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1. GENOME-WIDE ORGANIZATION OF TRANSCRIPTION MACHINERY DETECTED AT SINGLE NUCLEOTIDE RESOLUTION

open_access
Open Access
Author:
Rhee, Ho Sung
Title:
GENOME-WIDE ORGANIZATION OF TRANSCRIPTION MACHINERY DETECTED AT SINGLE NUCLEOTIDE RESOLUTION
Graduate Program:
Biochemistry, Microbiology, and Molecular Biology
Keywords:
ChIP-seq
genomic binding locations
transcription factors
File:
Download Rhee_Thesis.pdf
Committee Members:
Benjamin Franklin Pugh, Dissertation Advisor/Co-Advisor
Benjamin Franklin Pugh, Committee Chair/Co-Chair
David Scott Gilmour, Committee Member
Stephan Schuster, Committee Member
Istvan Albert, Committee Member
Debashis Ghosh, Committee Member

3. Computational Approaches for Integrative Detection of Protein-DNA Interactions

open_access
Open Access
Author:
Chen, Kuanbei
Title:
Computational Approaches for Integrative Detection of Protein-DNA Interactions
Graduate Program:
Computer Science and Engineering
Keywords:
Computational Biology
Bioinformatics
Peak-Calling
ChIP-seq
Gene regulation
Comparative Genomics
File:
Download Kuan-Bei.dissertation.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Dr Yu Zhang, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Member
Padma Raghavan, Committee Member
Kamesh Madduri, Committee Member

4. GENOMIC PROFILING OF THE CONSTITUTIVE ANDROSTANE RECEPTOR IN RODENT MODELS REVEAL NOVEL TUMORIGENESIS TARGETS AND SPECIES VARIATIONS

open_access
Open Access
Author:
Niu, Ben
Title:
GENOMIC PROFILING OF THE CONSTITUTIVE ANDROSTANE RECEPTOR IN RODENT MODELS REVEAL NOVEL TUMORIGENESIS TARGETS AND SPECIES VARIATIONS
Graduate Program:
Cell and Developmental Biology
Keywords:
Constitutive androstane receptor
CAR
ChIP-seq
ChIP-exo
Phenobarbital
PB
HCC
Carcinogenesis
File:
Download Ben_Niu_thesis_final_3.pdf
Committee Members:
Curtis John Omiecinski, Dissertation Advisor/Co-Advisor
Curtis John Omiecinski, Committee Chair/Co-Chair
Istvan Albert, Committee Member
Jack Vanden Heuvel, Committee Member
Joshua D Lambert, Outside Member
Kumble Sandeep Prabhu, Committee Member

5. STATISTICAL METHODS FOR COMAPRING NEXT-GENERATION SEQUENCING DATA REPRODUCIBILITY, SIMILARITY AND DIFFERENTIATION

open_access
Open Access
Author:
Yang, Tao
Title:
STATISTICAL METHODS FOR COMAPRING NEXT-GENERATION SEQUENCING DATA REPRODUCIBILITY, SIMILARITY AND DIFFERENTIATION
Graduate Program:
Bioinformatics and Genomics
Keywords:
sequencing
reproducibility
quality control
ChIP-seq
Hi-C
differential interaction
genomics
File:
Download TaoYang_dissertation_2018_FinalVersion.pdf
Committee Members:
Qunhua Li, Dissertation Advisor/Co-Advisor
Qunhua Li, Committee Chair/Co-Chair
Shaun Mohany, Committee Member
Yu Zhang, Committee Member
Ross Hardison, Outside Member
Feng Yue, Dissertation Advisor/Co-Advisor

6. Computational methods to characterize protein-DNA interactions in ChIP-exo data

open_access
Open Access
Author:
Yamada, Naomi
Title:
Computational methods to characterize protein-DNA interactions in ChIP-exo data
Graduate Program:
Bioinformatics and Genomics
Keywords:
protein-DNA interactions
regulatory complexes
ChIP-exo
ChIP-seq
transcription factors
protein-DNA binding event detection
File:
Download NaomiYamada_Dissertation.final.pdf
Committee Members:
Shaun Mahony, Dissertation Advisor/Co-Advisor
Shaun Mahony, Committee Chair/Co-Chair
Benjamin Franklin Pugh, Committee Member
Ross Cameron Hardison, Committee Member
Qunhua Li, Outside Member
George H Perry, Program Head/Chair