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Author:

Lengerich, Benjamin J

Title:

On the Origin of Sequences: Computational Analysis of Somatic Hypermutation for Probabilistic Immunoglobulin Predecessor Identification

Area of Honors:

Computer Science

Keywords:

Computer Science
Machine Learning
Bioinformatics
Somatic Hypermutation
Immunoglobulin Predecessor Identification

File:

Download Lengerich_Benjamin_thesis.pdf

Thesis Supervisors:

Raj Acharya, Thesis Supervisor
Dr. Jesse Louis Barlow, Thesis Honors Advisor

Author:

Jayakar, Gopal

Title:

Random Forest Classification in Copy Number Variation Discovery

Area of Honors:

Biochemistry and Molecular Biology

Keywords:

CNV
Machine Learning
Sequencing
Genomics
Bioinformatics
Random Forest

File:

Download Thesis_Jayakar.pdf

Thesis Supervisors:

Santhosh Girirajan, Thesis Supervisor
Santhosh Girirajan, Thesis Honors Advisor
Shaun Mahony, Faculty Reader

Author:

Setar, Nathaniel

Title:

The Effect of Overlapping Generations on Inferences of Genetic Population Structure

Area of Honors:

Statistics

Keywords:

Population Genetics
fastSTRUCTURE
Overlapping Generations
Coral
Bioinformatics

File:

Download Thesis_Final_Setar.pdf

Thesis Supervisors:

Iliana Brigitta Baums, Thesis Supervisor
Le Bao, Thesis Honors Advisor

Author:

Wertz, Adam

Title:

Structural and Functional Analysis of Two Novel Iron- and Oxygen-Dependent Halogenases

Area of Honors:

Biochemistry and Molecular Biology

Keywords:

Enzyme Structure
Halogenases
BesD
Wel05
Homology
Bioinformatics

File:

Download Thesis_FINAL_Wertz__1_.pdf

Thesis Supervisors:

Amie Kathleen Boal, Thesis Supervisor
David Scott Gilmour, Thesis Honors Advisor

Author:

Thomas, Isaac

Title:

Genome-Metagenome Similarity Graph: a Novel Data Structure for Containment-Based Metagenome Comparison

Area of Honors:

Computer Science

Keywords:

Metagenomics
Bioinformatics
Mathematics
Computer Science
Metagenomic Similarity

File:

Download SHCThesis_IsaacThomas_Final.pdf

Thesis Supervisors:

David Koslicki, Thesis Supervisor
John Joseph Hannan, Thesis Honors Advisor

Author:

Cooper, Rachel

Title:

An Enhancer-Based Deep Learning Approach for Studying Viral Regulation

Area of Honors:

Computer Science

Keywords:

Deep Learning
Bioinformatics
Gene Regulation
Enhancers
Virus
HSV-1

File:

Download Cooper_Rachel_An_Enhancer-Based_Deep_Learning_Approach_For_Studying_Viral_Regulation.pdf

Thesis Supervisors:

Shaun Mahony, Thesis Supervisor
John Joseph Hannan, Thesis Honors Advisor

Author:

Millward, Andrew

Title:

L2-UniFrac

Area of Honors:

Computer Science

Keywords:

UniFrac
Bioinformatics
Comparative Metagenomics
Representative Microbiome
Distance Metric
Differential Abundance

File:

Download L2_Unifrac-Andrew_Millward-Schreyer.pdf

Thesis Supervisors:

David Koslicki, Thesis Supervisor
Danfeng Zhang, Thesis Honors Advisor
Paul Medvedev, Faculty Reader

Author:

Reiss, Hailey

Title:

Whole-genome sequence-based molecular characterization of antimicrobial genes in Salmonella enterica subsp. Dublin and Salmonella enterica subsp. Heidelberg isolated from veal calves

Area of Honors:

Immunology and Infectious Disease

Keywords:

Salmonella
Salmonella Dublin
Salmonella Heidelberg
Pennsylvania
Veal
Genomics
Bioinformatics
Whole-genome sequence analysis
Antimicrobial resistance

File:

Download reiss_hailey_thesis_iid.pdf

Thesis Supervisors:

Bhushan M Jayarao, Thesis Supervisor
Robert Paulson, Thesis Honors Advisor

Author:

Agarwala, Vandana

Title:

Cross-Species Prediction of Transcription Factor Binding

Area of Honors:

Computer Science

Keywords:

Gene Regulation
Deep Learning
Transfer Learning
Domain Adaptation
Computational Biology
Bioinformatics
Machine Learning

File:

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Thesis Supervisors:

Shaun Mahony, Thesis Supervisor
John Joseph Hannan, Thesis Honors Advisor

Author:

Sollenberger, Renee

Title:

Characterizing the Microbial Community of Anaerobically Digested High Lignin Fermentation Byproduct and Composted Material with Corn Stover as the Feedstock

Area of Honors:

Biological Engineering

Keywords:

Bioinformatics
Diversity Analysis
Compost
Anaerobic Digestion
Biofuels
Corn Stover
Bioprocessing

File:

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Thesis Supervisors:

Tom Richard, Thesis Supervisor
Ali Demirci, Thesis Honors Advisor

Author:

Jacob, Nolan

Title:

Binding Analysis of Ubiquitin Ligase SPOP with Intrinsically Disordered Proteins

Area of Honors:

Chemistry

Keywords:

Chemistry
Biochemistry
Biophysics
Biothermodynamics
Pdx1
SPOP
Intrinsically Disordered Proteins
Diabetes
NMR
Fluorescence Anisotropy
Bioinformatics

File:

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Thesis Supervisors:

Scott A Showalter, Thesis Supervisor
Lauren Dell Zarzar, Thesis Honors Advisor
David D Boehr, Faculty Reader