Speaker: Dr. Jared Simpson, Ontario Institute for Cancer Research
Title: Algorithms for Genome Assembly and Reference-free Genomics
The widespread adoption of high-throughput DNA sequencing required the development of new algorithms and data structures for working with vast amounts of short reads. This is especially true for the de novo assembly problem, where the genome is reconstructed from the sequence reads without the use of a reference genome. In this talk, I will highlight the major developments in assembly algorithms over the last 10 years, with an emphasis on the use of compressed text indices, like the FM-index. I will discuss how efficient algorithms have enabled new applications of assembly methods, like finding mutations in cancer samples and inferring properties of genomes and populations without the use of a reference. Finally, I will discuss algorithms for existing and emerging long-read sequencing platforms.
Jared Simpson is a Principal Investigator in Informatics and Biocomputing at the Ontario Institute for Cancer Research. Jared completed his PhD at the Wellcome Trust Sanger Institute and the University of Cambridge. His research interests are on the development of efficient algorithms for sequence analysis and genomics. Prior to entering bioinformatics, Jared pursued an interest in computer graphics and rendering with a position developing video games at Electronic Arts. His undergraduate education was in Computer Science at the University of British Columbia in Vancouver.