[Colloquium] Reminder: Olson/MS Presentation/Aug 22, 2014

[Margaret Jaffey]

This is an announcement of Anna Olson's MS Presentation on August
22nd.

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Date:  Friday, August 22, 2014

Time:  10:00 AM

Place:  Ryerson 276

M.S. Candidate:  Anna Olson

M.S. Paper Title: Modified Bootstrapping and K-Means Clustering for
Taxonomic Binning

Abstract:
Metagenomics is the study of microbial ecology using genetics as an
access point. We seek to understand the microbial communities in
environments such as tidal pools, soil, mine runoff, or even the human
gut, so that we can understand the impact that microbes have on our
world and our health. Metagenomic analysis usually involves the
determination of what species are present in a given sample, and, if
possible, what each species' genome looks like. Because the vast
majority of microbial organisms cannot be cultured easily in a generic
lab setting, we look instead to the DNA taken from a sample, and try
to assign the DNA to different species (the taxonomic binning
problem). Many methods for solving the taxonomic binning problem
exist, but they are extremely computationally intensive, reliant on
woefully incomplete reference databases, or insufficiently accurate.\\
In this paper, we put forward a new taxonomic binning algorithm called
Horatio. Horatio is a modified bootstrapping and k-means clustering
algorithm for taxonomic binning that uses compositional information
about DNA subsequences. Horatio requires relatively little setup, and
has tunable parameters that can reflect users' preferences. We compare
and contrast Horatio to other extant taxonomic binning algorithms and
evaluate its performance against simulated and real metagenomic
datasets.

Anna's advisor is Prof. Rick Stevens

Login to the Computer Science Department website for details:
 https://www.cs.uchicago.edu/phd/ms_announcements#olsona

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Margaret P. Jaffey            margaret at cs.uchicago.edu
Department of Computer Science
Student Support Rep (Ry 156)               (773) 702-6011
The University of Chicago      http://www.cs.uchicago.edu
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