Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. - Mattia Prosperi; Brittany Rife Magalis; Simone Marini; Marco Salemi (BIBM, 2022)

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. - Simone Marini; Carla Mavian; Alberto Riva; Mattia Prosperi; Marco Salemi; Brittany Rife Magalis (Bioinform., 2022)

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. - Chaoyue Sun; Ruogu Fang; Marco Salemi; Mattia Prosperi; Brittany Rife Magalis (PLoS Comput. Biol., 2024)