We are a diverse group of scientists and clinicians seeking to advance the understanding of infectious and inflammatory diseases by bridging patient-based research, metagenomics, immunophenotyping and computational biology. We focus on pneumonia, sepsis, and the acute respiratory distress syndrome- studying host/pathogen biology, developing novel diagnostics and tracking emerging microbes. We have pioneered methods for infectious disease diagnosis that integrate simultaneous assessment of host immune response and microbes, and have demonstrated their utility in adult and pediatric cohorts in the US and globally. We have extended these methods to deeply characterize the pathogenesis of SARS-CoV-2 infection in different populations and across the age spectrum, and more recently to discover novel molecular subphenotypes that correlate with outcomes. Further, we deploy genomic sequencing to track outbreaks of emerging pathogens in UCSF hospitals and in the community. Together, our team bridges basic science and clinical investigation by leveraging multiomic technologies to understand the relationships between microbes, host response, and clinical outcomes.