Winfree, Erik

Committee Member — 64 thesises

• Schkolne, Steven — 3-D Interfaces for Spatial Construction (2004, Dissertation (Ph.D.))
• Zadeh, Joseph N. — Algorithms for Nucleic Acid Sequence Design (2010, Dissertation (Ph.D.))
• Bois, Justin S. — Analysis of Interacting Nucleic Acids in Dilute Solutions (2007, Dissertation (Ph.D.))
• Franco, Elisa — Analysis, Design, and in vitro Implementation of Robust Biochemical Networks (2012, Dissertation (Ph.D.))
• Huang, Jining — Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens (2023, Dissertation (Ph.D.))
• Beierholm, Ulrik Ravnsborg — Bayesian Modeling of Sensory Cue Combinations (2007, Dissertation (Ph.D.))
• Woo, Sungwook — Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions (2013, Dissertation (Ph.D.))
• Xiao, Fangzhou — Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism (2022, Dissertation (Ph.D.))
• Wang, Zhiying — Coding for Information Storage (2013, Dissertation (Ph.D.))
• Ortiz-Muñoz, Andrés — Combinatorics and Stochasticity for Chemical Reaction Networks (2022, Dissertation (Ph.D.))
• Poole, William — Compilation and Inference with Chemical Reaction Networks (2022, Dissertation (Ph.D.))
• Fornace, Mark Evan — Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics (2022, Dissertation (Ph.D.))
• Hanewich-Hollatz, Mikhail Henning — Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology (2020, Dissertation (Ph.D.))
• Robinson, Noah Evan — Construction of Long, Complex, and Diverse DNA Sequences (2025, Dissertation (Ph.D.))
• Evans, Constantine Glen — Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly (2014, Dissertation (Ph.D.))
• Riedel, Marcus D. — Cyclic Combinational Circuits (2004, Dissertation (Ph.D.))
• Jain, Siddharth — Decoding the Past (2019, Dissertation (Ph.D.))
• Wolfe, Brian Robert — Design and Analysis of Nucleic Acid Reaction Pathways (2014, Dissertation (Ph.D.))
• Kapasiawala, Manisha Kaushik — Design Considerations for Synthetic Cells (2026, Dissertation (Ph.D.))
• Zhang, David Yu — Dynamic DNA Strand Displacement Circuits (2010, Dissertation (Ph.D.))
• Dunlop, Mary Julia — Dynamics and Correlated Noise in Gene Regulation (2008, Dissertation (Ph.D.))
• Raghavan, Guruprasad — Engineering Artificial Systems with Natural Intelligence (2023, Dissertation (Ph.D.))
• Zou, Olivia Aoli — Engineering DNA liquids Towards Macroscopic Separation of Biomolecules (2026, Dissertation (Ph.D.))
• Petersen, Philip Fai — Engineering Molecular Self-assembly and Reconfiguration in DNA Nanostructures (2018, Dissertation (Ph.D.))
• Porubsky, Nicholas James — Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways (2020, Dissertation (Ph.D.))
• Guareschi, Matteo Michele — Enriching Architectures for Biosensing and Motor-Filament Systems Through the Programmability of DNA (2025, Dissertation (Ph.D.))
• Johnson, Robert Francis — Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks (2020, Dissertation (Ph.D.))
• Levine, Joseph H. — Genetic Regulatory Circuit Dynamics: Analysis and Synthesis (2012, Dissertation (Ph.D.))
• Ross, Tyler David — Guiding Self-Organization in Active Matter with Spatiotemporal Boundary Conditions (2021, Dissertation (Ph.D.))
• Liang, Joe Chih Yao — High-Throughput Strategies for the Scalable Generation of RNA Component Functions (2012, Dissertation (Ph.D.))
• Kim, Jongmin — In Vitro Synthetic Transcriptional Networks (2007, Dissertation (Ph.D.))
• Hart, Christopher Edward — Inferring Genetic Regulatory Network Structure: Integrative Analysis of Genome-Scale Data (2005, Dissertation (Ph.D.))
• Christianson, Gestur Björn — Information Processing in the Interaural Time Difference Pathway of the Barn Owl (2006, Dissertation (Ph.D.))
