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Author:

Yin, Shuang

Title:

DIVERSITY OF SHIGA TOXIN-CONVERTING PHAGE AND CRISPR LOCI IN SHIGA TOXIN-PRODUCING ESCHERICHIA COLI: EVOLUTIONARY AND PATHOGENICITY IMPLICATIONS

Graduate Program:

Food Science

Keywords:

Escherichia coli
Shiga toxin
Phage
CRISPR

File:

Download ShuangYin-Dissertation.pdf

Committee Members:

Edward G Dudley, Dissertation Advisor/Co-Advisor
Edward G Dudley, Committee Chair/Co-Chair
Robert F Roberts, Committee Member
Stephen John Knabel, Committee Member
Dr Rodolphe Barrangou, Committee Member
Chitrita Debroy, Committee Member
James Landis Rosenberger, Committee Member

Author:

Farasat, Iman

Title:

Sequence-to-function models for efficient optimization of metabolic pathways and genetic circuits

Graduate Program:

Chemical Engineering

Keywords:

metabolic pathway
genetic circuit
CRISPR
Cas9
modeling
combinatorial optimization
protein expression
optimization

File:

Download Farasat_PhD_dissertation.pdfDownload 1-Farasat_PhD_dissertation.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Ali Borhan, Committee Member
Timothy Charles Meredith, Committee Member
Costas D Maranas, Committee Member

Author:

Halper, Sean

Title:

Design Optimization Algorithms for Synthetic Biology Applications

Graduate Program:

Chemical Engineering

Keywords:

Synthetic Biology
Metabolic Engineering
CRISPR
Design Optimization
Gene Synthesis

File:

Download Halper_Dissertation_Design_Optimization.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Andrew Zydney, Committee Member
Phillip E Savage, Committee Member
Reka Z Albert, Outside Member
Phillip E Savage, Program Head/Chair

Author:

Reis, Alexander

Title:

Sequence-Level Design of Evolutionary-Robust Genetic Systems

Graduate Program:

Chemical Engineering

Keywords:

synthetic biology
biophysics
CRISPR
genetic circuits
translation initiation

File:

Download Alex_Reis_Dissertation.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Phillip E Savage, Committee Member
Kristen Fichthorn, Committee Member
Philip C Bevilacqua, Outside Member
Phillip E Savage, Program Head/Chair

Author:

Schleicher, Emily

Title:

Using CRISPR Screens to Identify Genetic Vulnerabilities to Cancer Treatment

Graduate Program:

Biomedical Sciences (PHD)

Keywords:

CRISPR
CRISPR Screen
ATM inhibitors
ATR inhibitors
PARP10
Resistance
Sensitivity
CRISPR Knockout
CRISPR Activation

File:

Download EmilySchleicher_FINAL.pdf

Committee Members:

Hong-Gang Wang, Major Field Member
James Broach, Major Field Member
George Moldovan, Chair & Dissertation Advisor
Ralph Keil, Program Head/Chair
David Degraff, Outside Unit & Field Member
Katherine Aird, Special Member

Author:

Hossain, Ayaan

Title:

Advanced algorithms for the design and analysis of synthetic genetic parts

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

automated
design
synthetic
genetic
parts
combinatorial
optimization
machine
learning
algorithm
promoter
mRNA
transcription
translation
decay
repression
CRISPR
repeats
interference
graph
theory
path
finding
nonrepetitive
repetitive
gene
synthesis
assembly
oligopool
discovery
barcodes
primers
counting
NGS
reads
classifier
classification
regressor
regression
random
forest
LASSO
ridge
homologous
recombination
instability
tuning
efficiency
plasmids
genome
engineering
degenerate
IUPAC
vertex
cover
independent
set
initiation

File:

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Committee Members:

Paul Babitzke, Outside Unit Member
Howard Salis, Chair & Dissertation Advisor
Costas Maranas, Major Field Member
Reka Albert, Outside Field Member
George Perry, Program Head/Chair

Author:

O'Connor, Michael

Title:

PARP14 regulates cyclin D1 expression to promote cell cycle progression

Graduate Program:

Biomedical Sciences (PHD)

Keywords:

cell cycle
cyclin D1
CDK4/6 inhibitors
CRISPR
PARP14
breast cancer

File:

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Committee Members:

Thomas Spratt, Committee Member & Major Field Represnt
James Broach, Committee Member & Major Field Represnt
Ralph Keil, Committee Member & Major Field Represnt
Lisa Shantz, Committee Member & Related Areas Repres
George Moldovan, Chair & Major Field Represnt
Ralph Keil, Program Head/Chair

Author:

Wheatley, Matthew

Title:

Improving Fungal Genome Editing and Plant Disease Diagnostics with CRISPR/Cas Technologies

Graduate Program:

Plant Pathology

Keywords:

CRISPR
Genome-editing
Fungal Genetics
Pathogen Detection
Phytopathology

File:

Download Wheatley_PhD_2020_Dissertation_Final_v2-4.pdf

Committee Members:

Yinong Yang, Dissertation Advisor/Co-Advisor
Yinong Yang, Committee Chair/Co-Chair
Seogchan Kang, Committee Member
David Michael Geiser, Committee Member
John Edward Carlson, Outside Member
Carolee Theresa Bull, Program Head/Chair

Author:

Han, Jeong Hoon

Title:

Evaluation of CRISPR Activation Toolkit for Targeted Activation of Regulatory Elements in Chickens

Graduate Program:

Animal Science (MS)

Keywords:

Chicken
CRISPR
dCas9
Activation

File:

Download Thesis_Jeong_Hoon_Han_2023_funding_edited.pdf

Committee Members:

Adele Turzillo, Program Head/Chair
Tae Hyun Kim, Thesis Advisor/Co-Advisor
Wansheng Liu, Committee Member
Ramesh Ramachandran, Committee Member

Author:

Jiang, Yuqian

Title:

Application of human pluripotent stem cells and genetic engineering to treating and modeling pancreatic and cardiovascular degenerative diseases

Graduate Program:

Bioengineering (PHD)

Keywords:

Human pluripotent stem cells
CRISPR
Gene editing
RNA editing
Pancreatic differentiation
cardiomyocyte characterization
Nucleic acid detection

File:

Download Dissertation_Yuqian_Jiang_final.pdf

Committee Members:

Xiaojun Lian, Chair & Dissertation Advisor
Daniel Hayes, Major Field Member
Daniel Hayes, Program Head/Chair
Jian Yang, Major Field Member
Weihua Guan, Outside Unit & Field Member