Complexity of restricted and unrestricted models of molecular computation. - Erik Winfree (DNA Based Computers, 1995)

On the computational power of DNA annealing and ligation. - Erik Winfree (DNA Based Computers, 1995)

Universal computation via self-assembly of DNA: Some theory and experiments. - Erik Winfree; Xiaoping Yang; Nadrian C. Seeman (DNA Based Computers, 1996)

A Sticker-Based Model for DNA Computation. - Sam T. Roweis; Erik Winfree; Richard Burgoyne; Nickolas V. Chelyapov; Myron F. Goodman; Paul W. K. Rothemund; Leonard M. Adleman (J. Comput. Biol., 1998)

Error correction in DNA computing: Misclassification and strand loss. - Kevin Chen; Erik Winfree (DNA Based Computers, 1999)

Experimental progress in computation by self-assembly of DNA tilings. - Thomas H. LaBean; Erik Winfree; John H. Reif (DNA Based Computers, 1999)

On Applying Molecular Computation to the Data Encryption Standard. - Leonard M. Adleman; Paul W. K. Rothemund; Sam T. Roweis; Erik Winfree (J. Comput. Biol., 1999)

On the Reduction of Errors in DNA Computation. - Sam T. Roweis; Erik Winfree (J. Comput. Biol., 1999)

String Tile Models for DNA Computing by Self-Assembly. - Erik Winfree; Tony Eng; Grzegorz Rozenberg (DNA Computing, 2000)

The program-size complexity of self-assembled squares (extended abstract). - Paul W. K. Rothemund; Erik Winfree (STOC, 2000)

In-vitro Transcriptional Circuits. - Erik Winfree (UMC, 2000)

Self-Assembled Circuit Patterns. - Matthew Cook 001; Paul W. K. Rothemund; Erik Winfree (DNA, 2003)

One Dimensional Boundaries for DNA Tile Self-Assembly. - Rebecca Schulman; Shaun Lee; Nick Papadakis; Erik Winfree (DNA, 2003)

Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. - Erik Winfree; Renat Bekbolatov (DNA, 2003)

DNA Hybridization Catalysts and Catalyst Circuits. - Georg Seelig; Bernard Yurke; Erik Winfree (DNA, 2004)

Neural Network Computation by In Vitro Transcriptional Circuits. - Jongmin Kim; John J. Hopfield; Erik Winfree (NIPS, 2004)

Complexity of Compact Proofreading for Self-assembled Patterns. - David Soloveichik; Erik Winfree (DNA, 2005)

Self-replication and Evolution of DNA Crystals. - Rebecca Schulman; Erik Winfree (ECAL, 2005)

The computational power of Benenson automata. - David Soloveichik; Erik Winfree (Theor. Comput. Sci., 2005)

Self-healing Tile Sets. - Erik Winfree (Nanotechnology: Science and Computation, 2006)

Fault-Tolerance in Biochemical Systems. - Erik Winfree (UC, 2006)

Complexity of Self-Assembled Shapes. - David Soloveichik; Erik Winfree (SIAM J. Comput., 2007)

Thermodynamic Analysis of Interacting Nucleic Acid Strands. - Robert M. Dirks; Justin S. Bois; Joseph M. Schaeffer; Erik Winfree; Niles A. Pierce (SIAM Rev., 2007)

Toward molecular programming with DNA. - Erik Winfree (ASPLOS, 2008)

A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. - Lulu Qian; Erik Winfree (DNA, 2008)

DNA as a Universal Substrate for Chemical Kinetics. - David Soloveichik; Georg Seelig; Erik Winfree (DNA, 2008)

How crystals that sense and respond to their environments could evolve. - Rebecca Schulman; Erik Winfree (Nat. Comput., 2008)

Combining self-healing and proofreading in self-assembly. - David Soloveichik; Matthew Cook 001; Erik Winfree (Nat. Comput., 2008)

Computation with finite stochastic chemical reaction networks. - David Soloveichik; Matthew Cook 001; Erik Winfree; Jehoshua Bruck (Nat. Comput., 2008)

Programmability of Chemical Reaction Networks. - Matthew Cook 001; David Soloveichik; Erik Winfree; Jehoshua Bruck (Algorithmic Bioprocesses, 2009)

Error suppression mechanisms for DNA tile self-assembly and their simulation. - Kenichi Fujibayashi; David Yu Zhang; Erik Winfree; Satoshi Murata (Nat. Comput., 2009)

Programmable Control of Nucleation for Algorithmic Self-Assembly. - Rebecca Schulman; Erik Winfree (SIAM J. Comput., 2009)

