Research Interests and Goals
During graduate, post-doc, and early faculty years, I conducted basic research in molecular biology, microbial ecology, and bioinformatics. My research really took off at the University of Washington (UW). I wanted to study microbial dynamics in ecosystems using high-throughput DNA microarrays -- however, I quickly discovered that microarrays yield inconsistent output. As a consequence, I shifted my research to understanding the physicochemistry of microarrays in order to provide a solution to the inconsistency problem. After nine years, my team produced a large body of research on the physicochemistry underpinnings of DNA microarrays and, from that newfound knowledge, developed an accurate and statistically robust approach to quantify genes in biological samples. Today, we know about the physicochemistry of DNA microarrays, and this new information lead to the development of Gene Meters that can accurately determine gene abundances in a biological sample (PlosOne 9:e91295; Nucl. Acids Res. 41:2779).
My current research builds on these accomplishments and is highly interdisciplinary: (1) the death microbiome (i.e., thanatomicrobiome) in humans, (ii) postmortem gene expression in zebrafish and mice (i.e., thanatotranscriptome), (iii) oral microbiome transplantation for the prevention of periodontitis, (iv) biofilm development on aeration diffusers in wastewater treatment plants, and (v) biocorrosion of titanium dental implants.