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Author:

Wall, P. Kerr

Title:

COMPUTATIONAL TOOLS AND THEIR APPLICATIONS IN PLANT COMPARATIVE GENOMICS

Graduate Program:

Biology

Keywords:

Transcriptomics
Phylogenomics
Evolutionary Biology
Gene Family Evolution
Comparative Genomics
Computational Biology
Bioinformatics
Next Generation Sequencing

File:

Download P._Kerr_Wall_PhD_Dissertation.pdf

Committee Members:

Claude Walker Depamphilis, Committee Chair/Co-Chair
Webb Colby Miller, Committee Chair/Co-Chair
Hong Ma, Committee Member
Naomi S Altman, Committee Member
John Edward Carlson, Committee Member

Author:

Chung, Wen-Yu

Title:

Uncovering hidden genomic features using computational approaches

Graduate Program:

Computer Science and Engineering

Keywords:

Computational Biology
Bioinformatics
Systems Biology
Molecular Evolution

File:

Download wychung-Dissertation.pdf

Committee Members:

Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Anton Nekrutenko, Committee Member
Raj Acharya, Committee Member
Padma Raghavan, Committee Member
Reka Z Albert, Committee Member

Author:

Chen, Kuanbei

Title:

Computational Approaches for Integrative Detection of Protein-DNA Interactions

Graduate Program:

Computer Science and Engineering

Keywords:

Computational Biology
Bioinformatics
Peak-Calling
ChIP-seq
Gene regulation
Comparative Genomics

File:

Download Kuan-Bei.dissertation.pdf

Committee Members:

Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Dr Yu Zhang, Dissertation Advisor/Co-Advisor
Ross Cameron Hardison, Committee Member
Padma Raghavan, Committee Member
Kamesh Madduri, Committee Member

Author:

Ranganathan, Sridhar

Title:

Using computations to analyze and redesign metabolism

Graduate Program:

Integrative Biosciences

Keywords:

Metabolic Engineering
Metabolic Modeling
OptForce
Bioinformatics
Systems Biology

Author:

Li, Ruowang

Title:

USING LARGE-SCALE GENOMICS DATA TO UNDERSTAND THE GENETIC BASIS OF COMPLEX TRAITS

Graduate Program:

Integrative Biosciences

Keywords:

Bioinformatics
Genomics
Statistics
Data Integration
Bayesian Network
Epistasis

File:

Download Ruowang_Dissertation.pdf

Committee Members:

Marylyn Deriggi Ritchie, Dissertation Advisor/Co-Advisor
Marylyn Deriggi Ritchie, Committee Chair/Co-Chair
Ross Cameron Hardison, Committee Member
Shaun A Mahony, Committee Member
Le Bao, Outside Member

Author:

Wang, Wanyan

Title:

GENOMICS OF GENOTYPE-BY-ENVIRONMENT INTERACTIONS IN SHRUB WILLOW (SALIX SPP.): INSECT HERBIVORY AND SOIL MICROBIOMES

Graduate Program:

Plant Biology

Keywords:

Bioenergy
Bioinformatics
Shrub Willow
Pest-resistance
Soil Microbiome
Genomics
Genotype-by-environment Interaction

File:

Download PhD_Dissertation_Wanyan_Wang.pdf

Committee Members:

John Edward Carlson, Dissertation Advisor/Co-Advisor
John Edward Carlson, Committee Chair/Co-Chair
Yinong Yang, Committee Member
Mary Ann Victoria Bruns, Committee Member
Surinder Chopra, Outside Member

Author:

Pandey, Utsav

Title:

Comparative Genomics Provides Insights into Herpesvirus Transmission, Spread, and Virulence

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Herpes Simplex Virus
Marek's Disease Virus
Bioinformatics
Molecular Biology
Virology
Genomics

File:

Download Utsav_Pandey_PhD_dissertation.pdf

Committee Members:

Moriah Louise Szpara, Dissertation Advisor/Co-Advisor
Moriah Louise Szpara, Committee Chair/Co-Chair
Anthony Paul Schmitt, Committee Member
Istvan Albert, Committee Member
Andrew Fraser Read, Outside Member
Timothy Charles Meredith, Committee Member

Author:

Sun, Chen

Title:

Scalable and Accurate Algorithms for Search in Genomic Big Data and Analysis of Genetic Variants

Graduate Program:

Computer Science and Engineering

Keywords:

Algorithm
Big Data
Database
Genomics
Probabilistic Data Structures
Data Mining
Parallel Computing
Bioinformatics
Genetic Variants
SNP
Computational Biology

File:

Download ChenSun_dissertation_v0830.pdf

Committee Members:

Paul Medvedev, Dissertation Advisor/Co-Advisor
Paul Medvedev, Committee Chair/Co-Chair
Daniel Kifer, Committee Member
Kamesh Madduri, Committee Member
Michael Degiorgio, Outside Member

Author:

Messina, Kyle

Title:

Influence of biological small molecules on the twister ribozyme and development of methodologies to study and discover small ribozymes

Graduate Program:

Chemistry

Keywords:

RNA
Twister Ribozyme
Kinetics
Small Molecule
Cryo-EM
Bioinformatics

File:

Download Messina_KJ_2019_Dissertation.pdf

Committee Members:

Philip C Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C Bevilacqua, Committee Chair/Co-Chair
Carsten Krebs, Committee Member
David D Boehr, Committee Member
Craig Eugene Cameron, Outside Member
Philip C Bevilacqua, Program Head/Chair

Author:

Hu, Kai

Title:

Bioinformatics discovery of chemical diversity in enzyme superfamilies

Graduate Program:

Molecular, Cellular and Integrative Biosciences

Keywords:

Ribonucleotide Reductase (RNR)
Bioinformatics
Radical chemistry
Class Ie RNR
Deep Mutational Scanning (DMS) strategy

File:

Download Kai_Hu_dissertation_for_submission.pdf

Committee Members:

Benjamin D Allen, Dissertation Advisor/Co-Advisor
Joseph M Bollinger, Jr., Committee Chair/Co-Chair
Amie Kathleen Boal, Outside Member
Ross Cameron Hardison, Committee Member
Melissa Rolls, Program Head/Chair

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:

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

Author:

Millward, Andrew

Title:

L2-UniFrac

Graduate Program:

Computer Science and Engineering

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:

Ma, Zhao

Title:

Error in Scale Reliant Covariation Analysis

Graduate Program:

Informatics

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:

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

Keywords:

RNA
Ribozyme
pKa
Cheminformatics
Bioinformatics
Molecular Dynamics

File:

Login to Download

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:

Kumar, Balaji

Title:

Characterizing Nuclear genes of Mitochdonrial origin in avian clades

Graduate Program:

Biology

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:

Jonaid, G M

Title:

ADVANCING WORKFLOWS FOR STRUCTURE DETERMINATION OF DISEASE-RELEVANT MACRO-MOLECULES

Graduate Program:

Bioinformatics and Genomics (PhD)

Keywords:

Bioinformatics
data analysis

File:

Login to Download

Committee Members:

Dajiang Liu, Outside Unit Member
Susan Hafenstein, Outside Field Member
David Koslicki, Program Head/Chair
David Koslicki, Chair & Dissertation Advisor
Santhosh Girirajan, Major Field Member