<h1>Winfree, Erik</h1>
<h2>Monograph from <a href="https://data.caltech.edu">CaltechTHESIS committee</a></h2>
<ul>
<li>Cherry, Kevin Matthew (2024) <a href="https://resolver.caltech.edu/CaltechTHESIS:04292024-172707491">Molecular Pattern Recognition and Supervised Learning in DNA-Based Neural Networks</a>; <a href="https://doi.org/10.7907/529f-kf62">10.7907/529f-kf62</a></li>
<li>Kiliç, Kordağ Mehmet (2024) <a href="https://resolver.caltech.edu/CaltechTHESIS:06032024-055145735">On the Complexity of Neural Network Representations</a>; <a href="https://doi.org/10.7907/trse-ff38">10.7907/trse-ff38</a></li>
<li>Raghavan, Guruprasad (2023) <a href="https://resolver.caltech.edu/CaltechTHESIS:03172023-050019811">Engineering Artificial Systems with Natural Intelligence</a>; <a href="https://doi.org/10.7907/374f-1202">10.7907/374f-1202</a></li>
<li>Huang, Jining (2023) <a href="https://resolver.caltech.edu/CaltechTHESIS:01172023-195222304">Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens</a>; <a href="https://doi.org/10.7907/54tw-ym95">10.7907/54tw-ym95</a></li>
<li>Fornace, Mark Evan (2022) <a href="https://resolver.caltech.edu/CaltechTHESIS:12212021-202554260">Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics</a>; <a href="https://doi.org/10.7907/ayeg-at42">10.7907/ayeg-at42</a></li>
<li>Ortiz-Muñoz, Andrés (2022) <a href="https://resolver.caltech.edu/CaltechTHESIS:04182022-222416729">Combinatorics and Stochasticity for Chemical Reaction Networks</a>; <a href="https://doi.org/10.7907/s9mc-3d59">10.7907/s9mc-3d59</a></li>
<li>Galstyan, Vahe (2022) <a href="https://resolver.caltech.edu/CaltechTHESIS:08242021-212959886">Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling</a>; <a href="https://doi.org/10.7907/1fzr-1240">10.7907/1fzr-1240</a></li>
<li>Xiao, Fangzhou (2022) <a href="https://resolver.caltech.edu/CaltechTHESIS:05302022-235732314">Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism</a>; <a href="https://doi.org/10.7907/rtwq-v497">10.7907/rtwq-v497</a></li>
<li>Clamons, Samuel Eric (2022) <a href="https://resolver.caltech.edu/CaltechTHESIS:09262021-022402778">Three Problems in the Design and Specification of Biomolecular Circuits</a>; <a href="https://doi.org/10.7907/9b4h-8f95">10.7907/9b4h-8f95</a></li>
<li>Poole, William (2022) <a href="https://resolver.caltech.edu/CaltechTHESIS:11102021-210013472">Compilation and Inference with Chemical Reaction Networks</a>; <a href="https://doi.org/10.7907/x3qc-je74">10.7907/x3qc-je74</a></li>
<li>Ross, Tyler David (2021) <a href="https://resolver.caltech.edu/CaltechTHESIS:07082020-113341068">Guiding Self-Organization in Active Matter with Spatiotemporal Boundary Conditions</a>; <a href="https://doi.org/10.7907/q85h-j730">10.7907/q85h-j730</a></li>
<li>Parkin, James Michael (2021) <a href="https://resolver.caltech.edu/CaltechTHESIS:03262021-160841703">Signal Amplification in Synthetic Bacterial Communication</a>; <a href="https://doi.org/10.7907/50p8-bd89">10.7907/50p8-bd89</a></li>
<li>Porubsky, Nicholas James (2020) <a href="https://resolver.caltech.edu/CaltechTHESIS:10062019-213347699">Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways</a>; <a href="https://doi.org/10.7907/M8CZ-MW98">10.7907/M8CZ-MW98</a></li>
<li>Johnson, Robert Francis (2020) <a href="https://resolver.caltech.edu/CaltechTHESIS:04292020-052418975">Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks</a>; <a href="https://doi.org/10.7907/a74v-kv80">10.7907/a74v-kv80</a></li>
