Advances in research. I transformed epigenomic analysis by creating the genome annotation method Segway. Segway analyzes multiple epigenomic datasets, integrates them, and categorizes each base in a genome (e.g. transcription start, enhancer, insulator, repressed). Segway enables simple interpretation and visualization of large multivariate genomic datasets. I led an effort to annotate the human genome using Segway—a linchpin of the ENCODE analysis, which shifted thinking about the biomedical importance of noncoding DNA.
Segway's global impact is demonstrated by the many scientists who run the software or use our annotations on human cell types. These annotations are displayed by both the Ensembl (50,000 unique users/week), and UCSC (38,000 unique/week) genome browsers. Segway annotations also form a building block for highly-used noncoding interpretation tools like CADD and the Ensembl Regulatory Build. In other work, I created Sunflower, a theoretical framework to predict effects of genetic variation on transcription factor (TF) binding, originating a widespread "motif-breaker" approach.
Training a new generation. My past students are in PhD programs at Princeton, University of Toronto, University of Washington, and University of Maryland. They have received the NSF Graduate Research Fellowship, Canadian Graduate Scholarship, and Ontario Graduate Scholarships.