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Author:

Hollingshead, Brett David

Title:

In vitro and in vivo analysis of aryl hydrocarbon receptor regulation by the hepatitis B virus X-associated protein 2

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

aryl hydrocarbon receptor
XAP2
HSP90
gene regulation
chaperone proteins
AIP

File:

Download Hollingshead_thesis.pdf

Committee Members:

Gary H Perdew, Committee Chair/Co-Chair
Jeffrey Maurice Peters, Committee Member
Ross Cameron Hardison, Committee Member
Ming Tien, Committee Member
Scott Trent Feldman, Committee Member

Author:

Venters, Bryan Jacob

Title:

HIGH-RESOLUTION GENOME-WIDE ORGANIZATION OF THE YEAST TRANSCRIPTION MACHINERY

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

ChIP-chip
Tiling microarrays
Pre-initiation complex
Chromatin
Saccharomyces
Mot1

File:

Download 080724_Venters_Thesis.pdf

Committee Members:

Benjamin Franklin Pugh, Committee Chair/Co-Chair
Joseph C. Reese, Committee Member
Ross Cameron Hardison, Committee Member
David Scott Gilmour, Committee Member
Naomi S Altman, Committee Member

Author:

Hsu, Chih-Hao

Title:

INFERENCE OF ORTHOLOGS, WHILE CONSIDERING GENE CONVERSION, TO EVALUATE WHOLE-GENOME MULTIPLE SEQUENCE ALIGNMENTS

Graduate Program:

Computer Science and Engineering

Keywords:

Evolution
Gene conversion
Orthology
Multiple-Sequence Alignment

File:

Download Dissertation.pdf

Committee Members:

Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Raj Acharya, Committee Member
Wang Chien Lee, Committee Member
Ross Cameron Hardison, Committee Member

Author:

Lin, Chiao-Feng

Title:

EVOLUTIONARY DYNAMICS OF THE U12-TYPE SPLICEOSOMAL INTRONS IN MULTICELLULAR ORGANISMS

Graduate Program:

Biology

Keywords:

spliceosomal introns
U12-type intron
intron evolution

File:

Download Chiao-Feng_Lin_thesis.pdf

Committee Members:

Wojciech Makalowski, Committee Chair/Co-Chair
Edward C Holmes, Committee Chair/Co-Chair
Webb Colby Miller, Committee Member
Ross Cameron Hardison, Committee Member
Stephen M Mount, Committee Member

Author:

Ruan, Chun

Title:

The DNA Repair Protein yKu80 Regulates the Recombination Enhancer during Yeast Mating Type Switching

Graduate Program:

Integrative Biosciences

Keywords:

yKu80
mating type switching
chromatin structure
recombination enhancer

File:

Download final_thesis.pdf

Committee Members:

Song Tan, Committee Chair/Co-Chair
Ross Cameron Hardison, Committee Member
Hong Ma, Committee Member
Jerry L Workman, Committee Member

Author:

King, David

Title:

PHYLOGENETIC CONSERVATION OF CIS-REGULATORY REGIONS USING SEQUENCE ALIGNABILITY AND CLADISTIC MOTIFS

Graduate Program:

Integrative Biosciences

Keywords:

lineage-specific regulatory elements
cis-regulatory modules

File:

Download thesis-DCK.pdf

Committee Members:

Ross Cameron Hardison, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Member
Webb Colby Miller, Committee Member
Benjamin Franklin Pugh, Committee Chair/Co-Chair
Kateryna Dmytrivna Makova, Committee Member
Francesca Chiaromonte, Committee Member

Author:

Abebe, Demesew F

Title:

EVOLUTION AND ACTIVITY OF AN ERYTHROID CIS-REGULATORY MODULE IN MULTIPLE MAMMALIAN LINEAGES

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

boreoeutheria
Motif constraint
CIS-REGULATORY MODULE
GATA1

File:

Download DA-Thesis-Final.pdf

Committee Members:

Ross Cameron Hardison, Thesis Advisor/Co-Advisor
Ross Cameron Hardison, Thesis Advisor/Co-Advisor

Author:

Blankenberg, Daniel James

Title:

Galaxy, a web-based framework for the integration of genome analysis

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Sequence Analysis
Genome
Databases
Algorithms
Molecular Sequence Data
Software

File:

Download blankenberg_Galaxy_a_web-based_framework_for_the_integration_of_genome_analysis.pdf

Committee Members:

Anton Nekrutenko, Dissertation Advisor/Co-Advisor
Anton Nekrutenko, Committee Chair/Co-Chair
Webb Colby Miller, Committee Member
Ross Cameron Hardison, Committee Member
Stephan Schuster, Committee Member
Andrey S Krasilnikov, Committee Member

Author:

Chalkia, Dimitra

Title:

ORIGINS AND EVOLUTION OF THREE MULTIDOMAIN GENE FAMILIES CONCERNED WITH BASIC CELLULAR AND DEVELOPMENTAL PROCESSES IN EUKARYOTES

Graduate Program:

Biology

Keywords:

evolution
protein domain
functional divergence
formin

File:

Download Dimitra_Chalkia_PhD_Thesis.pdf

Committee Members:

Douglas Cavener, Committee Chair/Co-Chair
Masatoshi Nei, Committee Member
Jan Klein, Committee Member
Bernhard Luscher, Committee Member
Ross Cameron Hardison, Committee Member

Author:

Wu, Dai-Chen

Title:

FROM EXPLORING ROLES OF SIGNALS IN STRESS ERYTHROPOIESIS TO IN VITRO EXPANDING STRESS ERYTHROID PROGENITORS THAT ALLEVIATE ANEMIA

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Hedgehog
BMP4
hypoxia
hematopoiesis
erythropoiesis
GDF15
anemia
stem cell

File:

Download DC_Wu_Dissertation_Final_renumbered.pdf

Committee Members:

Robert Paulson, Dissertation Advisor/Co-Advisor
Robert Paulson, Committee Member
Douglas Cavener, Committee Member
David Scott Gilmour, Committee Member
Pamela Hankey Giblin, Committee Member
Ross Cameron Hardison, Committee Member