HIV-1 sequence diversity is affected by selection pressures arising from host genomic
factors. Using paired human and viral data from 1071 individuals, we ran> 3000 genome …

Viruses such as HIV and Hepatitis C (HCV) replicate rapidly and with high transcription error
rates, which may facilitate their escape from immune detection through the encoding of …

Background Understanding the genetic interplay between human hosts and infectious
pathogens is crucial for how we interpret virulence factors. Here, we tested for associations …

The vertebrate adaptive immune system provides a flexible and diverse set of molecules to
neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as …

Advances in human genomics are now being effectively applied to the search for host
factors underlying susceptibility to common diseases. From the steady stream of studies …

The impact of host genetic variation on determining the differential outcomes after HIV
infection has been studied by two approaches: targeting of candidate genes and genome …

Genetic variation in the peptide-binding groove of the highly polymorphic HLA class I
molecules has repeatedly been associated with HIV-1 control and progression to AIDS …

Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of
within-host diversification is less understood. Here we develop a novel computational tool …

Analysis of HIV-1 gene sequences sampled longitudinally from infected individuals can
reveal the evolutionary dynamics that underlie associations between disease outcome and …

HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV
transmission. These variable transmission rates are primarily driven by host risk behavior; …