We have broad interests in using microbial genomics to understand how microbes interact with each other and their hosts. This interest includes the roles played by both beneficial and harmful bacteria, fungi, and viruses and how they interact with the immune system. We study single microbes and microbial communities, primarily using high-throughput sequencing methods. We have a particular interest in developing new experimental and analytical methods that leverage the power of high-throughput sequencing. We are also interested in using deep learning in microbiology research.