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