Search

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:

Login to Download

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:

Wright, Dynisty

Title:

Inferring inversion breakpoint evolution in homozygotes by examining chromatin architecture in Drosophila pseudoobscura

Graduate Program:

Biology (PHD)

Keywords:

Chromatin Architecture
Topologically Associated Domains (TADs)
Inversions
Breakpoints

File:

Download Penn_State_Dissertation.pdf

Committee Members:

Stephen Schaeffer, Major Field Member & Dissertation Advisor
George Perry, Chair of Committee
Shaun Mahony, Outside Unit & Field Member
David Toews, Major Field Member
Elizabeth Mcgraw, 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:

Login to Download

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:

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

File:

Login to Download

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:

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:

Srivastava, Divyanshi

Title:

Computational Methods For Characterizing The Sequence And Chromatin Determinants Of Transcription Factor Binding

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Transcription Factors
Gene Regulation
Chromatin
Neural Networks
Neural Networks for Biological Sequences
Interpretable Models For DNA Sequences
Protein-DNA Binding

File:

Download Srivastava-Dissertation-Revised-2021-July.pdf

Committee Members:

Frank Pugh, Major Field Member
Shaun Mahony, Chair & Dissertation Advisor
Ross Hardison, Outside Field Member
Daniel Kifer, Outside Unit Member
George Perry, Program Head/Chair

Author:

Manickavasagam Pounraja, Vijay Kumar

Title:

Computational methods for dissecting the genetic basis of neurodevelopmental disorders

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

exome-sequencing
CNV
machine learning
rare variant genetics
genomics
neurodevelopmental disorders
random forest
apriori algorithm
rare combinations
combinatorial analysis

File:

Download Vijay_Kumar_Dissertation.pdf

Committee Members:

Naomi Altman, Major Field Member
Vasant Honavar, Outside Field Member
Yifei Huang, Major Field Member
Santhosh Girirajan, Chair & Dissertation Advisor
Reka Albert, Outside Unit Member
George Perry, Program Head/Chair