.

Bio:  Yu Lin is a postdoctoral fellow at the Department of Computer Science and Engineering, University of California, San Diego. He received his PhD in Computer Science from École Polytechnique Fédérale de Lausanne (EPFL), Switzerland. His research focuses on computational biology, and he has been working on algorithms for genome assembly, the analysis of genome rearrangements, and phylogenetic reconstruction. He has received two awards from the Swiss National Science Foundation.

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