Department of Mathematics

Speaker: Peter Kim
Title: Pyrosequencing and Computational Topology: A Tale of Two Homologies
Affiliation: Department of Mathematics and Statistics, University of Guelph
Department of Pathology and Molecular Medicine, McMaster University
SAMSI Program Leader LDHD
Date: Friday, April 4, 2014
Place and Time: Room 101, Love Building, 3:35-4:30 pm
Refreshments: Room 204, Love Building, 3:00 pm

Abstract. With the introduction of massively parallel sequencing (MPS) technologies, we are in a position to capture pictures of the microbiome at specific timepoints. MPS allows us to consider interactions between bacteria and their environment with an accuracy greater than achieved in vitro. We describe the process from microbiome sampling to sequence production and cleaning, and the first of two homologies. We describe some of the transformations possible, including the generation of phylogenetic trees for the bacteria in a sample. We propose a means of applying persistent homology to phylogenetic trees, and speculate on the future of this application.