[Colloquium] Bun/Dissertation Defense/Nov 9, 2016

[Margaret Jaffey via Colloquium]

       Department of Computer Science/The University of Chicago

                     *** Dissertation Defense ***


Candidate:  Christopher Bun

Date:  Wednesday, November 9, 2016

Time:  9:00 AM

Place:  Ryerson 277

Title: Integrative Methods for Reference-Independent Genome Assembly
and Error Detection

Abstract:
High-throughput genetic sequencing technologies have driven the
proliferation of new genomic data. From the advent of long-read Sanger
sequencing to the now low-cost, short-read generation and upcoming era
of single-molecule techniques, methods to address the complex genome
assembly problem have evolved alongside and are introduced at an
expiditious pace. These algorithms attempt to produce an accurate
representation of a target genome from datasets filled with errors and
ambiguities. Many of the challenges introduced, unfortunately, must be
addressed through an algorithm's ad-hoc criteria and heuristics, and
as a result, can output assembly hypotheses that contain significant
errors. Without an inexpensive or computational approach to assess the
quality of a given assembly hypothesis, researchers must make due with
draft-level genome projects for downstream analysis. Solving three
fundamental challenges will alleviate this issue: (i) automation and
incorporation of algorithms from the dynamic landscape of genome
assembly tools, (ii) developing optimal assembly algorithms best
suited for various types, or mixtures, of sequencing data, and (iii)
developing an approach to assess de novo genome assembly quality
independence of a reference genome.

We provide several contributions towards this effort: We first
introduce AssemblyRAST, a general compute orchestration framework and
accompanying domain-specific language that facillitates rapid workflow
design for rapid genome assembly, analysis, and method discovery.
Next, we demonstrate the improvement of genome assemblies through
novel integrative algorithm techniques. Finally, we devise a method
for reference-independent assembly evaluation and error identification
through supervised learning, along with several applications to
further improve existing techniques.

Christopher's advisor is Prof. Rick Stevens

Login to the Computer Science Department website for details,
including a draft copy of the dissertation:

 https://www.cs.uchicago.edu/phd/phd_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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