Dissertations
Expand to see dissertation authors, titles, and advisors Heading link
Summer 2023
| Name | Thesis Title | Advisor |
|---|---|---|
| Lin, Shujun | Development of in vivo Human Brain DTI-MRE | Klatt, Dieter |
| Liu, Songyun | Chemical Alterations of Periprosthetic Tissue and Joint Replacements: A Vibrational Spectroscopy Study | Pourzal, Robin |
| Salehabadi, Melika | Decoupling Uniaxial Prestress and Waveguide Effects from Dynamic Elastography | Royston, Thomas |
| Wang, Boshen | Predicting Pathological Effect of Mutation and Identifying Cancer Driver Event Based on Protein Structure | Liang, Jie |
Spring 2023
| Name | Thesis Title | Advisor |
|---|---|---|
| Brown, Grace | Micropatterned Co-cultures of the Liver and the Heart for Drug Screening and Cell Therapy | Khetani, Salman |
| Choi, Hyunjun | The Development of Alginate-Based Microspheres for Endovascular Applications | Kim, Dong-Hyun |
| Kefi, Amira | Improving the Human Genome Annotation Using Integrative Analysis and Deep Learning Methods. | Liu, Chunyu |
| Le, David | Quantitative Image Analysis for Objective Classification of Retinal Diseases | Yao, Xincheng |
| Manuchehrfar, Farid | Probability Landscape and Its Rotational Flux in Complex Systems: Construction and Topological Structure | Liang, Jie |
| Phakatkar, Abhijit | TEM Studies of Multielement Nanomaterials and Bacteria Interactions in the Aqueous Environments | Shokuhfar, Tolou; Shahbazian-Yassar, Reza |
| Sun, Michael | Evaluation of Corneal Biomechanics Using Silk Biomaterials and Optical Coherence Elastography | Rosenblatt, Mark |
| Wang, Wangfei | Role of Post-transcriptional Dysregulation and Aberrant Microbiota in Obstructive Lung Disease | Perkins, David; Finn, Patricia |
Fall 2022
| Name | Thesis Title | Advisor |
|---|---|---|
| Gao, Shang | Machine Learning Approaches for the Integrative Analysis of Multi-omics Data | Dai, Yang; Rehman, Jalees |
| Liu, Jennifer | Design of Engineered Substrates to Modulate Human Liver Cell Phenotype for Disease Modeling | Khetani, Salman |
| Saha, Soumya | The Role of Ethanol in Inherently Selective Atomic Layer Deposition and in Making Bioactive Coating | Takoudis, Christos |
| Wu, Shanshan | Energy Flow Perspective on the Mechanism of Conformational Dynamics in Biomolecules | Ma, Ao |
Summer 2022
| Name | Thesis Title | Advisor |
|---|---|---|
| Bandela, Mounica | Role of Cortactin in Cigarette Smoke-Induced Lung Endothelial Dysfunction | Dudek, Steven |
| Gao, Hua | Viscoelastic and Inertial Focusing of Asymmetric Cells in Spiral Channels | Papautsky, Ian |
| Geng, Xue | Neuroprotective Effects of Docosahexaenoic Acid on Neuronal Cell Function | Lee, James |
| Monckton, Chase | Engineering High Content and Multicellular Human Liver Platforms for Drug Development | Khetani, Salman |
| Tangen, Kevin | Virtual CNS Test Station for Computational Prediction of Species Transport in the CSF | Linninger, Andreas |
| Zhang, Zhehao | Multiplexed Electrochemical Sensors Based on Printed Circuit Board | Papautsky, Ian |
Spring 2022
| X | Thesis Title | Advisor |
|---|---|---|
| Kim, Taehoon | Functional Optical Tomography of the Retina in Mouse Models with Neurodegenerative Diseases | Yao, Xincheng |
| Lam, Trinh | Microfluidic Device for Studies of Bacterial Genetic Transformation in Streptococcus pneumoniae | Eddington, David |
Fall 2021
| Name | Thesis Title | Advisor |
|---|---|---|
| Chang, Claire | The Role of G alpha 13 in Integrin-dependent Neutrophil Migration | Du, Xiaoping |
| Khan, Mohammed | Biomimetic Surfaces for the Study of Outside-In Signaling in Neutrophils | Malik, Asrar |
| Mukherjee, Prithviraj | Fractionation and Focusing of Leukocytes using Inertial Microfluidics | Papautsky, Ian |
| Reiman, Derek | Deep Learning Frameworks for Multi-omics Analyses of the Microbiome in Disease Studies | Dai, Yang |
| Sheth, Nihar | Development of an Autonomous Platform for Surgical Simulation and Training | Luciano, Cristian |
