James I. Mullins

The paper uses long-read sequencing to study HIV transmission and population dynamics in acute infection, finding high multilineage transmission rates and rapid viral evolution.

This paper develops updated HIV-1 pseudovirus panels to better detect and assess B cell lineages with potential to produce broadly neutralizing antibodies against contemporary HIV-1 variants.

The paper analyzes HIV breakthrough virus populations in antibody-mediated prevention trials, finding high rates of multilineage infections and recombination under VRC01 treatment.

This study identifies VRC01-mediated viral escape mutations in HIV-infected participants from antibody-mediated prevention trials, showing that VRC01 can select for escape variants with cross-resistance to other CD4bs bnAbs.

The paper identifies rare twin cysteine residues in HIV-1 Env V1 linked to neutralization escape and breadth development.

The paper presents an optimized SMRT-UMI protocol and bioinformatics pipeline to generate highly accurate sequence datasets from diverse pathogens, demonstrated on HIV-1 quasispecies.

This paper introduces a microfluidic method to sequence HIV proviruses and their integration sites, achieving >90% capture and sequencing of paired genomes from treated patients.