Bioengineering

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2026

• Caldera, Luis Fernando — Engineering Immunological Solutions for Pandemic-Level Threats (Dissertation (Ph.D.))
• Chadly, Duncan Matthew — High-Resolution Phylogenetic Lineage Recording with CRISPR Base Editors (Dissertation (Ph.D.))
• Chen, Linlin — A Platform for High Throughput Discovery of Sequence Defined Affinity Reagents (Dissertation (Ph.D.))
• Du, Rongrong — Build Synthetic Circuits at Different Scales (Dissertation (Ph.D.))
• Huang, Jianyi — Construction of Unconstructable DNA Constructs in Synthetic Chassis (Dissertation (Ph.D.))
• Kapasiawala, Manisha Kaushik — Design Considerations for Synthetic Cells (Dissertation (Ph.D.))
• Kratz, Matthieu Francois — Naturally-Inspired Circuits for Microbial Composition Control and Biosensing (Dissertation (Ph.D.))
• Lipschitz, Mikel — SLIM: Stochastic Lineage-Based Iterative Minimization (Dissertation (Ph.D.))
• Liu, Shichen — Reconstituting Cellular Intelligence in Nonliving Biomolecular Matter (Dissertation (Ph.D.))
• Pang Wan Rion, Marion — Deep Profiling of the Single-Cell Proteome (Dissertation (Ph.D.))
• Salmon, Gabriel L. — To see a World in a Grain of Cells: Statistical Auguries of Nonequilibrium (Dissertation (Ph.D.))
• Shaker, Sammy — 3D Vat Photopolymerization of Microarchitected Magnetic Metal Alloys for Chemotherapy Capture Filters (Dissertation (Ph.D.))
• Wexler, Helen — Algae as a Platform for Sustainable Biocomposites: Process–Structure–Property Relations (Dissertation (Ph.D.))
• White, Jonathan Alexander — Untangling Overlapping Barcodes in Image-Based Spatial Genomics (Dissertation (Ph.D.))
• Yu, Changhua — Understanding Kinase-Substrate Interaction with Deep Learning and High-Throughput Scanning (Dissertation (Ph.D.))
• Zou, Olivia Aoli — Engineering DNA liquids Towards Macroscopic Separation of Biomolecules (Dissertation (Ph.D.))

2025

• Davidson, Samuel Ryan — Localized Catalytic DNA Circuits for Integrated Information Processing in Molecular Machines (Dissertation (Ph.D.))
• Fang, Meichen — A Biophysical Approach to Normalization and Trajectory Inference in Single-Cell RNA Sequencing Data Analysis (Dissertation (Ph.D.))
• Guareschi, Matteo Michele — Enriching Architectures for Biosensing and Motor-Filament Systems Through the Programmability of DNA (Dissertation (Ph.D.))
• Larsson, Elin Maria — Domestication of Environmental Bacteria for Biosensing Applications (Dissertation (Ph.D.))
• Li, Francesca-Zhoufan — Evaluation of the Generalizability of Machine Learning-Assisted Protein Engineering Methods (Dissertation (Ph.D.))
• Robinson, Noah Evan — Construction of Long, Complex, and Diverse DNA Sequences (Dissertation (Ph.D.))
• Shivaei, Shirin — A Viral Toolkit for Ultrasound Imaging of Cellular Activity and Gene Expression (Dissertation (Ph.D.))
• Yang, Zheng — SpLacZ-MERCS-Coupled CRISPRi Screening Identifies Novel Mitochondria-ER Contact Sites Regulators (Dissertation (Ph.D.))

2024

• Bhamidipati, Pranav Subramanyam — Modeling and Design of Synthetic Biochemical Circuits for Biological Phenotypes (Dissertation (Ph.D.))
• Chari, Tara Varada — Perturbing the Genome: From Bench to Biophysics (Dissertation (Ph.D.))
• Cherry, Kevin Matthew — Molecular Pattern Recognition and Supervised Learning in DNA-Based Neural Networks (Dissertation (Ph.D.))
• Duan, Mengtong (Tom) — Expanding Frontiers in Biomedical Imaging and Synthetic Biology: Dynamic Acoustic Reporter Gene Imaging and Ratio-Tuning of Mammalian mRNA Polycistronic Expression (Dissertation (Ph.D.))
• Griffiths, Jessica Anne — Bidirectional Interactions Between the Gut Microbiome and Nervous System (Dissertation (Ph.D.))
• Johnston, Kadina Elizabeth — Acquiring Enzyme Sequence-Fitness Data at Scale Toward Predictive Methods for Enzyme Engineering (Dissertation (Ph.D.))
• Lee, Justin — Ultrasound Control and Imaging of Cellular Immunotherapy (Dissertation (Ph.D.))
• Mayfield, Acacia Michelle Hori — Customized and Modular Control of Gene Expression for Precision Gene Therapies (Dissertation (Ph.D.))