| Teng, Tao | Membrane-Cytoskeleton Connectivity in Alzheimer’s Disease: From Aβ Clearance to TauSpreading by Microglia | Lee, James |
summer 2021 dissertations
| Name | Title | Advisor |
|---|---|---|
| Adiraj Iyer, Maheshwar | Control of Cell Culture Microenvironment Using Programmable Systems | Eddington, David |
| Fortel, Igor | Excitation-Inhibition Balance: A Study of Brain Network Dynamics Using Statistical Mechanics | Leow, Alex and Schonfeld, Dan |
| Marjanovic, Nicholas | Augmented Reality Haptic Trainer for Urinary Catheterization | Niederberger, Craig |
| Pandya, Shrikant | Sperm Hunter - Neural Network Model for Sperm Identification in Azoospermic Males | Niederberger, Craig |
| Yazdanpanah, Ghasem | Fabricating Natural Tunable Bioactive Biomaterials for Corneal Repair and Regeneration | Djalilian, Ali |
spring 2021 dissertations
| Name | Title | Advisor |
|---|---|---|
| Kukla, David | Multiscale Human Liver Platforms for Disease Modeling, Drug Development, and Regenerative Medicine | Khetani, Salman |
| Kunzer, Brian | Development and Application of Computational Tools for Multi-Electrode Electroretinography | Hetling, John |
| Lenzini, Stephen | The Biophysical Characteristics of Extracellular Vesicle Production and Transport | Shin, Jae-Won |
| Maharathi, Biswajit | Spatial-Temporal Network of Epileptic Spikes in Human Neocortex | Patton, James; Loeb, Jeffrey |
| Perez-Rathke, Alan | Mechanisms of Biological Functions Through Polymer Deep Sampling: Protein Gating and Chromatin Folding | Liang, Jie |
| Scotti, Alessandro | A Novel Z-Spectrum MRI For The Detection Of Brown And Browning Adipose Tissue | Cai, Kejia |
| Zhong, Zheng | Advancing Spatial and Temporal Resolution of MRI for Biological and Physical Applications | Zhou, Xiaohong Joe |
fall 2020 dissertations
| Name | Title | Advisor |
|---|---|---|
| Mehta, Rahul | Learning Patterns of Somatic Mutations and Medical Images in Human Cancer With Machine Learning | Karaman, Muge |
| Parmar, Pritesh | Optimal Process Modeling for Assessment and Enhancement of Error-Based Motor Learning | Patton, James |
Summer 2020
| Name | Title | Advisor |
|---|---|---|
| Alam, Minhaj | Quantitative Analysis and Automated Classification of Retinal Images | Yao, Xincheng |
| Jambusaria, Ankit | Computational Investigation of Endothelial Heterogeneity During Homeostasis and Inflammation | Rehman, Jalees; Malik, Asrar |
| Majumdar, Shreyan | Development of Magnetic Resonance Elastography for Assessing Small Regions of Interest in Murine Models | Klatt, Dieter |
a
| Name | Title | Advisor |
|---|---|---|
| Majeed, Yazan | Computational Modeling to Predict and Affect Recovery After Stroke | Patton, James |
| Banner, David | vTEM of Biologically Induced Reactions: Kidney Stone Mineralization and E. coli-Fiber Interactions | Shokuhfar, Tolou |
| Guidetti, Martina | Understanding Mechanical Wave Propagation in Anisotropic Samples through Magnetic Resonance Elastography | Royston, Thomas |
| Hartung, Grant | Multi-Scale Simulation of Cerebral Blood Flow and Oxygen Exchange for the Entire Mouse Brain | Linninger, Andreas |
| Lu, Yiming | Quantitative Investigation of Stimulus-evoked Intrinsic Optical Signal Change in Retinal Photoreceptors | Yao, Xincheng |
| Narayanan, Surya | In situ TEM to Study Iron Crystallization Mechanism in Ferritin | Shokuhfar, Tolou |
| Shareef, Farah | Light Attenuating Artificial Iris: Implantable and Contact Lens Designs | Cho, Michael |
a
| Name | Title | Advisor |
|---|---|---|
| Ghosh, Shreya | Quantum Dot Based Aptasensors for the Detection of Biomolecules with Related Raman/SERS Spectral Analysis | Stroscio, Michael |
| Meltem, Uyanik | Tissue Structure Analysis Using Anomalous Diffusion Signal Decay Models in Magnetic Resonance Imaging | Magin, Richard |
| Wright, Zachary | Distribution Analysis of Motor Actions for the Design of Customized Robot-Assisted Therapy | Patton, James |
