Winfree, Erik

Combined from CaltechTHESIS committee

• Davidson, Samuel Ryan (2025) Localized Catalytic DNA Circuits for Integrated Information Processing in Molecular Machines; 10.7907/831v-vq95
• Cherry, Kevin Matthew (2024) Molecular Pattern Recognition and Supervised Learning in DNA-Based Neural Networks; 10.7907/529f-kf62
• Kiliç, Kordağ Mehmet (2024) On the Complexity of Neural Network Representations; 10.7907/trse-ff38
• Huang, Jining (2023) Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens; 10.7907/54tw-ym95
• Raghavan, Guruprasad (2023) Engineering Artificial Systems with Natural Intelligence; 10.7907/374f-1202
• Clamons, Samuel Eric (2022) Three Problems in the Design and Specification of Biomolecular Circuits; 10.7907/9b4h-8f95
• Galstyan, Vahe (2022) Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling; 10.7907/1fzr-1240
• Ortiz-Muñoz, Andrés (2022) Combinatorics and Stochasticity for Chemical Reaction Networks; 10.7907/s9mc-3d59
• Poole, William (2022) Compilation and Inference with Chemical Reaction Networks; 10.7907/x3qc-je74
• Fornace, Mark Evan (2022) Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics; 10.7907/ayeg-at42
• Xiao, Fangzhou (2022) Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism; 10.7907/rtwq-v497
• Ross, Tyler David (2021) Guiding Self-Organization in Active Matter with Spatiotemporal Boundary Conditions; 10.7907/q85h-j730
• Parkin, James Michael (2021) Signal Amplification in Synthetic Bacterial Communication; 10.7907/50p8-bd89
• Porubsky, Nicholas James (2020) Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways; 10.7907/M8CZ-MW98
• Hanewich-Hollatz, Mikhail Henning (2020) Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology; 10.7907/NS2B-DJ96
• Johnson, Robert Francis (2020) Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks; 10.7907/a74v-kv80
• Singhal, Vipul (2019) Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts; 10.7907/g31j-ch52
• Jain, Siddharth (2019) Decoding the Past; 10.7907/K286-5N63
• Petersen, Philip Fai (2018) Engineering Molecular Self-assembly and Reconfiguration in DNA Nanostructures; 10.7907/7FXP-8402
• Srinivas, Niranjan (2015) Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement; 10.7907/Z9KD1VVJ
• Jones, Daniel Lawson III (2014) Sequence-Function Relationships in E. coli Transcriptional Regulation; 10.7907/4J7V-WD59
• Wolfe, Brian Robert (2014) Design and Analysis of Nucleic Acid Reaction Pathways; 10.7907/G4XZ-ZF47
• Evans, Constantine Glen (2014) Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly; 10.7907/7FMK-9403
• Woo, Sungwook (2013) Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions; 10.7907/4NZK-XK58
• Schaeffer, Joseph Malcolm (2013) Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands; 10.7907/JEBY-6X69
• Zhou, Hongchao (2013) Randomness and Noise in Information Systems; 10.7907/82KV-2H11
• Weir, Peter Thomas (2013) Polarization-Based Navigation in Drosophila; 10.7907/3VXQ-TE73
• Chandra, Fiona Adriani (2013) Limits and Tradeoffs in the Control of Autocatalytic Systems; 10.7907/Z1BQ-ZX85
• Wang, Zhiying (2013) Coding for Information Storage; 10.7907/TFHZ-RW88
• Wang, Zhiying (2013) Coding for Information Storage; 10.7907/TFHZ-RW88
