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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:

Hughey, Jordan

Title:

In-silico modeling gene expression utilizing genomic activity and 3D contact information

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

gene regulation
transcriptome
association studies
machine learning
epigenomics
epigenetics

File:

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Committee Members:

Dajiang Liu, Chair & Dissertation Advisor
Shaun Mahony, Major Field Member
James Broach, Outside Unit & Field Member
Santhosh Girirajan, Major Field Member
George H Perry, Program Head/Chair

Author:

Sutherland, Jeremy

Title:

The Impacts of Genotype-by-Environment Interactions on Switchgrass Rhizosphere Microbiome Composition and Insights for Breeding in Sustainable Agriculture

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

switchgrass
microbiome
genotype-by-environment interactions
microbial heritability

File:

Download Thesis_formatted_JS_05242023.pdf

Committee Members:

Jia Li, Outside Unit & Field Member
Terrence Bell, Co-Chair & Dissertation Advisor
Jesse Lasky, Co-Chair & Dissertation Advisor
Emily Davenport, Major Field Member
George Perry, Program Head/Chair

Author:

Rimal, Bipin

Title:

MULTI-OMICS INSIGHTS INTO MICROBIAL METABOLISM

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Microbiome
Metabolomics
Bile Acids
Bile Salt Hydrolase

File:

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Committee Members:

Andrew Patterson, Chair & Dissertation Advisor
David Koslicki, Major Field Member
Emily Weinert, Outside Unit Member
George Perry, Program Head/Chair
Gary Perdew, Outside Field Member

Author:

Chen, Jiaxing

Title:

ENGINEERING A NON-COMMUTATIVE COMBINATORIAL PROTEIN LOGIC CIRCUIT TO CONTROL CELL ORIENTATION

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Protein logic circuit
Synthetic biology
Protein engineering
Cell engineering
Src kinase
Chemogenetic
Optogenetic

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Committee Members:

Dajiang Liu, Major Field Member
Scott Showalter, Outside Unit Member
Nikolay Dokholyan, Chair & Dissertation Advisor
Keith Cheng, Outside Field Member
David Koslicki, Program Head/Chair

Author:

Khunsriraksakul, Chachrit

Title:

INTEGRATING GENOMIC, EPIGENOMIC, AND 3D GENOMIC DATA TO EMPOWER DISCOVERY, RISK PREDICTION, AND DRUG REPOSITIONING

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Transcriptome-wide association studies
Genome-wide association studies
Systemic lupus erythematosus
Computational drug repurposing
Functional genomics
3D genomics
Epigenomics

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Committee Members:

Dajiang Liu, Chair & Dissertation Advisor
Qunhua Li, Major Field Member
Laura Carrel, Major Field Member
James Broach, Major Field Member
Aron Lukacher, Outside Unit & Field Member
Nancy Olsen, Special Member
George Perry, Program Head/Chair

Author:

Wang, Chen

Title:

Statistical methods for replicability assessment of genotype-phenotype associations and polygenic risk score modeling in large-scale multi-ancestry consortium studies and electronic health record-based biobanks

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

GWAS meta-analysis
Replicability Assessment
Polygenic Risk Score
Electronic Health Record

File:

No files available due to restrictions.

Committee Members:

David Koslicki, Program Head/Chair
Dajiang Liu, Chair & Dissertation Advisor
Qunhua Li, Major Field Member
Helen Kamens, Outside Unit & Field Member
Yifei Huang, Major Field Member

Author:

Song, Fan

Title:

Unveiling Structural Variation: Detection, Characterization, Phasing, and Its Role In 3D Genome Reorganization in Cancer

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Structural Variation
Chromatin Structure
Acute Myeloid Leukemia
Epigenomics
Hi-C
DNA methylation
Histone modification

File:

Download PhD_Dissertation_May_2021_Fan_Song_final.pdf

Committee Members:

Zhonghua Gao, Major Field Member
Sinisa Dovat, Outside Unit & Field Member
George Perry, Program Head/Chair
Shaun Mahony, Chair & Dissertation Advisor
Ross Hardison, Major Field Member
Feng Yue, Special Member

Author:

Jensen, Matthew

Title:

Complex genetic interaction patterns determine the phenotypic trajectory of neurodevelopmental disorders

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Neurodevelopmental disorders
Copy-number variants
Genomics
Transcriptomics
Drosophila melanogaster
Whole genome sequencing
Network analysis

File:

Download Matthew_Jensen_dissertation.pdf

Committee Members:

Dajiang Liu, Outside Unit & Field Member
Ross Hardison, Major Field Member
Santhosh Girirajan, Chair & Dissertation Advisor
Reka Albert, Major Field Member
George Perry, Program Head/Chair

Author:

Eckert, Scott

Title:

Studying risk factors for antibiotic resistance from population-scale microbiome data and machine learning

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Microbiome
bioinformatics
antibiotic resistance
idiopathic pulmonary fibrosis
statistical genetics
machine learning

File:

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Committee Members:

Dajiang Liu, Chair & Dissertation Advisor
James Broach, Major Field Member & Dissertation Advisor
Leslie Parent, Outside Unit & Field Member
Emily Davenport, Major Field Member
David Koslicki, Program Head/Chair