Tootfinder

A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models
Haley Stone, Jing Du, Hao Xue, Matthew Scotch, David Heslop, Andreas Z\"ufle, Chandini Raina MacIntyre, Flora Salim
https://arxiv.org/abs/2506.09076

A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known sequences within defined transmission chains, using time-aware evolutionary distance modeling. The method estimates pairwise divergence from collection dates and observed genetic distances, enabling biologically plausible imputation grounded in observed divergence …