"I am inspired by the tremendous resources we have at Genentech, and by the unprecedented volumes of high-throughput data that are now available. Much of our motivation comes from the opportunity to use such data to discover biological phenomena and possible insights to develop new therapeutics."
I came to Genentech because it provided an interdisciplinary and open environment where I could apply my background in medicine and computer science to solve challenging and important problems.
Nature 488/7413 pg.660-664 2012 [0028-0836]
We are interested in analyzing the DNA and RNA content, or the genomes and transcriptomes, of various tissues. These sequences can now be studied at a detailed level using high-throughput sequencing methods, which generate enormous amounts of data that require intensive computational analysis. With appropriate analysis, DNA-Seq and RNA-Seq data can reveal patterns of abnormalities that can provide clues about the molecular basis of disease.
Much of our research explores the best ways to analyze high-throughput sequencing data. A critical step in the analysis involves the alignment of sequence fragments to a genome, and I have developed some of the most accurate programs for performing this task. We have distributed these programs publicly and they are used widely in the scientific community. I am also developing computational tools for subsequent analysis steps that can reveal sequence variants, splice variants, and gene fusions that occur in various diseases, including cancer. Some of our recent studies have discovered novel gene fusions in colon cancer and have shown that read through gene fusions are prevalent phenomena in normal transcription.