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Ph.D. Proposal: Peng Xiao

November 19, 2018 @ 10:00 am - 11:00 am UTC-5

Title: Efficient Algorithms for Motif Search and Related Problems

Ph.D. Candidate: Peng Xiao

Major Advisor: Dr. Sanguthevar Rajasekaran

Associate Advisors: Dr. Sheida Nabavi, Dr. Yufeng Wu

Date/Time: Monday, November 19, 2018 10:00am

Location: ITE 336

 

Abstract:

Information extraction from voluminous biological data is a challenging problem. Motif search is a fundamental problem in this direction. This problem can be stated as that of finding patterns from different biological sequences. Motif search has many applications in solving some crucial biological problems. For example, finding DNA motifs is very important for the determination of open reading frames, identification of gene promoter elements, location of RNA degradation signals, and the identification of alternative splicing sites.

Many motif models have been proposed in the literature. In this study we focus on Planted Motif Search (PMS) and Edit-distance-based Motif Search (EMS) problems. Both the problems are intractable. Although extensive studies have been carried out by previous researchers, existing PMS and EMS solvers still have their limitations in terms of solving large datasets and challenging instances. In this proposal, we offer efficient algorithms for PMS and EMS. Our algorithms are currently the state-of-the-art. We also propose a new model for motif search.

Details

Date:
November 19, 2018
Time:
10:00 am - 11:00 am UTC-5
Event Category:

Venue

ITE 336
438 Whitney Road Extension, Unit 1006
Storrs, CT 06269-1006 United States
+ Google Map
Phone:
(860) 486-3798
Website:
https://www.cse.uconn.edu/

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