Models and methods to integrate epidemiological and whole genome sequence data for effectively analysing infectious disease outbreak dataTools Marsh, J. S. (2024) Models and methods to integrate epidemiological and whole genome sequence data for effectively analysing infectious disease outbreak data. PhD thesis, University of Nottingham.
AbstractAdvances in sequencing technology and the reduction in associated costs have enabled scientists to obtain highly detailed genomic data on disease-causing pathogens on a scale never seen before. Combining genomic data with traditional epidemiological data (e.g. incidence data) provides a unique opportunity to determine the actual transmission pathway of the pathogen through a population. Despite recent advances, existing approaches have their own limitations, such as simplifications to the underlying biological processes, arbitrary phenomenological models or approximations to the likelihood function, to name a few.
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