Genome Center/ Biotechnology Center

Faculty Advisor: David C. Schwartz / C. David Page

Dissertation: Cognitive Economy and the Role of Representation in On-Line Learning


My research interests involve the development of a state-space analysis of genomic variation within single cancerous cells. The Laboratory for Molecular and Computational Genomics has fully integrated systems for the genomic analysis of ensembles of single molecules. The Optical Mapping system produces ordered restriction maps to reveal sequence dependent patterns that serve as “bar codes” that uniquely identify any given molecule. Optical maps taken from either single cells or ensembles will be used to characterize genomic aberrations that accumulate as a consequence of oncogenic progression. The maps will link mutated genomic loci with sequence and annotation derived from public databases. A collection of these genomic “time slices” will be considered as a Markov chain to confidently identify those regions showing variation as typified by indels, translocations, or rearrangements. As a first level of analysis, optical map differences will be used to identify clusters of the most frequent cellular states. Any such generalization over a state-space depends critically on the selection of important features for cluster identity. I will apply methods I had previously developed – for characterizing such features on the basis of their ability to make critical distinctions in robotic control tasks and otherwise generalize over similar states – to further parse genomic loci in terms of their oncogenic relevance in the development of the cells.

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