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JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale

2025-03-05 epidemiology Title + abstract only
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Transmission reconstruction--the inference of who infects whom in disease outbreaks--offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We developed JUNIPER (Joint Underlying Network Inference for Phylogenetic and Epidemiological Reconstructions), a highly-scalable pathogen outbreak reconstruction tool that incorporates intrahost variation, incomplete sampling, and algorithmic parallelization. Central to JUNIPER is a statistical model for...

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