Fatemeh Mohebbi

The paper develops a computational framework to detect emerging viral variants with altered phenotypes by analyzing epistatic networks, achieving early detection of known SARS-CoV-2 strains.

SOPHIE reconstructs viral transmission networks using a maximum likelihood framework integrating phylogenetic and random graph models, without requiring case-specific epidemiological data.

This paper clusters SARS-CoV-2 sequences to identify variants and subtypes, showing improved performance over existing methods and detecting rare variants in large datasets.