Abstract
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Grant Number:
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1R01GM078991-01
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PI Name:
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TANG, JIJUN
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PI Email:
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jtang@cse.sc.edu
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PI Title:
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Project Title:
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Phylogenetic Analysis with Complex Genome
Rearrangement Events
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Abstract: DESCRIPTION
(provided by applicant): Phylogenetic analysis is crucial to a wide range of
biological and medical research. A new type of data based on gene order and
gene content within whole genomes has attracted increasing interest from
researchers in the past several years. Specific Aims: The complexity of genome
evolution poses many exciting challenges to developers of mathematical models
and algorithms. However, the current tools can only be applied to small genomes
(such as organelle genomes) evolving via very simple rearrangements events,
hence their breadth of usage is limited. We will address these problems by: (1)
mathematical modeling and theoretical analysis of complex evolutionary events
such as gene duplication and loss; (2) algorithm design and implementation for
phylogenetics and gene order reconstruction (3) performance assessment of these
new algorithms through extensive testing on simulated and biological datasets;
(4) high-performance implementation of the algorithms using algorithm
engineering techniques and a flexible approach to parallelization.
Contributions and Broader Impact: The broader impacts of the proposed project
are several. (1) The development of new theories and algorithms for the
efficient reconstruction of phylogenies and inference of ancestral genomes
based on complex genome rearrangements will considerably enlarge the scope of
research in the field and give rise to interesting new problems in mathematical
and computational biology. (2) Efficient and accurate software for phylogenetic
analysis and genome comparison, tested on a large variety of real datasets and
on an extensive range of simulations, is expected to reveal new evolutionary
patterns and to enable the investigation of novel biological questions. (3) A
web server hosted by our group (or by our collaborators) will enable biologists
to submit their datasets through a user-friendly web interface and get results
back within reasonable amount of time, without the burden of installation and
learning parallel computation. (4) The project team combines expertise in
mathematic modeling, algorithm design, high-performance computing, comparative
genomics, and phylogenetics. Students (both undergraduate and graduate) and
postdocs on this project will receive valuable interdisciplinary training
experience. (5) Both universities have established programs to boost research
in computational biology. This project will enable the PIs to establish close
interdisciplinary collaborations among departments from both universities and
recruit graduate students (especially minorities) to this fast-growing research
field.
Thesaurus Terms:
biochemical evolution, gene rearrangement
computer data analysis, computer system design /evaluation, gene duplication,
interdisciplinary collaboration, mathematical model, method development,
statistics /biometry
molecular biology information system
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Institution:
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UNIVERSITY OF SOUTH CAROLINA AT COLUMBIA
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901 SUMTER STREET
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COLUMBIA, SC 29208
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Fiscal Year:
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2006
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Department:
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COMPUTER SCIENCE AND ENGINEERING
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Project Start:
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02-JUN-2006
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Project End:
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31-MAY-2009
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ICD:
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NATIONAL INSTITUTE OF GENERAL
MEDICAL SCIENCES
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IRG:
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ZGM1
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