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Start Over Graduate Program Bioinformatics and Genomics (PhD) Year 2022

1. Advanced algorithms for the design and analysis of synthetic genetic parts

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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

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

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Restricted (Penn State Only)
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

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

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Restricted (Penn State Only)
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:
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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