Dissertations
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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. -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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