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MSc Thesis Proposal Announcement by Musab Mushtaque Naik:"Finding Binding Sites via Linear-time Multi-level Thresholding Algorithm"

Thursday, February 20, 2020 - 12:00 to 13:00

SCHOOL OF COMPUTER SCIENCE

 
 

The School of Computer Science is pleased to present…

 

MSc Thesis Proposal by: Musab Mushtaque Naik

 

Date: Thursday February 20, 2020

Time:  12:00pm – 1:00pm

Location: Lambton Tower, 3105

 

Abstract:

 

Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) is a technique that provides quantitative and genome-wide mapping of target protein binding events. The proteins are first cross-linked to the DNA after which the DNA is fragmented. The fragments are filtered such that only the fragments containing the target protein are left behind. The fragments are sequenced and the resulting reads are aligned to the reference genome. This creates a histogram where the x-axis is the coordinate of the chromosome and the y-axis is the number of reads aligned.

 

Multi-level thresholding is widely-used technique in different problems of signal and image processing, including segmentation, classification and object discrimination. It is an excellent approach for one-dimensional clustering and is guaranteed to provide the optimal solution in linear time.  We aim to find the enriched regions by finding the peaks in the signal generated by the ChIP-Seq experiment using linear-time multi-level thresholding algorithm. Here the time-complexity of the algorithm is important as the length of the reads are anywhere between 50 million to 250 million base-pairs.

 

Thesis Committee:

Internal Reader: Dr. Ahmad Biniaz           

External Reader: Dr. Huapeng Wu

Advisor: Dr. Luis Rueda

MSc Thesis Proposal Announcement

 

 
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