Erik Winfree

According to our database, Erik Winfree authored at least 63 papers between 1995 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2023

Predicting DNA kinetics with a truncated continuous-time Markov chain method.

Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt, Anne Condon, Erik Winfree

Comput. Biol. Chem., June, 2023

Two-dimensional tile displacement can simulate cellular automata.

Erik Winfree, Lulu Qian

CoRR, 2023

The Tall Thin Molecular Programmer.

Erik Winfree

Proceedings of the IEEE International Solid- State Circuits Conference, 2023

Revisiting Hybridization Kinetics with Improved Elementary Step Simulation.

Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon

Proceedings of the 29th International Conference on DNA Computing and Molecular Programming, 2023

2022

Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly.

Constantine Glen Evans, Jackson O'Brien, Erik Winfree, Arvind Murugan

CoRR, 2022

Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines.

William Poole, Thomas E. Ouldridge, Manoj Gopalkrishnan, Erik Winfree

CoRR, 2022

2020

Verifying polymer reaction networks using bisimulation.

Robert F. Johnson, Erik Winfree

Theor. Comput. Sci., 2020

Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions.

Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree

Theor. Comput. Sci., 2020

2019

Verifying chemical reaction network implementations: A pathway decomposition approach.

Seung Woo Shin, Chris Thachuk, Erik Winfree

Theor. Comput. Sci., 2019

Verifying chemical reaction network implementations: A bisimulation approach.

Robert F. Johnson, Qing Dong, Erik Winfree

Theor. Comput. Sci., 2019

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly.

Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree

Nat., 2019

Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains.

Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon

Proceedings of the DNA Computing and Molecular Programming - 25th International Conference, 2019

Chemical Reaction Networks and Stochastic Local Search.

Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 25th International Conference, 2019

Reversible Computation Using Swap Reactions on a Surface.

Tatiana Brailovskaya, Gokul Gowri, Sean Yu, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 25th International Conference, 2019

2018

Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler.

Constantine G. Evans, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 24th International Conference, 2018

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, Chris Thachuk, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

Chemical Boltzmann Machines.

William Poole, Andrés Ortiz-Muñoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree, Manoj Gopalkrishnan

Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

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

Proceedings of the DNA Computing and Molecular Programming - 23rd International Conference, 2017

2016

Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model.

Nicholas Schiefer, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 22nd International Conference, 2016

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

Leakless DNA Strand Displacement Systems.

Chris Thachuk, Erik Winfree, David Soloveichik

Proceedings of the DNA Computing and Molecular Programming - 21st International Conference, 2015

Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model.

Nicholas Schiefer, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 21st International Conference, 2015

Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands.

Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 21st International Conference, 2015

2014

Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface.

Lulu Qian, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 20th International Conference, 2014

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

Proceedings of the Innovations in Theoretical Computer Science, 2013

DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly.

Constantine G. Evans, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 19th International Conference, 2013

2012

Simple evolution of complex crystal species.

Rebecca Schulman, Erik Winfree

Nat. Comput., 2012

2011

Erratum to "The computational power of Benenson automata" [Theoret. Comput. Sci. 344 (2005) 279-297]

David Soloveichik, Erik Winfree

Theor. Comput. Sci., 2011

Neural network computation with DNA strand displacement cascades.

Lulu Qian, Erik Winfree, Jehoshua Bruck

Nat., 2011

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

Proceedings of the 48th Design Automation Conference, 2011

2010

Efficient Turing-Universal Computation with DNA Polymers.

Lulu Qian, David Soloveichik, Erik Winfree

Proceedings of the DNA Computing and Molecular Programming - 16th International Conference, 2010

2009

Programmable Control of Nucleation for Algorithmic Self-Assembly.

Rebecca Schulman, Erik Winfree

SIAM J. Comput., 2009

Error suppression mechanisms for DNA tile self-assembly and their simulation.

Kenichi Fujibayashi, David Yu Zhang, Erik Winfree, Satoshi Murata

Nat. Comput., 2009

Programmability of Chemical Reaction Networks.

Matthew Cook, David Soloveichik, Erik Winfree, Jehoshua Bruck

Proceedings of the Algorithmic Bioprocesses, 2009

2008

Computation with finite stochastic chemical reaction networks.

