The focus of our laboratory is on defining genomic characteristics of human parasites and other pathogens. Our research is multidisciplinary and draws upon the tools of genomics, molecular virology, and computational biology. Projects include the study of influenza virus evolution and emergence, the analysis of the microbiome and mycobiome (fungal microbiota) associated with the pathogenesis of lung obstruction and emphysema in HIV patients, and the characterization of endosymbiotic interactions between filarial worms and Wolbachia.
The characterization of virus populations by deep sequencing is transforming our understanding of viral evolutionary dynamics by enabling the dissection of the mutational spectrum at an extraordinary level of precision. Using the same tools we can also query the host environment in which the virus evolves—such as host microbial ecology and local response to infection—to determine its effect on virus evolution. I will illustrate how immune status, the respiratory microbiome, mixed infections and transmission can shape influenza virus diversity. I will also discuss the epidemiological value of high-resolution mapping and haplotype reconstruction in modeling influenza transmission networks.