<li>Hanewich-Hollatz, Mikhail Henning (2020) <a href="https://resolver.caltech.edu/CaltechTHESIS:11042019-135312842">Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology</a>; <a href="https://doi.org/10.7907/NS2B-DJ96">10.7907/NS2B-DJ96</a></li>
<li>Singhal, Vipul (2019) <a href="https://resolver.caltech.edu/CaltechTHESIS:08262018-213846283">Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts</a>; <a href="https://doi.org/10.7907/g31j-ch52">10.7907/g31j-ch52</a></li>
<li>Jain, Siddharth (2019) <a href="https://resolver.caltech.edu/CaltechTHESIS:04032019-102853075">Decoding the Past</a>; <a href="https://doi.org/10.7907/K286-5N63">10.7907/K286-5N63</a></li>
<li>Petersen, Philip Fai (2018) <a href="https://resolver.caltech.edu/CaltechTHESIS:05312018-112853523">Engineering Molecular Self-assembly and Reconfiguration in DNA Nanostructures</a>; <a href="https://doi.org/10.7907/7FXP-8402">10.7907/7FXP-8402</a></li>
<li>Srinivas, Niranjan (2015) <a href="https://resolver.caltech.edu/CaltechTHESIS:06012015-171243593">Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement</a>; <a href="https://doi.org/10.7907/Z9KD1VVJ">10.7907/Z9KD1VVJ</a></li>
<li>Wolfe, Brian Robert (2014) <a href="https://resolver.caltech.edu/CaltechTHESIS:03272014-193400848">Design and Analysis of Nucleic Acid Reaction Pathways</a>; <a href="https://doi.org/10.7907/G4XZ-ZF47">10.7907/G4XZ-ZF47</a></li>
<li>Jones, Daniel Lawson III (2014) <a href="https://resolver.caltech.edu/CaltechTHESIS:06022014-165211576">Sequence-Function Relationships in E. coli Transcriptional Regulation</a>; <a href="https://doi.org/10.7907/4J7V-WD59">10.7907/4J7V-WD59</a></li>
<li>Evans, Constantine Glen (2014) <a href="https://resolver.caltech.edu/CaltechTHESIS:05132014-142306756">Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly</a>; <a href="https://doi.org/10.7907/7FMK-9403">10.7907/7FMK-9403</a></li>
<li>Woo, Sungwook (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:05302013-123041371">Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions</a>; <a href="https://doi.org/10.7907/4NZK-XK58">10.7907/4NZK-XK58</a></li>
<li>Schaeffer, Joseph Malcolm (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:02042013-110332492">Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands</a>; <a href="https://doi.org/10.7907/JEBY-6X69">10.7907/JEBY-6X69</a></li>
<li>Weir, Peter Thomas (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:07242012-154851161">Polarization-Based Navigation in Drosophila</a>; <a href="https://doi.org/10.7907/3VXQ-TE73">10.7907/3VXQ-TE73</a></li>
<li>Zhou, Hongchao (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:07122012-141803264">Randomness and Noise in Information Systems</a>; <a href="https://doi.org/10.7907/82KV-2H11">10.7907/82KV-2H11</a></li>
<li>Chandra, Fiona Adriani (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:06032013-143158080">Limits and Tradeoffs in the Control of Autocatalytic Systems</a>; <a href="https://doi.org/10.7907/Z1BQ-ZX85">10.7907/Z1BQ-ZX85</a></li>
<li>Wang, Zhiying (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:05312013-123819501">Coding for Information Storage</a>; <a href="https://doi.org/10.7907/TFHZ-RW88">10.7907/TFHZ-RW88</a></li>
<li>Wang, Zhiying (2013) <a href="https://resolver.caltech.edu/CaltechTHESIS:05312013-123819501">Coding for Information Storage</a>; <a href="https://doi.org/10.7907/TFHZ-RW88">10.7907/TFHZ-RW88</a></li>
