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Computational Techniques for the Analysis of Large Scale Biological Systems

Tae-Hyuk (Ted) Ahn, Oak Ridge National Laboratory

What
  • Computer Science Seminar
  • Colloquium
When Wed, Mar 11, 2015
from 04:00 PM to 04:50 PM
Where Ritter Hall 119
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Abstract:

An accelerated pace of discovery in biological sciences is made possible by a new generation of computational biology and bioinformatics tools. Computational biology and bioinformatics are emerging fields that use and develop computer science knowledge in order to provide solutions to important biological problems. Recently emerged next generation sequencing is the revolutionary high-throughput sequencing technology requiring critical need for efficient software to analyze massively large sequencing data. Important challenges in computational biology and bioinformatics arise from the large amounts of data, the difficulty to construct accurate mathematical models, and the computational complexity of the corresponding simulations. In this talk, I will describe these challenges in general and explore new computational, analytical, and high performance techniques for analyzing large-scale datasets generated from mixed microbial communities. Specifically, I will present the Sigma algorithm (Strain-level Inference of Genomes from Metagenomic Analysis, http://sigma.omicsbio.org) for metagenomic biosurveillance and taxonomic profiling. A novel Sigma probabilistic model was developed to identify and quantify genomes using the read mapping approach. The computation of Sigma can be scaled from desktops to supercomputers to achieve a short turnaround time for very large metagenomic datasets. This allows a prompt response of a metagenomic biosurveillance network to disease outbreaks using supercomputers. I will conclude the talk by outlining my future research agenda for the next couple of years.

 

Reception to precede at 3:30 p.m.

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