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Finlay Maguire's research aims to develop and collaboratively apply data-driven methods to mitigate health and social crises. He focuses on genomic epidemiology of infectious diseases and interdisciplinary health data science, collaborating with experts in medicine and social sciences. His work in genomic epidemiology involves creating novel microbial bioinformatics and machine learning approaches to understand the diagnosis, evolution, and dynamics of infectious diseases. This research often involves collaboration with national and international public health consortia to address issues related to antimicrobial resistance and the viral dynamics of the COVID-19 pandemic. In broader health data science, his work identifies and seeks to solve data-related problems pertinent to socially and health-focused academics, non-governmental organizations, and public health groups. This includes working with local shelters to identify gaps in service provision, and with physicians to improve healthcare access for refugees, and sociologists to explore online radicalization. He is also an active supporter of the MicroResearch initiative, a multinational community-based program aimed at building research capacity in the Global South and among underserved Canadian communities.