Our People

Haiyang Chang

Program: Ph.D.

Advisor: Dr. Steffen Graether

Co-advisor: Dr. Stefan Keller

 

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.

Michael Dube

Michael Dube

Program: Ph.D.
Advisors: Dr. Sheridan Houghten (Brock) and Dr. Steffen Graether
 
Research:
He has an undergraduate degree in Mathematics and Computer Science as well as a Master's degree in Computer Science, both from Brock University.  Michael's Master's thesis investigated epidemic modeling, simulation, and deployment of vaccination strategies on personal contact networks using evolutionary computation; work that he continues to pursue as part of his PhD given the reality of COVID-19. He has published 7 peer reviewed scientific publications and served as a reviewer for CIBCB 2018 and TCBB 2019.  Michael enjoys working in an inter-disciplinary fashion both to leverage insights from other fields of research and to satisfy his insatiable curiosity.

Thanuja Fernando

Thanuja Fernando

Program: Ph.D.

Advisor: Dr. Sarah Adamowicz

 

Research:

Biodiversity is important for ecosystem function. Building large and comprehensive phylogenetic trees, i.e., reconstructing the evolutionary relatedness among species, is valuable for diverse studies, including biomonitoring, evolutionary biology, and conservation biology. With phylogenetic trees, we can ask: how much unique evolutionary history is represented at a given site? High-throughput sequencing technologies are providing a great opportunity to build larger trees than ever before, but there is a gap in the literature regarding the performance of existing bioinformatics tools. Therefore, the objective of this study is to test and develop new approaches for quantifying evolutionary history and identifying biodiversity using molecular data. My approach is to combine the best of two methods: DNA barcoding projects sequence many species for few genes, while phylogenomics projects study few species for many genes. I am benchmarking existing methods for phylogenetic placement, including distance-based and likelihood-based methods, considering the taxonomic coverage of backbone phylogenies, phylogenetic patterns in missing data, and generality of the findings across animal taxa. In combining these techniques, this project will open new avenues for biodiversity, evolutionary, and conservation research in species-rich groups of life and under-studied environments.

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.