Department of Pathology
Stanford University School of Medicine
300 Pasteur Drive, Lane 235
Stanford, CA 94305-5324
Doctor of Philosophy in Computer Science, 2011. University of California, Santa Cruz, CA, USA.
Thesis: Past, Present, and Future of Sequence Alignment.
Bachelor of Science in Computer Science with Highest Honors, 2002. University of California, Santa Cruz, CA, USA.
Bachelor of Arts in Mathematics with Highest Honors, 2002. University of California, Santa Cruz, CA, USA.
My interest and participation in genomic research began in 2002, my first year in graduate school at the University of California Santa Cruz. In the wake of the sequencing of the human genome, the often cited scientific goal was personalized medicine: therapies tailored to individual patients based on their genome. When I began working with Dr David Haussler analyzing data from the Mouse Genome Sequencing Consortium our focus was on using the mouse genome to find regions of the human genome that are conserved not because of chance but because of evolutionary constraint. These regions are likely to be functional and might elucidate causes of human disease or help determine disease susceptibility and thus be possible therapeutic targets. For the first time, there was sufficient data to allow a large scale of comparison of the mouse and human genomes. I was fortunate to be part of the birth of mammalian comparative genomics. My work with that consortium, and later with the Rat Genome Sequencing Consortium, led to major original results on the share of the human genome under purifying selection and variations in genomic divergence, both between species and between individuals, across the genome. These results help distinguish functional regions of the human genome and have given rise to many subsequent studies and is an area of active research to this day. After studying the whole human genome, I became interested in the immunoglobulin and T cell receptor loci. Like the genome as a whole, these loci undergo a specialized form of somatic evolution. High-throughput DNA sequencing and computational sequence analysis of the these regions will play a major role in understanding the human immune system and the mechanisms of immune-mediated diseases. Our understanding of human immune responses will be critical in bringing about the dream of personalized medicine. This is what drew me to become a post-doctorate researcher in the laboratory of Dr Scott Boyd at Stanford University. The Boyd laboratory's focus, in collaboration with the laboratories of Dr Andrew Fire and Dr Mark Davis, is on extending sequence-based immune system monitoring to better understand the range of human immune responses, including vaccination responses and immune system aging. My postdoctoral work is devoted to applying my skills and computational insights gained from full genome comparative analyses to this area currently deluged with new and exciting data requiring interpretation.
| Jan. 2011—present | Postdoctoral Research Fellow, Boyd Laboratory, Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. Designed and developed a pipeline and data infrastructure for storing, processing, and annotating Ig and TCR sequences created with various sequencing platforms, including tracking of participant and sample metadata. Studied vaccine immune responces and immune deficiencies. |
| Sep. 2002—Jan. 2011 | Graduate Student Researcher, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA. Worked on projects including UCSC's contribution to The Encyclopedia of DNA Elements project and large scale alignment problems. |
| Jun. 2001—Sep. 2002 | Staff Researcher, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA. Worked on UCSC's contribution to the International Human Genome Mapping Consortium, a crucial component of the Human Genome Project. |
| Mar. 2001—Jun. 2001 | Course Assistant, Computer Science Department, University of California, Santa Cruz, CA, USA. Was the teaching assistant for a class on the analysis of algorithms consisting of over ninety students. Ran five discussion sections a week, created solution sets to weekly homeworks, and gave review sections. |
| Jun. 1999—Jun. 2001 | Undergraduate Student Researcher, Computer Science Department, University of California, Santa Cruz, CA, USA. As part of a research group in the Advanced Visualization and Interactive System laboratory, developed algorithms for scalar and vector topology extraction and visualization and created interactive user interfaces for topology visualization. |
| Sep. 1998—Jun. 1999 | Chancellor's Undergraduate Intern, Chancellor's Undergraduate Internship Program, University of California, Santa Cruz, CA, USA. Working with the School of Engineering and the Multicultural Engineering Participation program as part of an outreach program, designed and held workshops for transfer students to prepare them for entry into the UCSC School of Engineering. |
| Sep. 1998—Jun. 1999 | Teaching Assistant, Mathematics, Engineering, and Science Achievement Transfer Center, Cabrillo College, Aptos, CA, USA. Lead discussion sections in mathematics, especially vector calculus and linear algebra. Tutored physics, and computer science. |