The department includes faculty with expertise in genomics, including members of the Institute for Genome Sciences. These researchers use genome-enabled approaches to study microbial isolates, the microbiome, and host–microbe interactions at the molecular level. Their work seeks to uncover mechanisms of pathogenesis, determinants of disease outcomes, and the role of beneficial microbial communities in health.

Research in this area spans from mechanistic studies aimed at discovering new drugs and therapies to investigations of how pathogens and microbial populations adapt to selective pressures such as drugs, vaccines, and interactions with other microbes. Faculty employ state-of-the-art technologies on diverse infection models —including single-cell transcriptomics, single-nucleus multiomics, spatial genomics, dual-species transcriptomics, epitranscriptomics, RNA structure analysis, single-cell proteomics, and immuno- and phospho-proteomics.