Alumni Ph.D. Dissertations

Chad Creighton (Arul Chinnaiyan, Kerby Shedden)

Comparisons of Gene Expression Profiles from Cell Culture Models with Profiles from Tumor Xenografts and Patient Tumors: Implications for Lung and Breast Cancers

 

Daniel Rhodes (Eric Fearon)

Development and Integrative Analysis of a Cancer Gene Expression Database

 

Dongxiao Zhu (Alfred O. Hero III)

Reconstructing Signaling Pathways From High Throughput Data

 

Yu (Alex) Chen (Gordon Crippen)

Protein Structural Alignment and Application to Fold Recognition

 

Ji Chen (David States)

Identification of Global and Specific Gene Expression Patterns Based on Microarray

 

Damian Fermin (David States)

Use of Proteomics as a Method of Enhancing Genome Annotation

 

Stewart Chang (Denise Kirschner; Jennifer Linderman)

Multi-Scale Modeling of Antigen Presentation With Applications to Tuberculosis

 

Yili Chen (Tom Kerppola / David States)

Integrative Analysis of Transcriptional Regulation Using Computational Approaches

 

Jianjun Yu (Arul Chinnaiyan)

Bioinformatics Analysis of 'Omics' Data Towards Cancer Diagnosis and Prognosis

 

Jayson Falkner (Phil Andrews)

Aggregation, dissemination, and analysis of high-throughput scientific data sets in the field of proteomics

 

Carlos Santos (Brian Athey, David States)

Automated natural language processing for curation and integration of biological signal transduction pathways

 

Pete Ulintz (Philip Andrews)

Mining Deeper into the proteome: computational strategies for improving depth and breadth of coverage in high-throughput protein indentification studies

 

Arvind Rao (Doug Engel, Alfred O. Hero III, David States)

Prospective Identification of Long-range Transcriptional Enhancers

 

Subramanian Shankar Ajay (Brian Athey, Inhan Lee)

Novel Bioinformatics Approaches for microRNA Detection and Target Prediction

 

Mark Benson (Heather Carlson)

Binding MOAD (Mother of All Databases)

 

Xing Li (Deb Gumucio)

Bioinformatic Analysis of Epithelial: Mesenchymal Crosstalk during Mouse Gut Development and Patterning

 

Reagan Kelly (Sharon Kardia)

The Development & Application of a Risk Index to Predict the Individualized Chronic Disease Risk

 

Viktoriya Strumba (Margit Burmeister)

Association Analysis of Known Genetic Variants with Gene Expression in the Brain

 

Junguk Hur (Eva Feldman)

Integration of Text Mining with Systems Biology Provides New Insight into the Pathogenesis of Diabetic Neuropathy

 

Jung Hei (Julie) Kim (Arul Chinnaiyan)

Characterization of Copy Number Aberrations & Epigenetic Modifications in Prostate Cancer

 

Casey Diekman (Daniel Forger, Unni Nair)

Modeling and Analysis of Electrical Network Activity in Neuronal Systems

 

Patrick Harrington (Alfred O. Hero III)

Inverse Problems in High Dimensional Stochastic Systems Under Uncertainty

 

Lan Dai (David Lubman)

The Application of Mass Spectrometry-based Quantitative Proteomic Strategies in Cancer Stem Cell Research

 

Yongsheng Huang (Alfred O. Hero III, Jay Hess)

Integrative Statistical Learning and Applications to Predicting Features of Diseases and Health

 

Abhik Shah (Brian Athey, Peter Woolf)

Mechanistic Bayesian Networks for Integrating Knowledge and Data to Unravel Biological Complexity

 

Raquel Assis (Alexey Kondrashov)

Origin and Evolution of Novel Sequences by Gene Duplication

 

Michael DeGiorgio (Noah Rosenberg)

Genetic Variation and Modern Human Origins

 

Andrew Hodges (Oliver He, Peter Woolf)

Bayesian Network Approaches for Refining and Expanding Cellular and Immunological Pathways

 

Juichi (Lucy) Huang (Noah Rosenberg)

Genotype imputation in diverse populations: Empirical and theoretical approaches

 

Arun Manoharan (John Kim)

The Landscape of C. elegans 3'UTRs

 

Huy Vuong (David Lubman)

Bioinformatics Analysis of Humoral Immune Response and Reverse Phase Protein Microarray for Biomarker Discovery

 

Nickolay Khazanov (Heather Carlson)

Large-scale Analysis of Protein-Ligand Binding Sites Using the Binding MOAD Database

 

Doug Jacobsen (Charles Brooks III, Matt Young)