• Stetson, Robert Chess Abernathy (2012) Interaction of Planning Regions in Cortex; 10.7907/VGS7-PZ20
• Franco, Elisa (2012) Analysis, Design, and in vitro Implementation of Robust Biochemical Networks; 10.7907/1C3S-FA59
• Liang, Joe Chih Yao (2012) High-Throughput Strategies for the Scalable Generation of RNA Component Functions; 10.7907/FQHC-EW36
• Rolfe, Jason Tyler (2012) Intrinsic Gradient Networks; 10.7907/YCB7-7X24
• Rolfe, Jason Tyler (2012) Intrinsic Gradient Networks; 10.7907/YCB7-7X24
• Levine, Joseph H. (2012) Genetic Regulatory Circuit Dynamics: Analysis and Synthesis; 10.7907/35A7-K421
• Hariadi, Rizal Fajar (2011) Non-Equilibrium Dynamics of DNA Nanotubes ; 10.7907/6GQW-YG26
• Shen, Kai (2010) Neural Encoding of Mixtures and Stimulus Generation in the Insect Brain; 10.7907/MDZC-0J48
• Zadeh, Joseph N. (2010) Algorithms for Nucleic Acid Sequence Design; 10.7907/20DG-NF39
• Pascal, Tod Augustin (2010) New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures; 10.7907/P0JH-QM60
• Zhang, David Yu (2010) Dynamic DNA Strand Displacement Circuits; 10.7907/Q4NR-CH87
• Cohen, Justin Delgado (2009) Programming Protein Patterns on DNA Nanostructures with Pyrrole-Imidazole Polyamides; 10.7907/CZ2K-MJ03
• Dunlop, Mary Julia (2008) Dynamics and Correlated Noise in Gene Regulation; 10.7907/AC8V-6S05
• Cox, Robert Sidney, III (2008) Transcriptional Regulation and Combinatorial Genetic Logic in Synthetic Bacterial Circuits; 10.7907/KRW6-DH88
• Soloveichik, David (2008) Molecules Computing: Self-Assembled Nanostructures, Molecular Automata,and Chemical Reaction Networks; 10.7907/ZGE0-AF38
• Kim, Jongmin (2007) In Vitro Synthetic Transcriptional Networks; 10.7907/Q9YA-N192
• Schulman, Rebecca Beth (2007) The Self-Replication and Evolution of DNA Crystals; 10.7907/3F8C-9D50
• Teal, Tracy Kristin (2007) Studies of the Spatial Organization of Metabolism in Shewanella oneidensis and Pseudomonas aeruginosa Biofilms; 10.7907/2gdf-yh13
• Bois, Justin S. (2007) Analysis of Interacting Nucleic Acids in Dilute Solutions; 10.7907/2JCJ-SX75
• Jayaraman, Vivek (2007) Neural Circuit Dynamics and Ensemble Coding in the Locust and Fruit Fly Olfactory System; 10.7907/A4VB-6C23
• Beierholm, Ulrik Ravnsborg (2007) Bayesian Modeling of Sensory Cue Combinations; 10.7907/K89B-XW75
• Papadantonakis, Karl Spyros (2006) Rigorous Analog Verification of Asynchronous Circuits; 10.7907/4R8F-WF03
• Christianson, Gestur Björn (2006) Information Processing in the Interaural Time Difference Pathway of the Barn Owl; 10.7907/3WJJ-7294
• Mihalas, Stefan (2006) Quantitative Model of Calcium/Calmodulin- Dependent Protein Kinase II Activation; 10.7907/d0zv-g984
• Drummond, David Allan (2006) Misfolding Dominates Protein Evolution; 10.7907/DH8E-2N10
• Cook, Matthew M. (2005) Networks of Relations; 10.7907/CVKM-D684
• Hart, Christopher Edward (2005) Inferring Genetic Regulatory Network Structure: Integrative Analysis of Genome-Scale Data; 10.7907/2JXP-3G71
• Schkolne, Steven (2004) 3-D Interfaces for Spatial Construction; 10.7907/8VWJ-TX38
• Riedel, Marcus D. (2004) Cyclic Combinational Circuits; 10.7907/410B-XR25
• Schkolne, Steven (2004) 3-D Interfaces for Spatial Construction; 10.7907/8VWJ-TX38