| Xu, Jingting | Computational Analysis of DNA Methylation and Gene Regulation | Dai, Yang |
a
| Name | Title | Advisor |
|---|---|---|
| Anderson, Nickolas | Deposition and Characterization of Electronics Materials in Bionanotechnology and Micro/Nano-electronics | Jursich, Gregory |
| Blank, Kenneth | Influence of Lumbar Fusion Alignment and Sitting Postures on the Biomechanics of Adjacent Segments | Patwardhan, Avinash |
| Chen, Chang | Structure-function Analysis of Inflammatory Bowel Disease Associated Proteins and Moonlighting Proteins | Jeffery, Constance |
| De, Ayushmita | Effect of Fusion Methods on Adjacent Segment Biomechanics in a Lumbar Spine with Preexisting Conditions | Natarajan, Raghu |
| Seonbyeong, Kim | Mathematical Modeling of Aquaporin 4 Intracellular Transport and Design of Complex Distillation Process | Linninger, Andreas |
| Thomas, Joel | Quantitative Evaluation of Electrical Stimulation Therapy for Eye Disease | Hetling, John |
| Terebus, Anna | Computing Landscape, Velocity and Flux of Probability Mass in Gene Regulatory Networks | Liang, Jie |
| Tian, Wei | Computational Investigation of Structural and Thermodynamic Properties of Beta-Barrel Membrane Proteins | Liang, Jie |
a
| Name | Title | Advisor |
|---|---|---|
| Ghodsi, Seyed | Graphene Liquid-Cell TEM Investigation of Confined Liquids | Shokuhfar, Tolou |
| Knowlton, Christopher | A Gait-Dependent Model of Wear from Retrieved Polyethylene Components of Total Knee Replacements | Wimmer, Markus |
| Naqib, Ankur | Evaluating PCR Bias Through Experimental Investigations of Complex Primer-Template Interactions | Green, Stefan |
| Xing, Mengqi | Using Electroencephalography-Based Connectomics for Pattern Learning on Psychiatric Disorders | Leow, Alex |
a
| Name | Title | Advisor |
|---|---|---|
| Christoforidis, Theodoros | Microfluidic Devices for Control of Gaseous Environments | Eddington, David |
| Jones, Taneka | Extrusion Based Bioprinting: An In Vitro Model for Dental Pulp Tissue Engineering | Alapati, Satish |
a
| Name | Title | Advisor |
|---|---|---|
| Bishal, Arghya | Functionalization of Biomaterials with Atomic Layer Deposition for Tunable Performance Enhancements | Takoudis, Christos |
| Ghaffari, Mahsa | Large-Scale Hemodynamic Analysis of Cerebral Arterial Tree with Parametric Mesh Generation Technique | Linninger, Andreas |
| Gould, Ian | Computational Mathematics Elucidates the Dependence of Brain Perfusion on Microcirculation | Linninger, Andreas |
| Metwally, Ahmed | Computational Methods for Longitudinal Microbiome Analysis: Identification, Modeling, and Classification | Perkins, David/Dai, Yang |
| Mkrtschjan, Michael | Mechanical Inputs to Cardiac Fibroblasts and Myocytes Affect Structure, Function, and Signaling Response | Russell, Brenda |
| Paredes, Andre | Effects of Variable Energy Delivery on Leukocyte Kinetics and Wound Healing | Bartholomew, Amelia |
| Suryadevara, Vidyani | Role of Phospholipase D in Idiopathic Pulmonary Fibrosis and FTIR Imaging to Detect Fibrogenesis | Natarajan, Viswanathan/Royston |
a
| Name | Title | Advisor |
|---|---|---|
| Bergau, Dennis | Machine Learning Prediction of Pre-Clinical Drug Induced QT Prolongation Liability and Pathway Analysis | Lu, Hui |
| Henry, Brian | The Audible Human Project: Geometric and Acoustic Modeling in The Airways, Lungs and Torso | Royston, Thomas |
| Patangay, Shresta | Pattern Electroretinograpy in Peripheral Retina: System Development and Validation in Human Subjects | Hetling, John |
| Qin, Wenyi | Novel Statistical Methods Through Data Integration for Disease-related Gene and Pathway Detection | Lu, Hui |
a
| Name | Title | Advisor |
|---|---|---|
| Michael, George | Tribocorrosion Studies of Dental Materials, and the Clinical Implications | Magin, Richard |
| Khansari, Maziyar | Quantitative Analysis of Ocular Microcirculation Images in Human Health and Disease | Shahidi, Mahnaz |
