Christian M. Gallardo

MrHAMER2 enables high-accuracy long-read RNA sequencing to detect and quantify viral isoform dynamics during HIV-1 latency in CD4+ T cells.

APHIX automates HIV-1 isoform analysis from long-read RNA sequencing data, providing accurate splice site quantification and non-coding exon detection across multiple HIV strains.

The paper develops a method to sequence full-length host and viral transcripts by ablating 3' RNA ends and using processive reverse transcriptases, improving coverage and detection of long transcripts.

The paper uses CoVaMa to analyze co-variation between SNVs and recombination events in viral genomes, finding correlations in FHV and HIV datasets.

MrHAMER enables accurate long-range viral sequencing, allowing analysis of intra-host evolution and genetic interactions in HIV.