2023

• Chen, Zhewei — Engineering Conditional Guide RNAs for Cell-Selective Regulation of CRISPR/Cas9 (Dissertation (Ph.D.))
• Chuapoco, Miguel Roberto Estella — Adeno-Associated Viral Vectors for Gene Delivery to the Non-Human Primate Brain (Dissertation (Ph.D.))
• Ding, Xiaozhe — Computation-Aided Protein Engineering for Targeted Therapeutic Delivery (Dissertation (Ph.D.))
• Goertsen, David Gerald — Expanding Adeno-Associated Viral Capsid Engineering to Multiple Variable Regions for Diversified Tropism (Dissertation (Ph.D.))
• Guan, Charles — Neural Coding of Finger Movements in Human Posterior Parietal Cortex and Motor Cortex (Dissertation (Ph.D.))
• Hsu, Alice — Neurotechnology for Multiplexed Interrogation of Brain Circuits and Synaptic Activity (Dissertation (Ph.D.))
• Huang, Jining — Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens (Dissertation (Ph.D.))
• Marken, John Paul — Experimental and Theoretical Frameworks for Enabling Environmental Synthetic Biology (Dissertation (Ph.D.))
• Melis, Johan Matthijs — A Neural Network Model of an Insect's Wing Hinge Reveals How Steering Muscles Control Flight (Dissertation (Ph.D.))
• Raghavan, Guruprasad — Engineering Artificial Systems with Natural Intelligence (Dissertation (Ph.D.))
• Sarraf, Namita — Towards Integrated Molecular Machines: Structural, Mechanical, and Computational Motifs (Dissertation (Ph.D.))
• Wang, Sheng — Synthetic Circuits for Multicellular Spatial Patterning (Dissertation (Ph.D.))

2022

• Aceves, Aiden Joseph — Machine Learning and Modeling Methods for Protein Engineering (Dissertation (Ph.D.))
• Barlow, Jacob T. — Quantitative Sequencing and its Application to Studies of the Human Small-Intestine Microbiota (Dissertation (Ph.D.))
• Clamons, Samuel Eric — Three Problems in the Design and Specification of Biomolecular Circuits (Dissertation (Ph.D.))
• da Veiga Beltrame, Eduardo — Stories in Single Cell RNA Sequencing (Dissertation (Ph.D.))
• Gong, Mengsha — Remodeling Jellyfish (Dissertation (Ph.D.))
• Jo, HyeongChan — Bidirectional Brain-Machine Interfaces for Modulating Stimulation and Neural Plasticity (Dissertation (Ph.D.))
• Savela, Emily Sue — Nucleic Acid Measurements for Antibiotic Susceptibility Testing and Early Detection of SARS-CoV-2 (Dissertation (Ph.D.))
• Shur, Andrey Sergeyvich — Serine Integrase-Based Event Recording in E. coli (Dissertation (Ph.D.))
• Watkins-Dulaney, Ella Jenná — Engineering the Tryptophan Synthase β-Subunit for Synthesis of Noncanonical Amino Acids (Dissertation (Ph.D.))
• Williams, Rory Logan — Development and Scaling of Differentiation Circuit Architectures for Improving the Evolutionary Stability of Burdensome Functions in E. coli (Dissertation (Ph.D.))
• Wittmann, Bruce James — Strategies and Tools for Machine Learning-Assisted Protein Engineering (Dissertation (Ph.D.))
• Xiao, Fangzhou — Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism (Dissertation (Ph.D.))

2021

• Abedi, Mohamad — Thermal Bioswitches for Non-Invasive Control of Cellular Therapies (Dissertation (Ph.D.))
• Bagherian, Dawna Paria — Artificial Neural Networks for Nonlinear System Identification of Neuronal Microcircuits (Dissertation (Ph.D.))
• Chour, William — Molecular Technologies for Antigen-Based Immunity (Dissertation (Ph.D.))
• Knight, Anders Matthew — Expanding the Scope of Metalloprotein Families and Substrate Classes in New-to-Nature Reactions (Dissertation (Ph.D.))
• McCardell, Reed Dillard — Genetic Circuits for the Control of Multi-Strain Bacterial Populations (Dissertation (Ph.D.))
• Merk, Liana Noor — Engineering Logical Inflammation Sensing and Secreting Circuit for Gut Modulation (Senior thesis (Major))
• Parkin, James Michael — Signal Amplification in Synthetic Bacterial Communication (Dissertation (Ph.D.))
• Roychoudhury, Ankita — Understanding the Lifetime and Rate of Protein Production in Cell-Free Reactions While Maximizing Energy Use (Senior thesis (Minor))
• Sawyer, Daniel Patrick — Enhanced Noninvasive Imaging of Acoustic Biomolecules (Dissertation (Ph.D.))

