Dr. Ray's laboratory is engaged in studying the evolution of RNA viruses, primarily hepatitis C virus (HCV) and HIV, and the ways in which viral evolution in vivo serves as a biological probe for the host-pathogen relationship. That work involves development and application of widely-used tools in computational biology of infectious diseases.

Areas of specific focus of the lab are immune escape and reversion driving HCV genomic evolution, antibody-mediated neutralization of HCV and its modulation by HIV infection, and HCV-related liver disease progression as revealed by HCV evolution and accelerated by HIV's effects on the liver.