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Author:

Wafula, Eric

Title:

Computational methods for comparative genomics of non-model species: a case study in the parasitic plant family Orobanchaceae

Graduate Program:

Biology

Keywords:

Computational biology
Evolutionary biology
Bioinformatics
Comparative genomics
Next-generation sequencing
de novo assembly
Genome annotation
Gene expression
Whole genome duplication
Gene duplication
Phylogenomics
Ancestral reconstruction
Transcriptomics
Orthogroups
Gene family evolution
Parasitic plants
Orobanchaceae
Striga

File:

Download Eric_wafula_dissertation_final_submission.pdf

Committee Members:

Claude Walker Depamphilis, Dissertation Advisor/Co-Advisor
James Harold Marden, Committee Chair/Co-Chair
Istvan Albert, Outside Member
Naomi S Altman, Outside Member
Stephen Wade Schaeffer, Program Head/Chair

Author:

Timilsena, Prakash Raj

Title:

Phylogenomics and comparative transcriptomic analyses of the monocots

Graduate Program:

Biology

Keywords:

Phylogenomics
Plant Biology
Taxonomy
Systematics
Monocots
Genomics
Bioinformatics
Botany
Evolution
Comparative Genomics
Evolutionary Genomics
Transcriptomics
RNASeq
Gene Annotation

File:

Download Supplementary_File_14Apr_2020.xlsxDownload PhD_Dissertation_2020_Prakash_Raj_Timilsena.pdf

Committee Members:

Claude Walker Depamphilis, Dissertation Advisor/Co-Advisor
Kateryna Dmytrivna Makova, Committee Chair/Co-Chair
Heather M Hines, Committee Member
John Edward Carlson, Outside Member
Tracy Langkilde, Program Head/Chair

Author:

Cooper, Rachel

Title:

An Enhancer-Based Deep Learning Approach for Studying Viral Regulation

Graduate Program:

Bioinformatics and Genomics

Keywords:

Deep Learning
Bioinformatics
Gene Regulation
Enhancers
Virus
HSV-1

File:

Download RCooper_BGEN_final_masters_thesis.pdf

Committee Members:

Shaun Mahony, Thesis Advisor/Co-Advisor
Moriah Louise Szpara, Committee Member
George H Perry, Program Head/Chair

Author:

Millward, Andrew

Title:

L2-UniFrac

Graduate Program:

Computer Science and Engineering (MS)

Keywords:

UniFrac
Bioinformatics
Comparative Metagenomics
Representative Microbiome
Distance Metric
Differential Abundance

File:

Download L2_Unifrac-Andrew_Millward.pdf

Committee Members:

Chitaranjan Das, Program Head/Chair
David Koslicki, Thesis Advisor/Co-Advisor
Paul Medvedev, Committee Member

Author:

Veenis, Andrew

Title:

Towards a Better Understanding of the Influence of Noncovalent Interactions on RNA Catalysis and the Properties of RNA Moieties

Graduate Program:

Chemistry (PHD)

Keywords:

RNA
Ribozyme
pKa
Cheminformatics
Bioinformatics
Molecular Dynamics

File:

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Committee Members:

Lasse Jensen, Major Field Member
Song Tan, Outside Unit & Field Member
Joseph Cotruvo, Major Field Member
Philip Bevilacqua, Chair & Dissertation Advisor
Philip Bevilacqua, Program Head/Chair

Author:

Agarwala, Vandana

Title:

Cross-Species Prediction of Transcription Factor Binding

Graduate Program:

Statistics (MS)

Keywords:

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

File:

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Committee Members:

Shaun Mahony, Thesis Advisor/Co-Advisor
Qunhua Li, Thesis Advisor/Co-Advisor
Ephraim Hanks, Professor in Charge/Director of Graduate Studies
Xiang Zhu, Committee Member

Author:

Kumar, Balaji

Title:

Characterizing Nuclear genes of Mitochdonrial origin in avian clades

Graduate Program:

Biology (MS)

Keywords:

Nuclear genes of mitochondrial origin
Phylogenetics
Evolution
Bioinformatics

File:

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Committee Members:

David Toews, Thesis Advisor/Co-Advisor
Zachary A Szpiech, Committee Member
Stephen Schaeffer, Professor in Charge/Director of Graduate Studies

Author:

Ma, Zhao

Title:

Error in Scale Reliant Covariation Analysis

Graduate Program:

Informatics (MS)

Keywords:

Covairation Analysis
Uncertainity Quantification
Sequence Count Data
Bioinformatics

File:

Download ZhaoMa-Thesis.pdf

Committee Members:

Jeffrey Bardzell, Program Head/Chair
Justin Silverman, Thesis Advisor/Co-Advisor
Sharon Xiaolei Huang, Committee Member

Author:

Sebastian, Aswathy

Title:

Advancing Genomic and Transcriptomic Knowledge Through Reproducible Bioinformatics Workflows

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Bioinformatics
Workflows
Genomics
Transcriptomics
Metabarcoding

File:

Download dissertation_AS.pdf

Committee Members:

Andrew Patterson, Major Field Member
Shaun Mahony, Chair of Committee
Istvan Albert, Major Field Member & Dissertation Advisor
Reka Albert, Outside Unit & Field Member
David Koslicki, Program Head/Chair

Author:

Aguilar, Morris

Title:

“Omics of Disease”: Automation, Weaving, and Capturing

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Multi-Omic Analysis
Genomics
Metabolomics
Small RNA
Precision Medicine
Bioinformatics
Disease Pathogenesis
Biomarker Discovery
Neurodegenerative Diseases
Computational Biology
Cardiovascular Disease

File:

Download Dissertation_Full_MAA.pdf

Committee Members:

David Koslicki, Program Head/Chair
Andrew Patterson, Major Field Member
Dajiang Liu, Outside Unit & Field Member
James Broach, Major Field Member
Dokyoon Kim, Special Member
Molly Hall, Chair & Dissertation Advisor