Group Members
We are looking for new enthusiastic and creative PhD students to join the team!
Finlay Maguire
Principal Investigator, started Jan 2022
Jointly appointed Assistant Professor in Community Health & Epidemiology and Computer Science at Dalhousie University. Pathogenomics Bioinformatics Lead at the Shared Hospital Laboratory, Faculty in the Institute for Comparative Genomics, and with an adjunct appointment at Sunnybrook Research Institute.
Precious Osadebamwen
CS PhD Student, starting January 2024
NSERC Discovery Grant-funded project developing automated clinical and public health tools for detection of evolving antimicrobial resistance threats. These tools will be used to triage predicted AMR genes in genomic data by incoporating multi-modal data (genomic, phylogenetic, and contextual metadata). This is being developed using data from the Shared Hospital Lab’s antimicrobial resistance organism outbreak and surveillance genomics.
David Mahoney
Interdisciplinary PhD Student, starting June 2023
NSERC Discovery Grant-funded project based on the development and application of tools to detect lateral gene transfer (LGT) of genes with important microbial functions (such as antimicrobial resistance) from metagenomic assembly graphs. This involves a One Health focus with a priority on identifying intersectoral LGT events (i.e., those between clinical, environmental, agricultural environments).
Malcolm Tait
Community Health & Epidemiology MSc Student, Starting Fall 2024
CIHR Team Grant funded project on factors influencing zoonotic transmissions of mpox
Yann Guerin
Research Assistant, started March 2023
SSHRC Insight Development Grant funded project on combining qualitative sociological analyses and natural language processing to characterise radicalisation in social media data. Yann is developing improved easy-to-use tooling to automate data scraping, perform network analyses, and further dissemination/knowledge translation of datasets via a custom database.
Committees
Sneha Murthy
Beiko Lab Interdisciplinary PhD student, started September 2022
CFIA/CS/NSERC-funded project developing improved approaches for the analysis of mobile AMR/VF genes and microbial eukaryotes from metagenomic data. Specifically, this largely focuses on metagenome-assembled genome binning methods and signals.
Alumni
Peter Jentsch
Postdoctoral Fellow 2021-11 to 2022-11. Now working as a scientific software developer.
Worked on improving use of genomic data in epidemiological modelling of SARS-CoV-2 (jointly supervised with Dr. Samira Mubareka at Sunnybrook).
Yuan Wang
Undergraduate Student Research Associate 2022-05 to 2023-05
Developing natural language processing (NLP) approaches to improve prediction of language-change/radicalisation in incel online communities (in collaboration with Dr. Michael Halpin in Sociology)
Zahraa Zeinou
Research Intern 2023-04 to 2023-06
Short-term project developing data analysis and plotting skills to explore genomic metadata in large sequencing databases. This is being used with global burden of disease data to measure the mismatch between AMR health burden and the availability of microbial sequencing.
Nathan Smith
Externship supervision for Yukiko Lab Community Health & Epidemiology PhD student 2023-04 to 2023-08. Postdoctoral fellow at NIH.
Working on a co-supervised externship at PHAC with genomic epidemiology modellers Dr. Carmen lia Murall and Dr. Michael Li focused on COVID-19 wave dynamics. Collaborator on health inequity simulation project led and completing a PhD on frailty epidemiology modelling with NIH’s Dr. Yukiko Asada.
Devarshi Shah
Microbiology & Immunology Honours student 2023-07 to 2024-04
Computational project as part of the WILD-EPI consortium with governmental, clinical, and academic researchers investigating viral spillovers between human and wildlife populations in Canada. This project is focused on identifying and characterising mutational and evolutionary signatures of animal adaptation associated with SARS-CoV-2 spillover and spillback.