David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck

Nat. Comput., 2008

Combining self-healing and proofreading in self-assembly.

David Soloveichik, Matthew Cook, Erik Winfree

Nat. Comput., 2008

How crystals that sense and respond to their environments could evolve.

Rebecca Schulman, Erik Winfree

Nat. Comput., 2008

DNA as a Universal Substrate for Chemical Kinetics.

David Soloveichik, Georg Seelig, Erik Winfree

Proceedings of the DNA Computing, 14th International Meeting on DNA Computing, 2008

A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits.

Lulu Qian, Erik Winfree

Proceedings of the DNA Computing, 14th International Meeting on DNA Computing, 2008

Toward molecular programming with DNA.

Erik Winfree

Proceedings of the 13th International Conference on Architectural Support for Programming Languages and Operating Systems, 2008

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

Complexity of Self-Assembled Shapes.

David Soloveichik, Erik Winfree

SIAM J. Comput., 2007

2006

Fault-Tolerance in Biochemical Systems.

Erik Winfree

Proceedings of the Unconventional Computation, 5th International Conference, 2006

Self-healing Tile Sets.

Erik Winfree

Proceedings of the Nanotechnology: Science and Computation, 2006

2005

The computational power of Benenson automata.

David Soloveichik, Erik Winfree

Theor. Comput. Sci., 2005

Self-replication and Evolution of DNA Crystals.

Rebecca Schulman, Erik Winfree

Proceedings of the Advances in Artificial Life, 8th European Conference, 2005

Complexity of Compact Proofreading for Self-assembled Patterns.

David Soloveichik, Erik Winfree

Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

2004

Neural Network Computation by In Vitro Transcriptional Circuits.

Jongmin Kim, John J. Hopfield, Erik Winfree

Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004

DNA Hybridization Catalysts and Catalyst Circuits.

Georg Seelig, Bernard Yurke, Erik Winfree

Proceedings of the DNA Computing, 10th International Workshop on DNA Computing, 2004

2003

Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly.

Erik Winfree, Renat Bekbolatov

Proceedings of the DNA Computing, 9th International Workshop on DNA Based Computers, 2003

One Dimensional Boundaries for DNA Tile Self-Assembly.

Rebecca Schulman, Shaun Lee, Nick Papadakis, Erik Winfree

Proceedings of the DNA Computing, 9th International Workshop on DNA Based Computers, 2003

Self-Assembled Circuit Patterns.

Matthew Cook, Paul W. K. Rothemund, Erik Winfree

Proceedings of the DNA Computing, 9th International Workshop on DNA Based Computers, 2003

2000

In-vitro Transcriptional Circuits.

Erik Winfree

Proceedings of the Unconventional Models of Computation, 2000

The program-size complexity of self-assembled squares (extended abstract).

Paul W. K. Rothemund, Erik Winfree

Proceedings of the Thirty-Second Annual ACM Symposium on Theory of Computing, 2000

String Tile Models for DNA Computing by Self-Assembly.

Erik Winfree, Tony Eng, Grzegorz Rozenberg

Proceedings of the DNA Computing, 6th International Workshop on DNA-Based Computers, 2000

1999

On the Reduction of Errors in DNA Computation.

Sam T. Roweis, Erik Winfree

J. Comput. Biol., 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

Experimental progress in computation by self-assembly of DNA tilings.

Thomas H. LaBean, Erik Winfree, John H. Reif

Proceedings of the DNA Based Computers, 1999

Error correction in DNA computing: Misclassification and strand loss.

Kevin Chen, Erik Winfree

Proceedings of the DNA Based Computers, 1999

1998

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

1996

Universal computation via self-assembly of DNA: Some theory and experiments.

Erik Winfree, Xiaoping Yang, Nadrian C. Seeman

Proceedings of the DNA Based Computers, 1996

1995

On the computational power of DNA annealing and ligation.

Erik Winfree

Proceedings of the DNA Based Computers, 1995

Complexity of restricted and unrestricted models of molecular computation.

Erik Winfree

Proceedings of the DNA Based Computers, 1995