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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