[Colloquium] Bun/MS Presentation/Jul 26, 2013

[Margaret Jaffey]

This is an announcement of Christopher Bun's MS Presentation.

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Date:  Friday, July 26, 2013

Time:  12:00 PM

Place:  Searle 240A

M.S. Candidate:  Christopher Bun

M.S. Paper Title: Optimizations of De Novo Genome and Metagenome
Assembly

Abstract:
Since the advent of genetic sequencing technologies, the genome
assembly problem has be- come a widely studied topic, for the
information gained from an organism’s completed genome offers myriad
biological insights. Most early genome projects that were completed,
beginning with the first microbial genome in 1995 through the Human
Genome Project in 2001, and be- yond, were high in cost and low in
throughput. Recently, technologies have led to the so-called era of
“Next-generation sequencing,” in which sequencing cost is plummeting
at a rate much faster than computation costs, creating a genomic data
crisis. Furthermore, cost and through- put benefits are gained at the
penalty of data usefulness, introducing obstacles into the genome
assembly computational problem. Accurate genome assembly is essential
to many biologic studies but its execution is far from trivial. Base
calling errors, indels, biases, translocation, and repeat regions are
only a portion of the challenges to be overcome. Many tools and
methods have been devised, but completely automatic and accurate
protocols are still imperfect; thus a solution to this deluge of new
data remains at large. This thesis introduces AssemblyRAST, a
service-oriented framework based on a variety of open-source
technologies that allows for workflow flexibility, extensibility, and
automation, for rapid genome and metagenome assembly, analysis, and
method discovery. By utilizing many of the known processing
algorithms, we attempt to study and achieve optimal assembly of next-
generation sequencing data through dynamic and integrative pipelines.

Christopher's advisor is Prof. Rick Stevens

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

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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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