2020

• Bogatyrev, Said R. — Development of Analytical Tools and Animal Models for Studies of Small-Intestine Dysbiosis (Dissertation (Ph.D.))
• Farhadi, Arash — Acoustic Reporter Genes for Noninvasive Imaging of Cellular Function (Dissertation (Ph.D.))
• Hanewich-Hollatz, Mikhail Henning — Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology (Dissertation (Ph.D.))
• Johnson, Robert Francis — Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks (Dissertation (Ph.D.))
• Jue, Erik Bradley — Improved Tools for Point-of-Care Nucleic Acid Amplification Testing (Dissertation (Ph.D.))
• Neumann, Adam Patrick — Towards Single Molecule Imaging Using Nanoelectromechanical Systems (Dissertation (Ph.D.))

2019

• Fowler, Trevor Michael — Silicon Neural Probes for Stimulation of Neurons and the Excitation and Detection of Proteins in the Brain (Dissertation (Ph.D.))
• Khazaei, Tahmineh — Metabolic Bi-Stability and Hysteresis in a Model Microbiome Community (Dissertation (Ph.D.))
• Lakshmanan, Anupama — Engineering Acoustic Protein Nanostructures for Non-Invasive Molecular Imaging using Ultrasound (Dissertation (Ph.D.))
• Lewis, Russell DeRieux — Evolution and Characterization of Carbene Transferases for Cyclopropanation and Carbon–Silicon Bond Formation (Dissertation (Ph.D.))
• Ramesh, Pradeep — Imaging and Control of Engineered Cells using Magnetic Fields (Dissertation (Ph.D.))
• Shao, Zixuan — Biological Responses to Therapeutic Treatments of Human Vascular Diseases (Dissertation (Ph.D.))

2018

• Barnes, Stephanie Loos — Decoding the Regulatory Genome: Quantitative Analysis of Transcriptional Regulation in Escherichia coli (Dissertation (Ph.D.))
• Bedbrook, Claire Nicole — Engineering Novel Rhodopsins for Neuroscience (Dissertation (Ph.D.))
• Belliveau, Nathan Maurice — Quantitative Dissection of the Allosteric and Sequence-Dependent Regulatory Genome in E. coli (Dissertation (Ph.D.))
• Gethers, Matthew Leroy, III — Therapeutic Opportunities and Approaches to Sequence Control for Nucleic Acids (Dissertation (Ph.D.))
• Lin, Ben Albert — Ultrasound Speckle Image Velocimetry: Studies on System Performance and Application to Cardiovascular Fluid Dynamics (Dissertation (Ph.D.))
• Mahmoudabadi, Gita — Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology (Dissertation (Ph.D.))
• Nandagopal, Nagarajan — New Capabilities of the Notch Signaling Pathway (Dissertation (Ph.D.))
• Park, Jin — Circuits of Dynamically Interacting Sigma Factors in Single Cells (Dissertation (Ph.D.))
• Schmidt, William Charles — What Makes a Narrative? Understanding the Portrayals of Hermenegild's Rebellion (Senior thesis (Major))
• Zhang, Carey Yuzhe — Partially Mixed Selectivity and Parietal Cortex (Dissertation (Ph.D.))

2017

• Thubagere Jagadeesh, Anupama — Programming Complex Behavior in DNA-based Molecular Circuits and Robots (Dissertation (Ph.D.))

2016

• Acharya, Aneesh — Multiplexed Analysis of Diverse RNA Classes via Hybridization Chain Reaction (Dissertation (Ph.D.))
• Hsiao, Victoria — Synthetic Circuits for Feedback and Detection in Bacteria (Dissertation (Ph.D.))
• Rios, Gustavo — Nanofabricated Neural Probe System for Dense 3-D Recordings of Brain Activity (Dissertation (Ph.D.))

