PhD Seminar • Bioinformatics • Application of Machine Learning to Taxonomic Classification of Emerging Astroviruses

Please note: This PhD seminar will take place online.

Fatemeh Alipour, PhD candidate
David R. Cheriton School of Computer Science

Supervisors: Professor Lila Kari, Yang Lu

Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astroviruses are classified into two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach.

This talk presents a classification method based on the k-mer composition of whole genome sequences along with host information for emerging and unclassified astroviruses. The proposed three-pronged classification method consists of a supervised learning method, an unsupervised learning method, and the consideration of host species. Finally, we show that the proposed approach, augmented by principal component analysis (PCA), supports the hypothesis that human astrovirus (HAstV) subgenus exists under the Mamastrovirus genus and goose astrovirus (GoAstV) subgenus exists under the Avastrovirus genus.

To attend this PhD seminar on Zoom, please go to https://uwaterloo.zoom.us/j/92240321532.