An Investigation of the Roles of Magnesium Ions in the Catalytic Cycle of the Protein Kinase CDK2: a Molecular Link between Allosteric Activation Catalytic Activity

 

Yu-Hsuan Lin (Doug Engel, Maureen Sartor)

Analysis of, and software development for, ChIP-Seq and RNA-Seq data

 

Conner Sandefur (Santiago Schnell)

Defining chemical reaction mechanisms associated with threshold phenomena in conformational diseases

 

Sira Sarntivijai (Brian Athey) 

A Novel Integrative Bioinformatics Approach to biomedical Ontology Practice for Translational Informatics

 

Yasin Senbabaoglu (Jun Li, George Michailidis)

Developing and Application of Statistical Algorithms for High-Dimensional Biological Data Analysis

 

Erin Shellman (Charles Burant, Santiago Schnell)

Network motifs provide signatures that characterize metabolism

 

Zachary Szpiech (Noah Rosenberg, Sebastian Zollner)

Human Migration, Population Divergence, and the Accumulation of Deleterious Alleles: Insights from Private Genetic Variation and Whole-exome Sequencing.

 

Chaolong Wang (Michael Boehnke, Noah Rosenberg)

Statistical Methods for Analyzing Human Genetic Variation in Diverse Populations

 

Yan Zhang (Philip Andrews)

Network discovery in equilibrium-state and dynamic data: Applications to phosphoproteomics and kinetics

 

Gang Su (Brian Athey, Fan Meng) 

Omics Data Mining: Across Scales and Dimensions

 

Ryan Welch (Michael Boehnke, Laura Scott)

Bioinformatics Software and Methods for Genome-wide Association and Chip-Seq Studies

 

Michelle Wynn (Sofia Merajver, Santiago Schnell)

Unraveling the Complex Regulatory Relationships between Metabolism and Signal Transduction in Breast Cancer

 

Chunchao Zhang (Philip Andrews)

Analysis of Post-translational Modifications of Histones and Myelin Basic Protein: Crosstalk and Beyond

 

Peng Zhang (Sebastian Zollner)

The Road to identifying disease causing genes: association test, genotype imputation, and sampling strategies for sequencing studies

 

Matthew Iyer (Arul Chinnaiyan)

Discovering cancer-associated transcripts by RNA sequencing

 

O. Alejandro Balbin (Arul Chinnaiyan, Alexey Nesvizhskii)

Identifying Novel Targetable Genes and Pathways in Cancer by Integrating Diverse Omics Data

 

Lee Sam (Arul Chinnaiyan, Alexey Nesvizhskii)

Integrative bioinformatics in the age of massive throughput sequencing: from the transcriptome to the proteome in prostate cancer

 

Bo Li (Li, Jun)

Development and Application of Novel Methods to Study Tumor Heterogeneity and Cancer Genome Evolution

 

Artur Veloso (Mats Ljungman)

Insights into RNA transcription through nascent RNA sequencing

 

Kraig Stevenson (Patricia Wittkopp)

The evolution of gene regulation in Drosophila

 

Shanshan Cheng (Charles Brooks III)

Delineating Structural Characteristics of Viral Capsid Proteins Critical for Their Functional Assembly

 

Datta Mellacheruvu (Alexey Nesvizhskii)

A computational and informatics framework for the analysis of affinity purification mass spectrometry data and reconstruction of protein interaction networks

 

Joseph Donohoe (Rajesh Balkrishnan)

Evaluating the Methodology and Clinical Utility of Spatial Access to Health Care Measures in Appalachia

 

Mallory Freeberg (John Kim)

Computational analysis of the post-transcriptional gene regulatory network

 

Jinrui Xu (Jianzhi Zhang)

Molecular evolutionary studies using structure genomics and proteomics

 

Daniel Zinder (Mercedes Pascual0

Phylodynamic Patterns in Pathogen Ecology and Evolution

 

Chang Gong (Denise Kirschner; Jennifer Linderman)

Quantifying the generation of T-cell immunity using a systems biology approach

 

Avinash Shanmugam (Alexey Nesvizhskii)

Integrative analysis frameworks for improved peptide and protein identification from tandem mass spectrometry data

 

Ellen Schmidt (Cristen Willer)

Insights into the genetic architecture underlying plasma lipids and related phenotypes from genome-wide human genetic variation

 

Katherine Gurdziel (Deb Gumucio)

Computational and biological approaches for identification of Hedgehog signaling targets and their application to intestinal visceral smooth muscle development in the mouse

 

Yanxiao Zhang (Maureen Sartor)

High-throughput bioinformatics approaches to understand gene expression regulation in head and neck tumors

 

Chih-Chiang Tsou (Alexey Nesvizhskii)

