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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:

Golkaram, Mahdi

Title:

Application of Reactive Molecular Dynamics in Biomaterial Science and Computational Biology

Graduate Program:

Mechanical Engineering

Keywords:

Reactive Molecular Dynamics
Computational Biology
Protein Denaturation
Graphene Oxide Toxicity

File:

Download LKGO.movDownload MY_Thesis_Final.pdf

Committee Members:

Adrianus C Van Duin, Thesis Advisor/Co-Advisor

Author:

Mueller, Thomas J

Title:

Modeling Metabolism and Regulation to Facilitate Strain Characterization and Design

Graduate Program:

Chemical Engineering

Keywords:

Optimization
Cyanobacteria
Systems Biology
Computational Biology
Metabolic Modeling

File:

Download Mueller_thesis_final.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Phillip E Savage, Committee Member
Manish Kumar, Committee Member
James Gregory Ferry, Outside 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:

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:

Agarwala, Vandana

Title:

Cross-Species Prediction of Transcription Factor Binding

Graduate Program:

Statistics

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