| Parikh, Paras | MRI-based Curvature Assessment and High-Resolution T1 Mapping to Detect Cardiac Structural Abnormalities | Ng, Jason; Royston, Thomas |
| Rexius, Megan | Engineered Systems for Controlled Hypoxia and Thermogenesis | Eddington, David |
| Wang, Benquan | Functional Optical Coherent Tomography of Stimulus-Evoked Intrinsic Optical Signals in the Retina | Yao, Xincheng |
| Xing, Yuan | Microfluidic Platform for In Vitro Study on the Development of Cell Therapy | Oberholzer, Jose |
| Larsen, Peter | Modeling Host-Microbiome Interactions | Dai, Yang |
| Liu, Cong | Investigation of Feature Selection Methods in High-Throughput Omics Data Analysis | Lu, Hui |
a
| Name | Title | Advisor |
|---|---|---|
| Ahn, Sang | Role of Endothelial Potassium Channels in Vasodilation Under Normal and Dyslipidemic Condition | Levitan, Irena |
| Bogdanowicz, Leszek | Diagnosis of Glaucoma by 3D Reconstruction of Optic Nerve Head with a Portable Ocular Imaging System | Hetling, John |
| Brennan, Martin | Devices for Biological Systems: On-Chip Horizontal Gene Transfer and 3D-Printed Microfluidic Applications | Eddington, David |
| Felder, Anthony | Multi-modal Imaging of Retinal Oxygenation | Shahidi, Mahnaz |
| Jaishankar, Dinesh | Engineering a Higher Efficacy Anti-Heparan Sulfate Peptide for an Entry-Based Antiviral Therapy | Shukla, Deepak |
| LeMaster, Elizabeth | Synergistic Effect of Hemodynamic Environment and Dyslipidemia on Endothelial Biomechanics | Levitan, Irena |
| Selner, Ashley | Three-Dimensional Finite Element Models of Corneal Electroretinogram Potentials in Rat | Hetling, John |
| Shah, Amit | Reshaping Movements Through Avoidance of Negative Events: A General Adaptive Controller | Patton, James |
| Srinivasan, Girish | Development of a Novel Data Acquisition Technique and a Software Tool for Quantitative Diffusion Imaging | Zhou, X. Joe |
| Varma, Vishal | QCL and FT-IR Spectroscopic Imaging to Identify Biomarkers for Transplant Outcome and Cancer | Walsh, Michael |
| Wang, Zhinan | Study of Hypoxia on Embryogenesis, Pharmaceutical Testing and Stem Cell Regulation Using Drosophila Model | Cheng, Jun |
a
| Name | Title | Advisor |
|---|---|---|
| Hsu, Chihyang | Medical Imaging Techniques for Characterizing Cerebral Angioarchitecture | Linninger, Andreas |
| Mashiatulla, Maleeha | Structural and Compositional Assessment of Bone and Articular Cartilage with Micro-Computed Tomography | Sumner, D. Rick |
| Mendoza-Elias, Joshua | Microfluidic-based Strategies to Improve Islet and Encapsulated Islet Transplant for Type I Diabetes | Oberholzer, Jose |
| Venugopal, Indu | Intrathecal Magnetic Drug Targeting for Treatment of Central Nervous System Diseases | Linninger, Andreas |
| Ye, Allen | Multiple-Scale Analysis on the Fractal Structure of the Brain using Diffusion Magnetic Resonance Imaging | Magin, Richard |
| Lin, Meishan | Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins | Liang, Jie |
a
| Name | Title | Advisor |
|---|---|---|
| Derafshi, Zahra | Multi-Electrode Electroretinography: Measuring Spatial Differences in Corneal Potentials | Hetling, John |
| Hall, Cierra | A Luminance Noise Approach to Target Post-Receptor Visual Pathways; Application to Optic Nerve Disease | McAnany, J. Jason |
| Gursoy, Gamze | Three-Dimensional Chromosome Organization in Eukaryotes: Novel Computational Approaches | Liang, Jie |
| Zhao, Jieling | Dynamic Cell Model with Cellular Signaling Network and Mechanical Forces for Tissue Pattern Formation | Liang, Jie |
a
| Name | Title | Advisor |
|---|---|---|
| Horowitz, Justin | Movement Intent and Its Construction | Patton, James L. |
| Gerardo Mauleon Ramos | 3D Oxygen Microfluidic Platform for In Vitro Hypoxic Studies | Eddington, David |
| Tang, Ke | Efficient Biased Sampling Methods for Biomacromolecules: Protein Loops and RNA Thermodynamic Prediction | Liang, Jie |