Computational Framework for Data-Independent Acquisition Proteomics

 

Chee Lee (Maureen Sartor)

Functional Interpretation of High-Throughput Sequencing Data

 

Jing Lu (Heather Carlson)

Data-Driven Insights into Ligands, Proteins, and Genetic Mutations

 

Brandon Govindarajoo (Yang Zhang, 

Template Based Modeling and Structural Refinement of Protein-Protein Interactions

 

Shiya Song (Jeff Kidd)

Demographic and population separation history inference based on whole genome sequences

 

Brendan Veeneman (Arul Chinnaiyan, Alexey Nesvizhskii)

Development and Application of Methods to Discover Cancer-Associated Transcript Variants

 

Bryan Moyers (Jianzhi Zhang)

On Gene Age, Gene Origins, and Evolutionary Trends

 

Andy Kong (Alexey Nesvizhskii)

Computational strategies for proteogenomics analyses 

 

Xuefang Zhao (Ryan Mills)

Understanding the complexity of human structural genomic variation through multiple whole genome sequencing platforms 

 

Sai Chen (Goncalo Abecasis)

Statistical methods and analysis to identify disease-related variants from genetics studies

 

Laura Seaman (Indika Rajapakse)

4D Nucleome of Cancer

 

Zhengting Zou (Jianzhi Zhang)

Model-based genomic studies of protein sequence evolution: convergence, epistasis, and amino acid acceptance rates

 

Raymond Cavalcante, Jr. (Maureen Sartor)

Beyond the transcriptome: Facilitating interpretation of epigenomics and metabolomics data

 

Craig Biwer (Kayvan Najarian)

Computing Obesity: Signal Processing and Machine Learning Applied to Predictive Modeling of Clinical Weight-Loss

 

Daniel Hovelson (Scott Tomlins)

Precision oncology opportunities and disease insights from next-generation sequencing profiling of routine clinical biospecimens

 

Sang ("Tony") Chun (Ryan Mills)

Development and Application of Next-Generation Sequencing Methods to Profile Cellular Translational Dynamics

 

Wei Zhou (Cristen Willer)

Computational and Statistical Approaches for Large-Scale Genome-Wide Association Studies

 

Ridvan Eksi (Yuanfang Guan)

Identification and functional annotation of alternatively spliced isoforms

 

Richard Alexander Smith (Edward Ionides, Aaron King) 

Inference of infectious disease dynamics from genetic data via Sequential Monte Carlo

 

Shweta Ramdas (Margit Burmeister, Jun Li)

Genomics of Complex Traits: Methods and Applications

 

Ari Allyn-Feuer (Brian Athey)

The Pharmacoepigenomics Informatics Pipeline and H-GREEN Hi-C Compiler: Discovering Pharmacogenomic Variants and Pathways with the Epigenome and Spatial Genome

 

Lauren Jepsen (David Sept)

Nucleotide and Polymerization Effects on Actin Structure and Dynamics

 

Xinqiang Ding (Charles Brooks III)

Methodological Advances for Drug Discovery and Protein Engineering

 

Alexandr Kalinin (Brian Athey, Ivo Dinov)

Cell Nuclear Morphology Analysis Using 3D Shape Modeling, Machine Learning and Visual Analytics

 

Jedidiah Carlson (Jun Li, Sebastian Zollner)

Mapping the Landscape of Mutation Rate Heterogeneity in the Human Genome: Approaches and Applications

 

Zhengda Li (Qiong Yang)

Molecular Circuits of Biological Oscillators

 

Fan Zhang (Hyun Min Kang)

Leveraging Genetic Variants for Rapid, Robust, and Scalable Analysis of Massive Sequence Datasets

 

Shashank Jariwala (David Sept)

Dynamics and Regulation of Cytoskeletal Proteins

 

Hongyang Li (Yuanfang Gua)

Computational Analysis of Physiological Systems at Multiple Time and Length Scales

 

Hongjiu Zhang (Yuanfang Guan, Margit Burmeister)

Computational methods for resolving heterogeneity in biological data

 

Scott Ronquist (Indika Rajapakse)

Methods for Analyzing the 4D Nucleome with Application to Cellular Reprogramming

 

Ricardo D'Oliveira Albanus (Stephen Parker)

Computational Methods to Dissect Tissue-Specific Landscapes of Transcription Factor and DNA Interactions

 

Peter Orchard (Stephen Parker)

Epigenomic and Transcriptomic Profiling for the Study of Monogenic and Polygenic Traits and Disease

 

Vy Nguyen (Justin Colacino, Olivier Jolliet)

Biomarker-Based Characterization of Chemical Exposures and Physiological Responses

