Seminar • Bioinformatics • Applied Biological Sequence Analysis with a Theoretical Flavour

Please note: This seminar will take place in DC 1304.

Jim Shaw, PhD candidate
Department of Mathematics, University of Toronto

DNA is life’s instruction manual, but mathematically, DNA is simply a string over an alphabet of four letters. DNA can now easily be read into a computer, and the associated string-processing algorithms are being leveraged by biologists for exciting discoveries. However, this has created a flood of data in the petabytes, requiring modern and faster tools.

In this talk, I argue that empowering biologists with modern algorithms requires a multidisciplinary approach. This requires a blend of biological knowledge, engineering know-how, but also theoretical techniques. I then show how studying seemingly esoteric topics such as k-gram sampling combinatorics or random paths in string-induced graphs has led to more accurate discovery of bacterial species and enhanced detection of microbes in the human gut.

This talk assumes no biological background, and I will introduce all necessary background knowledge throughout the talk.

Bio: Jim Shaw is a PhD candidate in the Department of Mathematics at the University of Toronto under the supervision of Prof. Yun William Yu. His research centers on developing efficient software and methods for computational biology from a mathematical point of view, with a heavy emphasis on bridging the gap between theory and biological discovery.

Jim is supported by an NSERC CGS-D, and prior to his PhD, he received a BASc in Engineering Physics and Mathematics from the University of British Columbia.