Fred Hutchinson Cancer Research Center

Faculty Member, Population Sciences Statistics

Other Affiliations: Fred Hutchinson Cancer Research Center, Computational Biology Program

Assistant Member

Vaccine and Infectious Disease Division

Thesis Title: Conditional Baum-Welch, Dynamic Model Surgery, and The Three-Poisson Dempster-Shafer Model

About

My background is rooted in computer science.  I have loved programming since I was a child: my parents, who are software engineers, taught me to program in C at age ten.  I received my BA in computer science in 2000 from Wesleyan University.  During college I spent some time abroad at the University of Sussex School of Cognitive and Computing Sciences, where my passion for machine learning and complex systems theory blossomed.  I am competent in several programming languages, and have done large projects in perl, R, C, C++, and Java.

  After college I became a software engineer at the Institute for Systems Biology in Seattle, in the lab of Dr. Leroy Hood.  At the Institute I worked closely with Drs. Andrew F. Siegel and Eugene Kolker.  My projects included a novel probability profile modeling algorithm (with Drs. Andrew F. Siegel, Eugene Kolker, and Arian Smit), an integrative systems biology software platform focusing primarily on protein interaction network data ("Cytoscape") with various collaborators, including Drs. Trey Ideker and Hamid Bolouri, and some genomic (sequence) and graph algorithms (with Dr. George Lake and others).

  During my three years at the Institute I learned a great deal about molecular biology and bioinformatics.  Dr. Hood and my other mentors at the ISB treated me like a student or a post-doc.  I audited courses and attended workshops and regular lecture series at the Institute and at the University of Washington.  My work with Dr. Andrew F. Siegel, a statistician, on modeling biological sequence families inspired my interest in pursuing statistics at the PhD level.

  I recently completed a PhD from the Statistics department at Harvard.  During my second year I received a Masters degree in statistics.  After passing my general exam I focused on teaching, earning me several awards including an especially prestigious accolade: The Derek Bok Award for Excellence in Teaching.

  I had two thesis advisors, with whom I continue to collaborate.  With Prof. Arthur P. Dempster, a famous and wise elder statistician, I work on applications of his theoretical framework ("Dempster-Shafer theory").  Our paper on an application to high-energy physics recently appeared in the Annals of Applied Statistics.  I also have projects with him on fast algorithms for computing DS statistics, and on an application to fingerprint identification ("object recognition").  With Prof. Jun S. Liu, a statistician focusing on bioinformatics, I have extended my earlier work on genomic sequence family modeling, improving procedures for finding maxima in the likelihood landscape of hidden Markov models.  My bioinformatics work continues to emphasize the integration of data sources, including sequence data, phylogenetics, and structural and functional data.

  My skills and research interests converge at the interface between computer science, statistics, and molecular biology.  I am particularly excited to contribute to the development of new informatics methods in genomics and post-genomics.  I seek opportunities to make contributions that both have concrete utility and that advance theory.

  In my free time I enjoy playing with my one-year-old daughter, Eleanor Iona (born in July!), playing music with my wife and friends, and biking around Seattle.

  I recently moved back to Seattle, where I am working as a biostatistician and bioinformatician in the Vaccine and Infectious Diseases Division and the Public Health Sciences Division of the Fred Hutchinson Cancer Research Center (FHCRC).  My research will primarily focus on the genomics and systems biology of infectious disease, especially towards the effective prevention of the spread of HIV.

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