 

Chengxin Zhang (Yang Zhang)

Deep Learning-based Ab Initio Protein Structure Prediction and Structure-based Protein Function Annotation

 

Shriya Sethuraman (Andrzej Wierzbicki)

Genome-wide identification of non-coding transcription by RNA polymerase V and its involvement in transcriptional gene silencing

 

Edison Ong (Oliver He)  

Rational Vaccine Design by Reverse & Structural Vaccinology and Ontology 

 

Narathip Reamaroon (Brian Athey, Kayvan Najarian)

Label Uncertainty and Learning Using Partially Available Privileged Information for Clinical Decision Support

 

Shengcheng Dong (Alan Boyle)

Computational Methods to Identify Regulatory Variants in the Non-coding Regions of the Human Genome

 

Louis Joslyn (Denise Kirschner, Jennifer Linderman)

Multiscale modeling of T cells in Mycobacterium tuberculosis infection

 

Negar Farzaneh (Kayvan Najarian)

Automated Decision Support System for Traumatic Injuries

 

Brooke Wolford (Michael Boehnke, Cristen Willer)

Genetic discovery and precision medicine in cardiovascular diseases using electronic health record-linked biobanks

 

Zena Lapp (Evan Snitkin)

Genomic insights into carbapenem-resistant Klebsiella pneumoniae transmission and adaptation in the healthcare environment

 

Nguyen Vo (Arul Chinnaiyan)

The Genetic Heterogeneity and Drug Resistance Mechanisms of Relapsed Refractory Multiple Myeloma

 

Yaya Zhai (Alfred O. Hero III)

Digital Biomarker Models for Prediction of Infectious Disease Susceptibility

 

Murchtricia Jones (born Charles) (Charles Brooks III)

Advancement of Molecular Mechanics Based Drug Discovery Through the Use of Machine Learning

 

Li Guan (Michael Boehnke, Laura Scott)

Identification of Potential Molecular Traits Underlying the Genetic Predisposition to Complex diseases Using Multi-omics and Meta-analysis

 

Marlena Duda (Danai Koutra, Chandra Sripada)

Informed Segmentation Approaches for Studying Time-Varying Functional Connectivity in Resting State fMRI

 

Carrie Li (Kayvan Najarian)

Cardiac Arrhythmia Monitoring and Severe Event Prediction System

 

Stephen Lindsly (Indika Rajapakse)

Disentangling the 4D Nucleome

 

Siyu Liu (Maureen Sartor)

Epigenetic Effects in Head and Neck Cancer and di-2-ethylhexyl phthalate (DEHP) Exposure

 

Heming Yao (Kayvan Najarian)

Machine Learning and Image Processing for Clinical Outcome Prediction: Applications in Medical data from Patients with Traumatic Brain Injury, Ulcerative Colitis, and Heart Failure

 

Ningxin Ouyang (Alan Boyle)

Deciphering Transcriptional Regulatory Circuits: Transcription Factor Binding and Regulatory Variants Identification

 

Vivek Rai (Stephen Parker)

Using integrative multiomics approaches to dissect type 2 diabetes genetic risk in pancreatic islets

 

Alexandra Weber (Ryan Mills)

Integrating Diverse Technologies for Genomic Variant Discovery

 

Ryan Crawford (Evan Snitkin)

Computational methods for large scale analysis of microbial genome evolution and application to antibiotic 

 

Daniel Geiszler (Alexey Nesvizhskii)

Computational Methods for Characterizing Post-translational and Chemical Modifications Found in Open Searches

 

Hani Habra (Alla Karnovsky)

Computational Approaches Enabling Disparately Acquired Untargeted LC-MS Metabolomics Data Analysis

 

Jess Millar (Robert Woods)

Modeling of infectious disease informed by investigative focus and data characteristics

 

Gabrielle Dotson (Indika Rajapakse)

4D Nucleome-Guided Cellular Reprogramming

 

Renaid Kim (Kayvan Najarian)

Applications of Machine Learning in Pharmacology and Clinical Decision Support

 

Marcus Sherman (Ryan Mills)

Cultivation of enhanced bioinformatic-specific pedagogical manipulatives, interventions, and professional development

 

Kuan-Han Wu (Cristen Willer, Xu Shi)

Integrating Electronic Health Records with Genetic Information to Advance Precision Medicine Approaches in Cardiovascular Diseases

 

Nicholas Wang (Arvind Rao)

Data, Model, Inference: Evaluating Glioma MRI Models on Clinically Informed Axes

 

Tingyang Li (Nambi Nallasamy)

Artificial Intelligence-Based Clinical Decision-Making System for Cataract Surgery