Published research
QUENTIN: Reconstruction of disease transmissions from viral quasispecies genomic data
Genomic analysis has become one of the major tools for disease outbreak investigations. This paper proposes a Quasispecies Evolution, Network-based Transmission Inference (QUENTIN) framework for conducting genomic analyses of outbreaks of highly mutable viruses associated with chronic infections, such as HIV and hepatitis C virus. The QUENTIN framework uses relevant properties of social networks to address previously identified shortcomings of existing computational frameworks for inference of transmission history from viral genomic data.