<li>Stetson, Robert Chess Abernathy (2012) <a href="https://resolver.caltech.edu/CaltechTHESIS:05262012-075609487">Interaction of Planning Regions in Cortex</a>; <a href="https://doi.org/10.7907/VGS7-PZ20">10.7907/VGS7-PZ20</a></li>
<li>Franco, Elisa (2012) <a href="https://resolver.caltech.edu/CaltechTHESIS:10192011-161454857">Analysis, Design, and in vitro Implementation of Robust Biochemical Networks</a>; <a href="https://doi.org/10.7907/1C3S-FA59">10.7907/1C3S-FA59</a></li>
<li>Liang, Joe Chih Yao (2012) <a href="https://resolver.caltech.edu/CaltechTHESIS:01312012-154032563">High-Throughput Strategies for the Scalable Generation of RNA Component Functions</a>; <a href="https://doi.org/10.7907/FQHC-EW36">10.7907/FQHC-EW36</a></li>
<li>Rolfe, Jason Tyler (2012) <a href="https://resolver.caltech.edu/CaltechTHESIS:04202012-133210844">Intrinsic Gradient Networks</a>; <a href="https://doi.org/10.7907/YCB7-7X24">10.7907/YCB7-7X24</a></li>
<li>Rolfe, Jason Tyler (2012) <a href="https://resolver.caltech.edu/CaltechTHESIS:04202012-133210844">Intrinsic Gradient Networks</a>; <a href="https://doi.org/10.7907/YCB7-7X24">10.7907/YCB7-7X24</a></li>
<li>Levine, Joseph H. (2012) <a href="https://resolver.caltech.edu/CaltechTHESIS:06052012-121432503">Genetic Regulatory Circuit Dynamics: Analysis and Synthesis</a>; <a href="https://doi.org/10.7907/35A7-K421">10.7907/35A7-K421</a></li>
<li>Hariadi, Rizal Fajar (2011) <a href="https://resolver.caltech.edu/CaltechTHESIS:06062011-122322347">Non-Equilibrium Dynamics of DNA Nanotubes  </a>; <a href="https://doi.org/10.7907/6GQW-YG26">10.7907/6GQW-YG26</a></li>
<li>Zadeh, Joseph N. (2010) <a href="https://resolver.caltech.edu/CaltechTHESIS:05112010-205335518">Algorithms for Nucleic Acid Sequence Design</a>; <a href="https://doi.org/10.7907/20DG-NF39">10.7907/20DG-NF39</a></li>
<li>Shen, Kai (2010) <a href="https://resolver.caltech.edu/CaltechTHESIS:09122010-130333994">Neural Encoding of Mixtures and Stimulus Generation in the Insect Brain</a>; <a href="https://doi.org/10.7907/MDZC-0J48">10.7907/MDZC-0J48</a></li>
<li>Zhang, David Yu (2010) <a href="https://resolver.caltech.edu/CaltechTHESIS:05262010-173410602">Dynamic DNA Strand Displacement Circuits</a>; <a href="https://doi.org/10.7907/Q4NR-CH87">10.7907/Q4NR-CH87</a></li>
<li>Pascal, Tod Augustin (2010) <a href="https://resolver.caltech.edu/CaltechTHESIS:10262009-204842274">New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures</a>; <a href="https://doi.org/10.7907/P0JH-QM60">10.7907/P0JH-QM60</a></li>
<li>Cohen, Justin Delgado (2009) <a href="https://resolver.caltech.edu/CaltechETD:etd-11232008-171327">Programming Protein Patterns on DNA Nanostructures with Pyrrole-Imidazole Polyamides</a>; <a href="https://doi.org/10.7907/CZ2K-MJ03">10.7907/CZ2K-MJ03</a></li>
<li>Cox, Robert Sidney, III (2008) <a href="https://resolver.caltech.edu/CaltechETD:etd-03042008-130011">Transcriptional Regulation and Combinatorial Genetic Logic in Synthetic Bacterial Circuits</a>; <a href="https://doi.org/10.7907/KRW6-DH88">10.7907/KRW6-DH88</a></li>
<li>Soloveichik, David (2008) <a href="https://resolver.caltech.edu/CaltechETD:etd-05292008-142339">Molecules Computing: Self-Assembled Nanostructures, Molecular Automata,and Chemical Reaction Networks</a>; <a href="https://doi.org/10.7907/ZGE0-AF38">10.7907/ZGE0-AF38</a></li>
<li>Dunlop, Mary Julia (2008) <a href="https://resolver.caltech.edu/CaltechETD:etd-05302008-141602">Dynamics and Correlated Noise in Gene Regulation</a>; <a href="https://doi.org/10.7907/AC8V-6S05">10.7907/AC8V-6S05</a></li>
