Pathogenomics researchers are generating and analyzing genome sequences of diverse bacterial, oomycete, fungal, and viral pathogens to identify genetic sources of virulence, understand differences observed among related pathogens, guide the development of diagnosis tools capable of discriminating among specific strains, reveal sources of host resistance, and understand the dynamics of host-microbe interactions and the diseases they cause. 

Some of the many projects include surveys of (i) fungal genome sequences to identify conserved patterns associated with genes encoding secondary metabolites and natural products, (ii) viral genome sequences to inform the course of disease spread, and (iii) bacterial genome sequences for comprehensive identification of secreted virulence factors and of commonly regulated genes associated with disease.

Genomic information for the model plants Arabidopsis thaliana and Nicotiana benthamiana, as well as an increasing number of crop species, is used to explore defense responses, and sequencing of pathogen genes transcribed under particular experimental conditions is being used for advancing our understanding of host-microbe interactions.