2015

• Bagert, John David — Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging (Dissertation (Ph.D.))
• Buhler, Vivian Huang — Mary and Magdalene Reintegrated Through Sisterhood in a Male-Dominated Goblin Market (Senior thesis (Major))
• Cornejo de los Santos, Emmanuel Lorenzo — Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits (Dissertation (Ph.D.))
• Mahdavi, Alborz — Synthetic Biology Tools for Targeted Incorporation of Non-Canonical Amino Acids into Cellular Proteins (Dissertation (Ph.D.))
• Malladi, Chaitanya Lakshmidhar — Shakespeare’s Crafting of the Ideal King in Henry V (Other)
• Szablowski, Jerzy Olgierd — Biological Activity of Pyrrole-Imidazole Polyamides in vivo (Dissertation (Ph.D.))
• Trivedi, Vikas — From Molecules to Organs : Microscopy and Multi-Scale Nature of Development (Dissertation (Ph.D.))

2014

• Tan, Alison — Eavan Boland and Paula Meehan : Irish Voices of the Past (Senior thesis (Major))
• Trudeau, Devin Lee — Engineering Enzyme Systems by Recombination (Dissertation (Ph.D.))
• Wolfe, Brian Robert — Design and Analysis of Nucleic Acid Reaction Pathways (Dissertation (Ph.D.))
• Yu, Jiun-Yann — Innovations of Wide-Field Optical-Sectioning Fluorescence Microscopy: Toward High-Speed Volumetric Bio-Imaging with Simplicity (Dissertation (Ph.D.))

2013

• Azizgolshani, Hesham — Tissue Engineering Active Biological Machines: Bio-Inspired Design, Directed Self-Assembly, and Characterization of Muscular Pumps Simulating the Embryonic Heart (Dissertation (Ph.D.))
• Chandra, Fiona Adriani — Limits and Tradeoffs in the Control of Autocatalytic Systems (Dissertation (Ph.D.))
• Pahlevan, Niema Mohammed — A Systems Approach to Cardiovascular Health and Disease with a Focus on Aortic Wave Dynamics (Dissertation (Ph.D.))
• Smith, Matthew Alexander — Non-Contiguous Protein Recombination (Dissertation (Ph.D.))
• Sternberg, Jonathan Ben-Zion — Signal Transduction with Hybridization Chain Reactions (Dissertation (Ph.D.))
• Wang, Ying Min — Deep Tissue Fluorescence Imaging with Time-Reversed Light (Dissertation (Ph.D.))
• Woo, Sungwook — Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions (Dissertation (Ph.D.))
• Wu, Indira — Engineering Thermostable Fungal Cellobiohydrolases (Dissertation (Ph.D.))

2012

• Dempsey, William P. — Establishing a Genetic and Exogenous Toolbox for Studying Multiple Stages of Vertebrate Development in vivo (Dissertation (Ph.D.))
• Lee, Lap Man — The Implementation of Optofluidic Microscopy on a Chip Scale and Its Potential Applications in Biology (Dissertation (Ph.D.))
• Michener, Joshua Kieran — Combining Rational and Evolutionary Approaches to Optimize Enzyme Activity in Saccharomyces cerevisiae (Dissertation (Ph.D.))

2011

• Fuller, Sawyer Buckminster — Steady as She Goes: Visual Autocorrelators and Antenna-Mediated Airspeed Feedback in the Control of Flight Dynamics in Fruit Flies and Robotics (Dissertation (Ph.D.))
• Shin, Young Shik — Micro- and Nanotechnology-Based Platforms to Study Biology at Small Scale: From DNAs to Single Cells (Dissertation (Ph.D.))
• Vermesh, Udi Benjamin — Technologies for Protein Analysis and Tissue Engineering, with Applications in Cancer (Dissertation (Ph.D.))

2010

• Choi, Harry Ming Tak — Programmable In Situ Amplification for Multiplexed Bioimaging (Dissertation (Ph.D.))
• Fong, Eileen — Wound Healing on Artificial Extracellular Matrix Proteins (Dissertation (Ph.D.))
• Kim, Jin-Hong — State Diagram for Contact-Inhibition of Proliferation: A Quantitative Framework for Modulating Growth Patterns in Epithelial Cell Clusters (Dissertation (Ph.D.))
• Lee, Cheng-Chung — Chemical Synthesis in Elastomer-Based Integrated Microfluidics (Dissertation (Ph.D.))
• Liu, Mike Chia-Chung — Integrated Microfluidic Devices for Cell Culture and Assay (Dissertation (Ph.D.))
• McDowell, Emily Jayne — Low Optical Signal Detection in Biological Materials: SNR Considerations and Novel Techniques (Dissertation (Ph.D.))
• Peng, Jifeng — A Lagrangian Approach to Transport of Momentum and Biomass in Aquatic Biological Systems (Dissertation (Ph.D.))
• Pope, Melissa Davis — Dynamics of Multicellular Aggregation and Disaggregation: Implications for Tissue Engineering and Cancer Metastasis (Dissertation (Ph.D.))
• Quach, Quoc Chan (Brandon) — A Parylene Real Time PCR Microdevice (Dissertation (Ph.D.))
• Wu, David Dah-wei — Biomechanical Information Transfer: Maximum Caliber, λ Genome Ejection Dynamics, and the Formation of Otoliths in Zebrafish (Dissertation (Ph.D.))
• Young, Kakani Katija — Effect of In Situ Animal-Fluid Interactions on Transport and Mixing (Dissertation (Ph.D.))
• Zadeh, Joseph N. — Algorithms for Nucleic Acid Sequence Design (Dissertation (Ph.D.))

