Previous M.Sc./Ph.D. Opportunities

Please note that these positions have been filled and are no longer available. Refer to Current M.Sc./Ph.D. Opportunities for available positions.


Graduate Student Opportunity in ECOLOGY/BIOINFORMATICS

Dr. Karl Cottenie (Integrative Biology)

ABOUT THE PROJECT

A MSc/PhD graduate student position is available in the laboratory of Dr. Cottenie in the Department of Integrative Biology in the College of Biological Science (www.cottenielab.org). The main research theme in my lab (www.cottenielab.org) centers around metacommunity dynamics, and we study this in a wide variety of systems, from fish to small mammals to macroinvertebrates to transposable elements within the genome. I am currently expanding my research focus to microbiome studies, and the first system that I will study is the microbiome of Canada Jays in Algonquin Park. Some of the questions we are interested in are determining the effect of very local dispersal (vertical transmission from parents to offspring) and regional dispersal (dispersal of parents and offspring in the landscape) on the oral and gut microbiome of Canada Jay individuals.

REQUIREMENTS

I am looking for an enthusiastic graduate student who wants a research project that combines ecological field work with bioinformatics to study relevant questions in ecology through advanced statistical analyses in R. This position is open to Canadian citizens or permanent residents. Other strong candidates are also welcome to apply.


Evaluating changes in the tonsil microbiome in Streptococcus suis disease in pigs

Dr. Nicole Ricker (Pathobiology)

There are two research opportunity focus possibilities:

1. Microbiology/AMR/Pathogenomics:

Through this work, students will develop important bioinformatics skills and techniques for analyzing genomic and metagenomic data from a diversity of next-generation sequencing technologies and relate these to the disease status of the animals and other research questions. Projects could include shotgun sequencing of microbiome samples and functional analysis of bacterial communities; mixed Enterobacteriaceae enrichment plasmid extractions and long-read sequencing assembly; bio-marker discovery and development of tools for monitoring AMR and pathogens in the food chain and the environment.

2. Predictive Modeling and Big Data Initiatives:

Students will utilize machine learning techniques to evaluate shotgun sequencing data for their ability to track bacterial pathogens and predict disease development.  Projects include comparative genomics of bacterial isolates for specific traits relating to disease development, as well as shotgun metagenomics of microbiome samples to reveal relevant functional categories that correlate with improved health outcomes.  Students will learn the importance of annotation and standardization in publicly available databases, and use data mining techniques to identify taxonomic or functional bio-markers that can be integrated into decision support tools for livestock production.


M.Sc. Position in Computational Biology (Dairy)

Dr. Dan Tulpan (Animal Biosciences)

The project will focus on computational/automatic detection and monitoring of antibiotic usage in dairy cattle. We will collaborate with OVC and Lactanet researchers.

Candidates must be interested in learning new computational analytical tools, advanced modeling techniques and learn how to write code to automate tasks.