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Author:

McGraw, Adam Philip

Title:

Protein-RNA interactions involved in regulation of the tryptophan biosynthesis operon (trpEDCFBA) in Bacillus subtilis

Graduate Program:

Chemistry

Keywords:

protein-RNA interactions
mRNA stability
TRAP
RNA structure

File:

Download AM_thesis_FINAL-2-101008.pdf

Committee Members:

Paul Lee Babitzke, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Chair/Co-Chair
Kenneth Charles Keiler, Committee Member
Christine Dolan Keating, Committee Member

Author:

Brown, Trevor S.

Title:

PROBLEM-ORIENTED INVESTIGATION OF THE pKa OF ACTIVE-SITE CYTOSINE 75 IN THE HEPATITIS DELTA VIRUS (HDV) RIBOZYME

Graduate Program:

Integrative Biosciences

Keywords:

31P NMR
hepatitis delta virus (HDV) ribozyme
Leadzyme
RNA folding
RNA structure
CD spectroscopy
UV spectroscopy and fluorescence spectroscopy

File:

Download Trevor_Brown_Thesis_print_for_GradSchool_4.pdf

Committee Members:

Philip C. Bevilacqua, Committee Chair/Co-Chair
Juliette T J Lecomte, Committee Chair/Co-Chair
Anne Milasincic Andrews, Committee Member
Stephen James Benkovic, Committee Member
Craig Eugene Cameron, Committee Member

Author:

Kwok, Chun Kit

Title:

Structural and Functional Roles of RNA Structure in Regulatory Processes in Plants

Graduate Program:

Chemistry

Keywords:

RNA
RNA structure
RNA folding
Plants
Arabidopsis thaliana
G-quadruplex
regulation
DMS
SHAPE
LMPCR
Structure-Seq

File:

Download Thesis_CKK_2014.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Sarah Mary Assmann, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Member
Tae Hee Lee, Committee Member
Song Tan, Committee Member

Author:

Quarles, Kaycee Andrea

Title:

The Impact of Primary MicroRNA Structure on Recognition by the Microprocessor Complex in MicroRNA Maturation

Graduate Program:

Chemistry

Keywords:

RNA structure
Microprocessor
microRNA
protein binding
DGCR8
EMSA

File:

Download Thesis_KayceeAQuarles.pdf

Committee Members:

Scott A Showalter, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Member
Christine Dolan Keating, Committee Member
Katsuhiko Murakami, Committee Member

Author:

Ritchey, Laura Elizabeth

Title:

PROBING RNA STRUCTURAL CHANGES GENOME-WIDE IN THREE IN VIVO SYSTEMS

Graduate Program:

Chemistry

Keywords:

RNA structure
Structure-seq
StructureFold
DMS

File:

Download Ritchey_LE_2018.pdf

Committee Members:

Philip C Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C Bevilacqua, Committee Chair/Co-Chair
Edward Patrick O'Brien Jr., Committee Member
Scott A Showalter, Committee Member
Sarah Mary Assmann, Outside Member
Paul Lee Babitzke, Outside Member

Author:

Renda, Andrew

Title:

TRANSLATIONAL ACTIVATION OF ESCHERICHIA COLI YMDA AND CHEMICAL DEVELOPMENT FOR IN VIVO RNA STRUCTURE PROBING

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Escherichia coli ymdA
RNA binding proteins
RNA structure
ymdA
Translational activation
Posttranscriptional regulation

File:

Download Andrew_Renda_MS_Thesis_BMMB_Final.pdf

Committee Members:

Paul Babitzke, Thesis Advisor/Co-Advisor
Philip C Bevilacqua, Thesis Advisor/Co-Advisor
Katsuhiko Murakami, Committee Member
Wendy Hanna-Rose, Program Head/Chair

Author:

Sha, Congzhou

Title:

Manifold Learning in Structural Biology: Docking, Folding, and Simulation

Graduate Program:

Engineering Science and Mechanics

Keywords:

differentiable programming
machine learning
neural networks
structural biology
Lie group
statistical mechanics
molecular dynamics
RNA structure
differential geometry

File:

Download Sha_dissertation-Final.pdf

Committee Members:

Albert Segall, Program Head/Chair
Elizabeth Proctor, Major Field Member
Mehrdad Mahdavi, Outside Field Member
Nikolay Dokholyan, Chair & Dissertation Advisor
Raymond Hohl, Outside Unit Member

Author:

Tang, Yin

Title:

HIDDEN RNA CODES REVEALED FROM THE PLANT IN VIVO RNA STRUCTUROME

Graduate Program:

Integrative Biosciences

Keywords:

RNA structure
Arabidopsis thaliana
oryza sativa
high-throughput sequencing

File:

No files available due to restrictions.

Committee Members:

Sarah M. Assmann, Dissertation Advisor/Co-Advisor
Sarah M. Assmann, Committee Chair/Co-Chair
Philip C. Bevilacqua, Committee Member
Anton Nekrutenko, Committee Member
Yu Zhang, Outside Member

Author:

Douds, Catherine

Title:

Approaches to improve in vivo RNA structure prediction through chemical structure probing

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

RNA
RNA structure
structure probing
E. coli ribosome

File:

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Committee Members:

Paul Babitzke, Major Field Member
Sarah Assmann, Outside Field Member
Shaun Mahony, Outside Unit Member
Lu Bai, Major Field Member
Philip Bevilacqua, Chair & Dissertation Advisor
Santhosh Girirajan, Program Head/Chair