My research interests are in the development and application of computational and mathematical techniques to understand biological systems. Over the past few years my research has focused on two areas: computational cancer genomics and algorithms for biological sequence analysis.
Computational Cancer Genomics
Cancer is driven by mutations in DNA including both single letter changes and more drastic, larger scale rearrangements of the genome; e.g. chromosomal inversions, translocations, deletions, and duplications. In some types of cancer, these large-scale rearrangements produce changes in gene structure and regulation that are directly implicated in cancer progression and are targets for cancer therapeutics. In 2003, I began developing algorithms for analyzing genome rearrangements in tumors through a technique called End Sequence Profiling. This work is an ongoing collaboration with Colin Collins, Joe Gray, and Stas Volik at the University of California, San Francisco Cancer Center. In addition to the obvious medical importance, the study of cancer presents numerous challenges that impact nearly every area of bioinformatics. I received a Career Award at the Scientific Interface from the Burroughs Wellcome Fund in 2005 to support this work.
Biological Sequence Analysis
The second focus of my research is the development of algorithms for biological sequence analysis, specifically methods for analyzing and annotating DNA and protein sequences including problems in multiple sequence alignment, motif finding, comparative genomics, and structural variation in the human genome. See my publications for further details.
Very recently, I began working on computational methods for assessing immunoglobulin diversity in patients with chronic lymphocytic leukemia (a collaboration with researchers at the UCSD Medical School). In addition, I am involved in a larger project on evolution of protein families.
Earlier Work and Scientific Biography
I received an S.B. in Mathematics with a minor in Biology from the Massachusetts Institute of Technology in 1996. As an undergraduate at MIT, I did research in combinatorics with Professor Jim Propp (now at University of Wisconsin) and did research in computational and experimental biology with Professor David Page at the Whitehead Institute for Biomedical Research.
I received my Ph.D. in Mathematics at the University of California, San Diego in 2002 under the supervision of Professor Jim Agler. My doctoral research was in operator theory, specifically on certain problems related to functional calculus of linear operators on Hilbert space. My thesis was titled "A Computational Investigation of Spectral Sets and Rational Dilations Over Multiply-Connected Domains". Many of the results from my thesis appear in this paper.
Following completion of my Ph.D. in mid-2002, I began a transition to Computational Biology with a generous Fellowship from the Alfred P. Sloan Foundation. I joined the Bioinformatics Group at UCSD led by Professor Pavel Pevzner.