| Trella, Katie | Haptic Simulation of Prostate Cancer Based on Magnetic Resonance Elastography | Luciano, Cristian J. |
a
| Name | Title | Advisor |
|---|---|---|
| Moria Fisher Bittmann | Customized Robotic Training Approaches Using the Statistics of Reaching Errors | Eddington |
| Zelenakova, Julia | Effect of Binge Alcohol Exposure on Intervertebral Disc Structure and Mechanical Properties in Adult Rats | Magin |
a
| Name | Title | Advisor |
|---|---|---|
| Bochenek, Matthew | Immuno-Isolation Strategies for Islet Transplantation into Rodent and Non-Human Primate Models | Oberholzer, Jose |
| Gutierrez, Diana | The Study of Non-Viral Nanoscale Delivery Systems for Islet Transplantation | Oberholzer, Jose |
| Khayatzadeh, Saeed | Effect of Sagittal Malalignment on Cervical Spine Biomechanics | Patwardhan, Avinash |
| Meshik, Xenia | Quantum Dot- and Aptamer-Based Nanostructures for Biological Applications | Stroscio, Michael |
| Nourmohammadzadeh, Mohammad | Application of Microfluidics in the Field of Diabetes and Islets | Oberholzer, Jose |
a
| Name | Titel | Advisor |
|---|---|---|
| Bang, Chi | The Role of Spectrosome and Centrosome in Asymmetric Stem Cell Division | Cheng, Jun |
| Butt, Arman | Functionalized Ti-V Surfaces for Improved Osseointegration and Tribocorrosion of Biomedical Implants | Takoudis, Christos |
| Parthasarathy, Rajni | Neprilysin-dependent Reduction of Amyloid-beta in Eye Tissues | Pepperberg, David |
| Hu, Hong | Identification of Transcriptional Regulatory Elements: Novel Machine Learning Approaches | Dai, Yang |
a
| Name | Title | Advisor |
|---|---|---|
| Eik Lang Lau | Designing and Evaluating Carbide-Derived Carbon As a Novel Biomaterial for Hip Implants | Cho/McNallan |
| Lueshen, Eric | Design of Drug Delivery Methods for the Brain and Central Nervous System | Linninger, Andreas |
| Sui, Yi | Multi-dimensional Excitation in MRI: New Development and Applications | Zhou, X. Joe |
a
| Name | Title | Advisor |
|---|---|---|
| Huang, Chun-Chieh | Synthesis And Characterization of Leucine Zipper Hydrogel For Tissue Regeneration | George, Anne |
| Faezeh Jahanmiri Nezhad | Surface EMG Examination of Amyotrophic Lateral Sclerosis | Rymer, William Zev |
| Kurani, Ajay | Resting State fMRI in Parkinson’s Disease and Progressive Supranuclear Palsy | Vaillancourt, David |
| Yenkie, Kirti | Stochastic Processes from Batch Crystallization to In-vitro Fertilization | Diwekar, Urmila |
a
| Name | Title | Advisor |
|---|---|---|
| Broughton, Kathleen | Bioengineering Approaches to Control Micromechanics for Analysis of Cardiomyocyte Contractility | Russell, Brenda |
| Schwartz, Benjamin | Dynamic Analysis of Multiply Connected Bodies for Magnetic Resonance Elastography | Magin |
| Teng, Pang-Yu | Quantification of Retinal Oxygen Extraction Fraction and Vascular Oxygen Tension Gradients | Shahidi, Mahnaz |
| Yin, Ziying | MR Relaxation, Diffusion, and Stiffness Characterization of Engineered Cartilage Tissue | Magin |
a
| Name | Title | Advisor |
|---|---|---|
| Doroudian, Golnar | Delivery of Mechanical and Chemical Stimuli to Advance Regeneration | Russell, Brenda |
| Kuo, Hsien-Chi | Development and Evaluation of Computerized Segmentation Algorithm for 3D Multimodality Breast Images | Giger, Maryellen |
| Parthiban, Sujeeth | A Novel Method to Determine the Impact of Different Saddle Designs on Male Cyclists' Perineal Blood Flow | Niederberger, Craig |
| Genchev, Georgi | Computational Studies of Mechanical Signal Transduction in Proteins | Lu |
| Xu, Yun | Protein Design and Chromatin Structure: Novel Computational Approaches | Liang |
a
| Name | Title | Advisor |
|---|---|---|
| Mulger, Emily | Investigation of Speech for Communicative Brain-Computer Interface | Patton |
| Roqueiro, Damian | Computational Methods to Study Gene Regulation Using Genomic, Epigenomic and Chromosome Conformation Data | Dai |