Efficient Turing-Universal Computation with DNA Polymers. - Lulu Qian; David Soloveichik; Erik Winfree (DNA, 2010)

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 (DAC, 2011)

Neural network computation with DNA strand displacement cascades. - Lulu Qian; Erik Winfree; Jehoshua Bruck (Nat., 2011)

Erratum to "The computational power of Benenson automata" [Theoret. Comput. Sci. 344 (2005) 279-297] - David Soloveichik; Erik Winfree (Theor. Comput. Sci., 2011)

Simple evolution of complex crystal species. - Rebecca Schulman; Erik Winfree (Nat. Comput., 2012)

DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly. - Constantine G. Evans; Erik Winfree (DNA, 2013)

Active self-assembly of algorithmic shapes and patterns in polylogarithmic time. - Damien Woods; Ho-Lin Chen; Scott Goodfriend; Nadine Dabby; Erik Winfree; Peng Yin (ITCS, 2013)

Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface. - Lulu Qian; Erik Winfree (DNA, 2014)

Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. - Joseph Malcolm Schaeffer; Chris Thachuk; Erik Winfree (DNA, 2015)

Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. - Nicholas Schiefer; Erik Winfree (DNA, 2015)

Leakless DNA Strand Displacement Systems. - Chris Thachuk; Erik Winfree; David Soloveichik (DNA, 2015)

A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures. - Casey Grun; Karthik Sarma; Brian Wolfe; Seung Woo Shin; Erik Winfree (CoRR, 2015)

Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. - Nicholas Schiefer; Erik Winfree (DNA, 2016)

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 (DNA, 2017)

Chemical Boltzmann Machines. - William Poole; Andrés Ortiz-Muñoz; Abhishek Behera; Nick S. Jones; Thomas E. Ouldridge; Erik Winfree; Manoj Gopalkrishnan (DNA, 2017)

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 001; Chris Thachuk; Erik Winfree (DNA, 2017)

Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler. - Constantine G. Evans; Erik Winfree (DNA, 2018)

Reversible Computation Using Swap Reactions on a Surface. - Tatiana Brailovskaya; Gokul Gowri; Sean Yu; Erik Winfree (DNA, 2019)

Chemical Reaction Networks and Stochastic Local Search. - Erik Winfree (DNA, 2019)

Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains. - Sedigheh Zolaktaf; Frits Dannenberg; Erik Winfree; Alexandre Bouchard-Côté; Mark Schmidt 001; Anne Condon (DNA, 2019)

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. - Damien Woods; David Doty; Cameron Myhrvold; Joy Hui; Felix Zhou 001; Peng Yin; Erik Winfree (Nat., 2019)

Verifying chemical reaction network implementations: A bisimulation approach. - Robert F. Johnson; Qing Dong; Erik Winfree (Theor. Comput. Sci., 2019)

Verifying chemical reaction network implementations: A pathway decomposition approach. - Seung Woo Shin; Chris Thachuk; Erik Winfree (Theor. Comput. Sci., 2019)

Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions. - Daniele Cappelletti; Andrés Ortiz-Muñoz; David F. Anderson; Erik Winfree (Theor. Comput. Sci., 2020)

Verifying polymer reaction networks using bisimulation. - Robert F. Johnson; Erik Winfree (Theor. Comput. Sci., 2020)

Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines. - William Poole; Thomas E. Ouldridge; Manoj Gopalkrishnan; Erik Winfree (CoRR, 2022)

Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. - Constantine Glen Evans; Jackson O'Brien; Erik Winfree; Arvind Murugan (CoRR, 2022)

Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. - Jordan Lovrod; Boyan Beronov; Chenwei Zhang; Erik Winfree; Anne Condon (DNA, 2023)

The Tall Thin Molecular Programmer. - Erik Winfree (ISSCC, 2023)

Two-dimensional tile displacement can simulate cellular automata. - Erik Winfree; Lulu Qian (CoRR, 2023)

Predicting DNA kinetics with a truncated continuous-time Markov chain method. - Sedigheh Zolaktaf; Frits Dannenberg; Mark Schmidt 001; Anne Condon; Erik Winfree (Comput. Biol. Chem., 2023)

Learning and Inference in a Lattice Model of Multicomponent Condensates. - Cameron T. Chalk; Salvador Buse; Krishna Shrinivas; Arvind Murugan; Erik Winfree (DNA, 2024)

Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. - Inhoo Lee; Salvador Buse; Erik Winfree (DNA, 2025)