Our People

Haiyang Chang

Program: M.Sc.

Advisor: Dr. Stefan Keller

Co-advisor: Dr. Dan Ashlock

Research: The adaptive immune response plays a key role in recognizing pathogens and determines health and disease in vertebrates. The protection mechanism of adaptive response is mediated by the antigen receptors (ARs) on the surface of lymphocytes. Specifically, an individual’s AR repertoire helps understand, diagnose and treat diseases. The data are from previously collected Canine immune repertoire sequencing data under normal and pathological conditions. The data analysis for this research will be confined to clustering of AR sequences (clonotypes) and a network map that displays the functional association of clonotypes within a given data set will be constructed. Finally we hope a database that integrates sequencing data from various projects based on variables such as species, disease, tissue, etc.. would be created.

Alicia Halhed

Alicia Halhed

Program: M.Sc.

Advisor: Dr. Karl Cottenie

Research: With the increase in access to DNA sequencing technologies and the bioinformatics software to manage the resulting data, microbial ecology has become a rapidly developing subdiscipline in ecology. Thus, my master's research lies at an intersection between metacommunity ecology and microbiology. I use a variety of multivariate statistical models to apply so-called "traditional" metacommunity theories to host-associated microbial communities. The host species I am interested in are the Canada Jay and the North American Red Squirrel, both of which have been part of long term research studies at the University of Guelph.

Nia Hughes

Program: M.Sc.

Advisor: Dr. Lewis Lukens

Research: My research focuses on RNA-dependent DNA methylation (RdDM) in maize, a process with significant implications for epigenetic variation and special importance in suppression of transposable elements, which make up ~85% of the maize genome. I am examining the difference in methylation patterns and expression levels between wild-type plants and those with a knocked out RNA-dependent RNA polymerase RdR2.

Laura Manerus

Laura Manerus

Program: M.Sc.

Advisors: Dr. Elizabeth Lee and Dr. Andy Robinson

Research: My research uses bioinformatics tools to determine ancestry of maize germplasm pools.

Jacqueline May

Jacqueline May

Program: Ph.D.

Advisors: Dr. Sarah Adamowicz, Dr. Zeny Feng

Research: Common evolutionary trends have been identified in the genomes of diverse taxonomic groups and have been linked to organismal traits. The substantial increase in the amount of available biological data due to advancements in sequencing technology offers unprecedented opportunities to examine these trends at deeper levels. My research entails identifying the sources of molecular evolutionary rate variation across diverse taxonomic groups and different genetic regions. Another project I am working on addresses the issue of missing values in trait datasets through use of phylogenetically-informed imputation techniques. Imputation techniques offer an alternative to removing cases with missing values from datasets and can contribute to trait-based analyses.

Jessmyn Niergarth

Program: Ph.D.

Advisors: Dr. Zeny Feng, Dr. Peter Kim

Research: My research is on the association between bacteriophage engraftment following fecal microbiota transplantation (FMT) and resolution of Clostridium difficile infection (CDI) in human patients. CDI frequently recurs in patients after traditional antibiotic therapies, so FMT has come to the fore as an effective alternative treatment. However, the exact mechanism behind the effectiveness of FMTs as well as their longterm effects require further study, so I am investigating possible correlations between the bacteriophages transferred from donors to patients and the patients' treatment outcomes using metagenomic sequencing, bioinformatic analysis pipelines, and machine learning techniques. 

Matthew Orton

Program: Ph.D.

Advisor: Dr. Sarah Adamowicz

 

Research: My Masters research is focused primarily on developing software pipelines for the analysis of DNA barcoding data from BOLD.  Current research focuses on:

  • Informatics approaches to studying the relationship between rates of molecular evolution and the latitudinal biodiversity gradient using geographical coordinate data and COI barcoding data.
  • Informatics approaches to studying Arctic Dipteran bio-geography and community similarity across the regions of Canada, Greenland and Norway.
  • Development and field validation of software used in primer design of in-situ qPCR assays of Trichopteran species in Churchill, Mb.

Andrew Riley

Program: Ph.D.

Advisors: Dr. Steffen Graether, Dr. Dan Ashlock

Research: My research involves determining the evolutionary origins of dehydrins, which are intrinsically disordered plant proteins associated with osmotic stress.

Amanda Saunders

Program: Ph.D.

Advisor: Dr. Dan Ashlock

Research: Investigating alternatives to previous hierarchical clustering methods in an attempt to improve the stability of output trees.  This includes exploring the new Bubble Clustering algorithm developed for my Masters as well as exploring possible alternative methods for measuring the association between points.