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Author:

Wang, Qingyu

Title:

Evaluation of whole exome sequencing technology in cohort dataset and quantification of phenotypic alterations in a model organism

Graduate Program:

Molecular, Cellular and Integrative Biosciences

Keywords:

Whole Exome Sequencing
low coverage
unevenness
Drosophila melanogaster
eye phenotype
image processing
quantitative assessment

File:

Download QWFinal_dissertation.pdf

Committee Members:

Naomi S Altman, Dissertation Advisor/Co-Advisor
Santhosh Girirajan, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Member
Shaun A Mahony, Committee Member
Cooduvalli S Shashikant, Committee Member

Author:

Reja, Rohit

Title:

Understanding Molecular Mechanisms of Gene Regulation using High Resolution ChIP-exo

Graduate Program:

Integrative Biosciences

Keywords:

ChIP-exo
gene regulation
ribosomal protein genes
architecture

File:

Download Thesis_Rohit_Reja.pdf

Committee Members:

Benjamin Franklin Pugh, Dissertation Advisor/Co-Advisor
Marylyn Deriggi Ritchie, Committee Chair/Co-Chair
Shaun A Mahony, Committee Member
Dr Yu Zhang, Special Member

Author:

Li, Ruowang

Title:

USING LARGE-SCALE GENOMICS DATA TO UNDERSTAND THE GENETIC BASIS OF COMPLEX TRAITS

Graduate Program:

Integrative Biosciences

Keywords:

Bioinformatics
Genomics
Statistics
Data Integration
Bayesian Network
Epistasis

File:

Download Ruowang_Dissertation.pdf

Committee Members:

Marylyn Deriggi Ritchie, Dissertation Advisor/Co-Advisor
Marylyn Deriggi Ritchie, Committee Chair/Co-Chair
Ross Cameron Hardison, Committee Member
Shaun A Mahony, Committee Member
Le Bao, Outside Member

Author:

Kakumanu, Akshay

Title:

COMPUTATIONAL MODELLING OF SEQUENCE FEATURES DRIVING TRANSCRIPTION FACTOR BINDING IN NEURONAL REPROGRAMMING

Graduate Program:

Integrative Biosciences

Keywords:

discriminative features
transcription factor binding sites
DNaseI hypersensitive sites
motif discovery
cellular reprogramming
transcription factor binding
spinal motor neurons
Ngn2
Ascl1
Lhx3
Isl1

File:

Download AkshayKakumanu_Dissertation_FINAL_11_22_2017.pdf

Committee Members:

Shaun A Mahony, Dissertation Advisor/Co-Advisor
Shaun A Mahony, Committee Chair/Co-Chair
Benjamin Franklin Pugh, Committee Member
Ross Cameron Hardison, Committee Member
Yu Zhang, Outside Member
Esteban O. Mazzoni, Committee Member

Author:

Verma, Shefali Setia

Title:

INVESTIGATING COMPUTATIONAL METHODS TO MODEL THE GENOTYPIC AND PHENOTYPIC COMPLEXITY OF ADVERSE HEALTH OUTCOMES: UNDERSTANDING UNDERCOVER HERITABILITY

Graduate Program:

Integrative Biosciences

Keywords:

Association Studies
GWAS
Rare Variants
Common Variants
Epistasis
Genetic Etiology
Complex Traits
Heritability

File:

Download Shefali_Thesis_Revised_FinalETDVersion.pdf

Committee Members:

Marylyn Deriggi Ritchie, Dissertation Advisor/Co-Advisor
Shaun A Mahony, Committee Chair/Co-Chair
Stephen Wade Schaeffer, Committee Member
Cooduvalli S Shashikant, Committee Member
William S. Bush, Outside Member

Author:

Baumann, Douglas G

Title:

CORE PROMOTER FUNCTION IN TRANSCRIPTIONAL REGULATION OF CONSTITUTIVELY EXPRESSED GENES IN DROSOPHILA

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Promoter
Transcription
Drosophila
Initiation
Glutathione
Motif 1
Pausing
GST
Housekeeping
TRF2
TBP-related factors
TBP
TFIID
DREF
M1BP
DRE
Motif 6
TADs
GFZF

File:

Download Dissertation_Baumann__Final.pdf

Committee Members:

David Scott Gilmour, Dissertation Advisor/Co-Advisor
David Scott Gilmour, Committee Chair/Co-Chair
Joseph C. Reese, Committee Member
Lu Bai, Committee Member
Tae-Hee Lee, Outside Member
Shaun A Mahony, Committee Member

Author:

Yan, Chao

Title:

Gene Regulation By Divergent Gene Pairs and Nucleosome Depleting Factors

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Nucleosome depleting factors
divergent gene pairs
divergent transcription
transcription
gene regulation

File:

Download 1810_Thesis_Draft_Chao_final.pdf

Committee Members:

Lu Bai, Dissertation Advisor/Co-Advisor
Lu Bai, Committee Chair/Co-Chair
Joseph C. Reese, Committee Member
Benjamin Franklin Pugh, Committee Member
William O Hancock, Outside Member
Shaun A Mahony, Committee Member