<li>Kim, Jongmin (2007) <a href="https://resolver.caltech.edu/CaltechETD:etd-12182006-115817">In Vitro Synthetic Transcriptional Networks</a>; <a href="https://doi.org/10.7907/Q9YA-N192">10.7907/Q9YA-N192</a></li>
<li>Schulman, Rebecca Beth (2007) <a href="https://resolver.caltech.edu/CaltechETD:etd-04302007-164103">The Self-Replication and Evolution of DNA Crystals</a>; <a href="https://doi.org/10.7907/3F8C-9D50">10.7907/3F8C-9D50</a></li>
<li>Teal, Tracy Kristin (2007) <a href="https://resolver.caltech.edu/CaltechETD:etd-05312007-190155">Studies of the Spatial Organization of Metabolism in Shewanella oneidensis and Pseudomonas aeruginosa Biofilms</a>; <a href="https://doi.org/10.7907/2gdf-yh13">10.7907/2gdf-yh13</a></li>
<li>Bois, Justin S. (2007) <a href="https://resolver.caltech.edu/CaltechETD:etd-05242007-211446">Analysis of Interacting Nucleic Acids in Dilute Solutions</a>; <a href="https://doi.org/10.7907/2JCJ-SX75">10.7907/2JCJ-SX75</a></li>
<li>Jayaraman, Vivek (2007) <a href="https://resolver.caltech.edu/CaltechETD:etd-05192007-195030">Neural Circuit Dynamics and Ensemble Coding in the Locust and Fruit Fly Olfactory System</a>; <a href="https://doi.org/10.7907/A4VB-6C23">10.7907/A4VB-6C23</a></li>
<li>Beierholm, Ulrik Ravnsborg (2007) <a href="https://resolver.caltech.edu/CaltechETD:etd-05212007-172639">Bayesian Modeling of Sensory Cue Combinations</a>; <a href="https://doi.org/10.7907/K89B-XW75">10.7907/K89B-XW75</a></li>
<li>Papadantonakis, Karl Spyros (2006) <a href="https://resolver.caltech.edu/CaltechETD:etd-01132006-152609">Rigorous Analog Verification of Asynchronous Circuits</a>; <a href="https://doi.org/10.7907/4R8F-WF03">10.7907/4R8F-WF03</a></li>
<li>Christianson, Gestur Björn (2006) <a href="https://resolver.caltech.edu/CaltechETD:etd-11212005-110457">Information Processing in the Interaural Time Difference Pathway of the Barn Owl</a>; <a href="https://doi.org/10.7907/3WJJ-7294">10.7907/3WJJ-7294</a></li>
<li>Mihalas, Stefan (2006) <a href="https://resolver.caltech.edu/CaltechETD:etd-06052006-142955">Quantitative Model of Calcium/Calmodulin- Dependent Protein Kinase II Activation</a>; <a href="https://doi.org/10.7907/d0zv-g984">10.7907/d0zv-g984</a></li>
<li>Drummond, David Allan (2006) <a href="https://resolver.caltech.edu/CaltechETD:etd-06022006-154329">Misfolding Dominates Protein Evolution</a>; <a href="https://doi.org/10.7907/DH8E-2N10">10.7907/DH8E-2N10</a></li>
<li>Hart, Christopher Edward (2005) <a href="https://resolver.caltech.edu/CaltechETD:etd-03152005-110423">Inferring Genetic Regulatory Network Structure: Integrative Analysis of Genome-Scale Data</a>; <a href="https://doi.org/10.7907/2JXP-3G71">10.7907/2JXP-3G71</a></li>
<li>Cook, Matthew M. (2005) <a href="https://resolver.caltech.edu/CaltechETD:etd-06032005-140944">Networks of Relations</a>; <a href="https://doi.org/10.7907/CVKM-D684">10.7907/CVKM-D684</a></li>
<li>Schkolne, Steven (2004) <a href="https://resolver.caltech.edu/CaltechETD:etd-05272004-003252">3-D Interfaces for Spatial Construction</a>; <a href="https://doi.org/10.7907/8VWJ-TX38">10.7907/8VWJ-TX38</a></li>
<li>Riedel, Marcus D. (2004) <a href="https://resolver.caltech.edu/CaltechETD:etd-05032004-153842">Cyclic Combinational Circuits</a>; <a href="https://doi.org/10.7907/410B-XR25">10.7907/410B-XR25</a></li>
<li>Schkolne, Steven (2004) <a href="https://resolver.caltech.edu/CaltechETD:etd-05272004-003252">3-D Interfaces for Spatial Construction</a>; <a href="https://doi.org/10.7907/8VWJ-TX38">10.7907/8VWJ-TX38</a></li>
</ul>