2009

• Brenner, Sarah Katherine — Engineering Synthetic Biofilm-Forming Microbial Consortia (Dissertation (Ph.D.))
• Card, Gwyneth Megan — Neural Control and Biomechanics of Flight Initiation in Drosophila melanogaster (Dissertation (Ph.D.))
• Chen, Yan — Integration of Dye Lasers and Microfluidics for Biochemical Analysis (Dissertation (Ph.D.))
• Kwong, Gabriel Abner — DNA Encoded Biotechnologies for Informative Cancer Diagnostics (Dissertation (Ph.D.))

2008

• Chow, Gang — Laser Tweezers for Moving Live Dissociated Neurons (Dissertation (Ph.D.))
• Erickson, Jonathan Christopher — The Neurochip: A Complete System for Long-Term Investigation of Cultured Neural Network Connectivity (Dissertation (Ph.D.))
• Grosberg, Anna — A Bioinspired Computational Model of Cardiac Mechanics: Pathology and Development (Dissertation (Ph.D.))
• Imoukhuede, Princess Ikhianosen Uerenikhosen — Visualizing the Membrane Confinement, Trafficking and Structure of the GABA Transporter, GAT1 (Dissertation (Ph.D.))
• Lu, Jian — Quantitative Three-dimensional Imaging of Droplet Convection and Cardiac Cell Motions Based on Micro DDPIV (Dissertation (Ph.D.))
• McHale, Kevin L. — Feedback Tracking and Correlation Spectroscopy of Fluorescent Nanoparticles and Biomolecules (Dissertation (Ph.D.))
• Rinderknecht, Derek Gresham — Development of a Microimpedance Pump for Pulsatile Flow Transport - Part 1: Flow Characteristics of the Microimpedance Pump. Part 2: A Systematic Study of Steady and Pulsatile Transport in Microscale Cavities (Dissertation (Ph.D.))
• Rodger, Damien Craig — Development of Flexible Parylene-based Microtechnologies for Retinal and Spinal Cord Stimulation and Recording (Dissertation (Ph.D.))
• Yung, Pun To (Douglas) — Detection of Aerobic Bacterial Endospores: From Air Sampling, Sterilization Validation to Astrobiology (Dissertation (Ph.D.))

2007

• Cai, Lance Lin-Lan — Robotics Training Algorithms for Optimizing Motor Learning in Spinal Cord Injured Subjects (Dissertation (Ph.D.))
• Kheradvar, Arash — The Role of Vortex Ring Formation and Pressure Drop on Dynamics of the Left Ventricle during Diastole (Dissertation (Ph.D.))
• Nasiraei Moghaddam, Abbas — Measurement and Analysis of Structure and Function of Myocardium in Embryonic and Adult Heart (Dissertation (Ph.D.))
• Sansom, Elijah Bodhi — Experimental Investigation on Patterning of Anchored and Unanchored Aligned Carbon Nanotube Mats by Fluid Immersion and Evaporation (Dissertation (Ph.D.))

2006

• Forouhar, Arian Soroush — Dynamic Views of Structure and Function during Heart Morphogenesis (Dissertation (Ph.D.))

2005

• Acevedo Bolton, Gabriel Alejandro — Blood Flow Effects on Heart Development and a Minimally Invasive Technique for in vivo Flow Alterations (Dissertation (Ph.D.))
• Dabiri, John Oluseun — Unsteady Fluid Mechanics of Starting-Flow Vortex Generators with Time-Dependent Boundary Conditions (Dissertation (Ph.D.))
• Endelman, Jeffrey B. — Design and Analysis of Combinatorial Protein Libraries Created by Site-Directed Recombination (Dissertation (Ph.D.))
• Hickerson, Anna Iwaniec — An Experimental Analysis of the Characteristic Behaviors of an Impedance Pump (Dissertation (Ph.D.))
• Zhou, Jijie — Nanowicking: Multi-scale Flow Interaction with Nanofabric Structures (Dissertation (Ph.D.))