Team

• Donald Hill Fellow (Computer Science) Dalhousie with Robert Beiko
• PhD (Bioinformatics) UCL & NHM with Thomas Richards
• MA (Life Sciences) Oxford

Jointly appointed Associate Professor in Community Health & Epidemiology and Computer Science at Dalhousie University. Pathogenomics Bioinformatics Lead at Toronto’s Shared Hospital Laboratory, Steering Committee/Workgroup Chair for PHA4GE.

• PhD (Evolutionary Biology) University of Sydney with Eddie Holmes
• BSc (Genetics, Honours I) University of Queensland with Mark Schembri

NFRF Explore grant-funded project on exploring evolutionary trends of coronaviruses circulating in North American wildlife, particularly drivers of zoonoses and cross-species transmission. Collaborative project with multidisciplinary team Wildlife-Emerging Pathogen Initiative.

• PhD (Bioinformatics) University of British Columbia with Jeff Joy.
• MSc (Population & Public Health) University of British Columbia with Jeff Joy.
• BSc (Microbiology & Immunology) University of British Columbia

CIHR Catalyst Grant-funded project on developing genomic and phylogenetic predictive models for highly pathogenic influenza A virus H5Nx host range and interspecies transmission. Jointly supervised with Zvonimir Poljak at the University of Guelph Ontario Veterinary College

• MSc (Bioinformatics), Covenant University, Nigeria
• MPH (Health Promotion & Education), University of Ibadan, Nigeria
• BSc (Biology), University of Benin, Nigeria

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.

• MSc (Food Science), University of British Columbia
• BSc (Microbiology), Dalhousie University

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).

• MSc (Bioinformatics), Pwani University, Kenya
• BSc (Biochemistry), Egerton University, Kenya

NSERC Discovery Grant funded project (co-supervised with Rob Beiko) developing genomic neighbourhood embedding based predictive models for phenotypic prediction.

• BHSc Honours (Health Sciences), Queen’s University

CIHR Team Grant funded project on factors influencing zoonotic transmissions of mpox

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.

Snacks and worklife balance

• MSc (Statistics), Dalhousie University
• BSc (Statistics), Dalhousie University

Project rigorously evaluating the utility and effectiveness of large language models for systematic literature reviews

• MSt (Bioinformatics), Rashtreeya Vidyalaya College of Engineering
• BEng (Biotechnology), People’s Education Society University

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.

• MSc (Computer Science), University of Tabriz
• BSc (Software Engineering)

Working on a NS Graduate Scholarship funded project to develop network-based approaches for predicting drug-drug interactions.

• MPH, Varendra University
• BSc (CS), Varendra University

Prediction of future use of mental health resources

• BSc (Medical science), Dalhousie university (in-progress).

Comparing different tools to identify wildlife-associated coronaviruses within massive raw sequencing databases.

• BSc (Microbiology & Immunology/Psychology), Dalhousie university (in-progress).

Evaluating long-read metagenomics for AMR detection

• BsC (Microbiology), Dalhousie university (in-progress).

Curate and analysing a dataset of nested Lateral Gene Transfer events in Bacteria with David Mahoney.

• PhD (Applied Maths) Waterloo, with Chris Bauch & Madhur Anand
• BSc Hons (Applied Maths), Waterloo

Worked on improving use of genomic data in epidemiological modelling of SARS-CoV-2 (jointly supervised with Dr. Samira Mubareka at Sunnybrook).

• BCS (Computer Science), Dalhousie/Peking University (in-progress)

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)

• CEGEP (Health Sciences), Collégial international Sainte-Anne (in-progress)

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.

• PhD (Community Health & Epidemiology), Dalhousie University
• MSc (Community Health & Epidemiology), Dalhouse University
• BSc (Neuroscience), Acadia University

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.

• BSc (Microbiology), Dalhousie University (in-progress)

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.