Link to the University of Pittsburgh Homepage
Link to the University Library System Homepage Link to the Contact Us Form

Genome-wide Open Chromatin and Nucleosome Identification for ATAC-seq

Zhu, Jiaping (2023) Genome-wide Open Chromatin and Nucleosome Identification for ATAC-seq. Master's Thesis, University of Pittsburgh. (Unpublished)

[img] PDF
Restricted to University of Pittsburgh users only until 14 September 2024.

Download (2MB) | Request a Copy


Eukaryotic genomes are hierarchically packaged into chromatin, with open chromatin and nucleosome occupancy playing a crucial role in gene regulation. Understanding the intricate structure of chromatin is of utmost importance in epidemiology. The emergence of ATAC-seq is revolutionary, as it allows for the identification of both open chromatin and nucleosome on the same data set. A significant challenge in ATAC-seq lies in detecting and distinguishing regions from open chromatin and nucleosome. We introduce a novel method, ATACR, which capitalizes on two key features of ATAC-seq experiments: the preference of transposase Tn5 cutting at open chromatin regions and the distinctive pattern of fragment length distribution. Through implementation on Saccharomyces cerevisiae data sets, ATACR shows remarkable performance in accurately identifying open chromatin and nucleosome regions, surpassing other existing computational methods. It achieves higher detection accuracy within a broader range, making it a valuable tool for researchers in exploring chromatin organization and its impact on gene regulation.


Social Networking:
Share |


Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Zhu, Jiapingjiapingzhu@pitt.edujiz261
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairHuang,
Committee MemberZhan,
Committee MemberMao,
Date: 14 September 2023
Date Type: Publication
Defense Date: 31 July 2023
Approval Date: 14 September 2023
Submission Date: 31 July 2023
Access Restriction: 1 year -- Restrict access to University of Pittsburgh for a period of 1 year.
Number of Pages: 37
Institution: University of Pittsburgh
Schools and Programs: Swanson School of Engineering > Electrical and Computer Engineering
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: Open Chromatin, Nucleosome, ATAC-seq
Date Deposited: 14 Sep 2023 13:45
Last Modified: 14 Sep 2023 13:45


Monthly Views for the past 3 years

Plum Analytics

Actions (login required)

View Item View Item