• Stetson, Robert Chess Abernathy — Interaction of Planning Regions in Cortex (2012, Dissertation (Ph.D.))
• Rolfe, Jason Tyler — Intrinsic Gradient Networks (2012, Dissertation (Ph.D.))
• Chandra, Fiona Adriani — Limits and Tradeoffs in the Control of Autocatalytic Systems (2013, Dissertation (Ph.D.))
• Davidson, Samuel Ryan — Localized Catalytic DNA Circuits for Integrated Information Processing in Molecular Machines (2025, Dissertation (Ph.D.))
• Drummond, David Allan — Misfolding Dominates Protein Evolution (2006, Dissertation (Ph.D.))
• Singhal, Vipul — Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts (2019, Dissertation (Ph.D.))
• Cherry, Kevin Matthew — Molecular Pattern Recognition and Supervised Learning in DNA-Based Neural Networks (2024, Dissertation (Ph.D.))
• Soloveichik, David — Molecules Computing: Self-Assembled Nanostructures, Molecular Automata,and Chemical Reaction Networks (2008, Dissertation (Ph.D.))
• Cook, Matthew M. — Networks of Relations (2005, Dissertation (Ph.D.))
• Jayaraman, Vivek — Neural Circuit Dynamics and Ensemble Coding in the Locust and Fruit Fly Olfactory System (2007, Dissertation (Ph.D.))
• Shen, Kai — Neural Encoding of Mixtures and Stimulus Generation in the Insect Brain (2010, Dissertation (Ph.D.))
• Pascal, Tod Augustin — New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures (2010, Dissertation (Ph.D.))
• Hariadi, Rizal Fajar — Non-Equilibrium Dynamics of DNA Nanotubes (2011, Dissertation (Ph.D.))
• Kiliç, Kordağ Mehmet — On the Complexity of Neural Network Representations (2024, Dissertation (Ph.D.))
• Weir, Peter Thomas — Polarization-Based Navigation in Drosophila (2013, Dissertation (Ph.D.))
• Gornet, James Andrew — Predictive Coding for Cognitive Mapping (2027, Dissertation (Ph.D.))
• Srinivas, Niranjan — Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement (2015, Dissertation (Ph.D.))
• Cohen, Justin Delgado — Programming Protein Patterns on DNA Nanostructures with Pyrrole-Imidazole Polyamides (2009, Dissertation (Ph.D.))
• Mihalas, Stefan — Quantitative Model of Calcium/Calmodulin- Dependent Protein Kinase II Activation (2006, Dissertation (Ph.D.))
• Zhou, Hongchao — Randomness and Noise in Information Systems (2013, Dissertation (Ph.D.))
• Subramanian, Arjuna Michael — Rewriting the Sequence and Structure Rules of Deep Protein Space (2026, Dissertation (Ph.D.))
• Papadantonakis, Karl Spyros — Rigorous Analog Verification of Asynchronous Circuits (2006, Dissertation (Ph.D.))
• Jones, Daniel Lawson III — Sequence-Function Relationships in E. coli Transcriptional Regulation (2014, Dissertation (Ph.D.))
• Parkin, James Michael — Signal Amplification in Synthetic Bacterial Communication (2021, Dissertation (Ph.D.))
• Schaeffer, Joseph Malcolm — Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands (2013, Dissertation (Ph.D.))
• Galstyan, Vahe — Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling (2022, Dissertation (Ph.D.))
• Teal, Tracy Kristin — Studies of the Spatial Organization of Metabolism in Shewanella oneidensis and Pseudomonas aeruginosa Biofilms (2007, Dissertation (Ph.D.))
• Schulman, Rebecca Beth — The Self-Replication and Evolution of DNA Crystals (2007, Dissertation (Ph.D.))
• Clamons, Samuel Eric — Three Problems in the Design and Specification of Biomolecular Circuits (2022, Dissertation (Ph.D.))
• Salmon, Gabriel L. — To see a World in a Grain of Cells: Statistical Auguries of Nonequilibrium (2026, Dissertation (Ph.D.))
• Cox, Robert Sidney, III — Transcriptional Regulation and Combinatorial Genetic Logic in Synthetic Bacterial Circuits (2008, Dissertation (Ph.D.))