John M. Coffin

The paper analyzes HERV-K(HML-2) structural variation and coding capacity across human pangenomes using long-read sequencing, revealing polymorphic loci and incomplete representation in reference genomes.

This study uses ultra-deep single-genome sequencing to show strong purifying selection in early HIV-1 infection, with limited early genetic divergence from founder viruses.

This study detects HIV-1 antisense transcripts in vivo, showing higher expression in ART-treated individuals compared to untreated ones, suggesting a regulatory role in viral expression.

This paper identifies HIV proviral integration into STAT3 as a driver of T cell persistence and lymphoma-like features in an ex vivo model.

The paper compares the fraction and total number of HIV-infected cells with unspliced RNA in controllers and non-controllers, finding that viremic control is linked to fewer infected cells, not a lower fraction of infected cells with HIV usRNA.

The paper identifies large T-cell clones producing infectious HIV-1 virus as a source of non-suppressible viremia despite ART adherence and no drug resistance.

HIV-DRLink detects linked HIV-1 drug resistance mutations in next-generation sequencing data to predict treatment failure.