Dr. Rouchka's research interests are in the broad field of bioinformatics, with a particular focus on algorithmic development for understanding transcriptional and translational control mechanisms.  Alternative splicing mechanisms and alternative 3' UTR utilization are of particular interest to his group.  Members of Dr. Rouchka's lab have extensive expertisse in high-throughput sequence analysis, including developing approaches for novel sequencing methods for identifying HIV, LVV, and CAR-T integrations within genomes using long-read sequencing.  Among the areas of expertise are transcriptomics, RNA-seq, single cell sequencing, single cell ISO-seq, ISO-seq, m6A modifications in RNA using Oxford Nanopore sequencing, detection of alternative splice junctions, and 16s and WGS metagenomics.  Dr. Rouchka's group has a number of internal and external collaborations, helping researchers to get the most out of their high-throughput sequencing data.