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Creation and Modification of Models of Nucleosome Occupancy and Their Applications Across Multiple Species

Title: Creation and Modification of Models of Nucleosome Occupancy and Their Applications Across Multiple Species.
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Name(s): Fincher, Justin Andrew, 1980-, author
Tyson, Gary, professor co-directing dissertation
Dennis, Jonathan, professor co-directing dissertation
Bass, Hank, university representative
Kumar, Piyush, committee member
Liu, Xiuwen, committee member
Department of Computer Science, degree granting department
Florida State University, degree granting institution
Type of Resource: text
Genre: Text
Issuance: monographic
Date Issued: 2012
Publisher: Florida State University
Place of Publication: Tallahassee, Florida
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: DNA is the fundamental storage for the genetic "blueprints" of all living organisms. It provides the information used to create the functional proteins in an organism. One of the key factors regulating the use of this blueprint is the interaction of DNA with protein complexes called histones forming chromatin. The basic subunit of chromatin is the nucleosome which is comprised of ~150 base pairs of DNA surrounding a histone octamer. As chromatin is the substrate for DNA-templated reactions, such as transcription, the distribution of nucleosomes throughout the genome is of particular interest. DNA sequence has been shown to influence the formation of nucleosomes and computational models predicting nucleosome occupancy from DNA sequence have been created. The most recent developments have been discriminative models, such as Support Vector Machines (SVMs). I show that these models can be effectively applied across species, and even kingdoms, to increase understanding of nucleosomal landscapes across genomic features and as a novel annotative tool. While the applicability of models derived from human chromatin data are broad in their usefulness, improvements can be made by creating models trained on specific organisms, such as Zea mays, or modifications to the representation of the DNA sequence that are then used as the training set for the SVM. Combined, the understanding of the sequence features contributing to the distribution of nucleosomes throughout the genome has expanded.
Identifier: FSU_migr_etd-4829 (IID)
Submitted Note: A Dissertation submitted to the Department of Computer Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Degree Awarded: Summer Semester, 2012.
Date of Defense: June 26, 2012.
Keywords: chromatin, nucleosome, SVM
Bibliography Note: Includes bibliographical references.
Advisory Committee: Gary Tyson, Professor Co-Directing Dissertation; Jonathan Dennis, Professor Co-Directing Dissertation; Hank Bass, University Representative; Piyush Kumar, Committee Member; Xiuwen Liu, Committee Member.
Subject(s): Computer science
Persistent Link to This Record: http://purl.flvc.org/fsu/fd/FSU_migr_etd-4829
Owner Institution: FSU

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Fincher, J. A. (2012). Creation and Modification of Models of Nucleosome Occupancy and Their Applications Across Multiple Species. Retrieved from http://purl.flvc.org/fsu/fd/FSU_migr_etd-4829