| 2025 | DNA | Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. | Inhoo Lee, Salvador Buse, Erik Winfree |
| 2024 | DNA | Learning and Inference in a Lattice Model of Multicomponent Condensates. | Cameron T. Chalk, Salvador Buse, Krishna Shrinivas, Arvind Murugan, Erik Winfree |
| 2023 | DNA | Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. | Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon |
| 2019 | DNA | Reversible Computation Using Swap Reactions on a Surface. | Tatiana Brailovskaya, Gokul Gowri, Sean Yu, Erik Winfree |
| 2019 | DNA | Chemical Reaction Networks and Stochastic Local Search. | Erik Winfree |
| 2019 | DNA | Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains. | Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Ct, Mark Schmidt, Anne Condon |
| 2018 | DNA | Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler. | Constantine G. Evans, Erik Winfree |
| 2017 | DNA | A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. | Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, Erik Winfree |
| 2017 | DNA | Chemical Boltzmann Machines. | William Poole, Andrs Ortiz-Muoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree, Manoj Gopalkrishnan |
| 2017 | DNA | Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates. | Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree |
| 2016 | DNA | Verifying Chemical Reaction Network Implementations: A Bisimulation Approach. | Robert F. Johnson, Qing Dong, Erik Winfree |
| 2016 | DNA | Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. | Nicholas Schiefer, Erik Winfree |
| 2015 | DNA | Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. | Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree |
| 2015 | DNA | Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. | Nicholas Schiefer, Erik Winfree |
| 2015 | DNA | Leakless DNA Strand Displacement Systems. | Chris Thachuk, Erik Winfree, David Soloveichik |
| 2014 | DNA | Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface. | Lulu Qian, Erik Winfree |
| 2013 | DNA | DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly. | Constantine G. Evans, Erik Winfree |
| 2011 | DAC | Joint DAC/IWBDA special session design and synthesis of biological circuits. | Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam P. Arkin, Erik Winfree, Chris Voigt |
| 2010 | DNA | Efficient Turing-Universal Computation with DNA Polymers. | Lulu Qian, David Soloveichik, Erik Winfree |
| 2010 | DNA | Simple Evolution of Complex Crystal Species. | Rebecca Schulman, Erik Winfree |
| 2008 | ASPLOS | Toward molecular programming with DNA. | Erik Winfree |
| 2008 | DNA | A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. | Lulu Qian, Erik Winfree |
| 2008 | DNA | DNA as a Universal Substrate for Chemical Kinetics. | David Soloveichik, Georg Seelig, Erik Winfree |
| 2006 | UC | Fault-Tolerance in Biochemical Systems. | Erik Winfree |
| 2005 | DNA | Complexity of Compact Proofreading for Self-assembled Patterns. | David Soloveichik, Erik Winfree |
| 2004 | DNA | Programmable Control of Nucleation for Algorithmic Self-assembly. | Rebecca Schulman, Erik Winfree |
| 2004 | DNA | DNA Hybridization Catalysts and Catalyst Circuits. | Georg Seelig, Bernard Yurke, Erik Winfree |
| 2004 | DNA | Complexity of Self-assembled Shapes. | David Soloveichik, Erik Winfree |
| 2003 | DNA | Self-Assembled Circuit Patterns. | Matthew Cook, Paul W. K. Rothemund, Erik Winfree |
| 2003 | DNA | One Dimensional Boundaries for DNA Tile Self-Assembly. | Rebecca Schulman, Shaun Lee, Nick Papadakis, Erik Winfree |
| 2003 | DNA | Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. | Erik Winfree, Renat Bekbolatov |
| 2000 | DNA | String Tile Models for DNA Computing by Self-Assembly. | Erik Winfree, Tony Eng, Grzegorz Rozenberg |
| 2000 | STOC | The program-size complexity of self-assembled squares (extended abstract). | Paul W. K. Rothemund, Erik Winfree |