Erik Winfree

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 21

Top Topics

Secondary Structure

Boltzmann Machine

Probability Distribution

Chemical Reaction

Top Venues

Theor. Comput. Sci.

Publications

Erik Winfree
The Tall Thin Molecular Programmer. ISSCC (2023)
Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon
Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. DNA (2023)
Erik Winfree, Lulu Qian
Two-dimensional tile displacement can simulate cellular automata. CoRR (2023)
Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt, Anne Condon, Erik Winfree
Predicting DNA kinetics with a truncated continuous-time Markov chain method. Comput. Biol. Chem. 104 (2023)
Constantine Glen Evans, Jackson O'Brien, Erik Winfree, Arvind Murugan
Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. CoRR (2022)
William Poole, Thomas E. Ouldridge, Manoj Gopalkrishnan, Erik Winfree
Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines. CoRR (2022)
Robert F. Johnson, Erik Winfree
Verifying polymer reaction networks using bisimulation. Theor. Comput. Sci. 843 (2020)
Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree
Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions. Theor. Comput. Sci. 801 (2020)
Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nat. 567 (7748) (2019)
Seung Woo Shin, Chris Thachuk, Erik Winfree
Verifying chemical reaction network implementations: A pathway decomposition approach. Theor. Comput. Sci. 765 (2019)
Tatiana Brailovskaya, Gokul Gowri, Sean Yu, Erik Winfree
Reversible Computation Using Swap Reactions on a Surface. DNA (2019)
Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon
Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains. DNA (2019)
Erik Winfree
Chemical Reaction Networks and Stochastic Local Search. DNA (2019)
Robert F. Johnson, Qing Dong, Erik Winfree
Verifying chemical reaction network implementations: A bisimulation approach. Theor. Comput. Sci. 765 (2019)
Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree
Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions. CoRR (2018)
Constantine G. Evans, Erik Winfree
Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler. DNA (2018)
Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, Erik Winfree
A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. DNA (2017)
William Poole, Andrés Ortiz-Muñoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree, Manoj Gopalkrishnan
Chemical Boltzmann Machines. DNA (2017)
Sedigheh Zolaktaf, Frits Dannenberg, Xander Rudelis, Anne Condon, Joseph M. Schaeffer, Mark Schmidt, Chris Thachuk, Erik Winfree
Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates. DNA (2017)
Robert F. Johnson, Qing Dong, Erik Winfree
Verifying Chemical Reaction Network Implementations: A Bisimulation Approach. DNA (2016)
Nicholas Schiefer, Erik Winfree
Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. DNA (2016)
Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree
Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. DNA (2015)
Nicholas Schiefer, Erik Winfree
Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. DNA (2015)
Chris Thachuk, Erik Winfree, David Soloveichik
Leakless DNA Strand Displacement Systems. DNA (2015)
Casey Grun, Karthik Sarma, Brian Wolfe, Seung Woo Shin, Erik Winfree
A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures. CoRR (2015)
Seung Woo Shin, Chris Thachuk, Erik Winfree
Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach. CoRR (2014)
Lulu Qian, Erik Winfree
Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface. DNA (2014)
Constantine G. Evans, Erik Winfree
DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly. DNA (2013)
Damien Woods, Ho-Lin Chen, Scott Goodfriend, Nadine Dabby, Erik Winfree, Peng Yin
Active self-assembly of algorithmic shapes and patterns in polylogarithmic time. ITCS (2013)
Damien Woods, Ho-Lin Chen, Scott Goodfriend, Nadine Dabby, Erik Winfree, Peng Yin
Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time CoRR (2013)
Rebecca Schulman, Erik Winfree
Simple evolution of complex crystal species. Nat. Comput. 11 (2) (2012)
Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam P. Arkin, Erik Winfree, Chris Voigt
Joint DAC/IWBDA special session design and synthesis of biological circuits. DAC (2011)
David Soloveichik, Erik Winfree
Erratum to "The computational power of Benenson automata" [Theoret. Comput. Sci. 344 (2005) 279-297] Theor. Comput. Sci. 412 (43) (2011)
Lulu Qian, Erik Winfree, Jehoshua Bruck
Neural network computation with DNA strand displacement cascades. Nat. 475 (7356) (2011)
Lulu Qian, David Soloveichik, Erik Winfree
Efficient Turing-Universal Computation with DNA Polymers. DNA (2010)
Rebecca Schulman, Erik Winfree
Simple Evolution of Complex Crystal Species. DNA (2010)
Rebecca Schulman, Erik Winfree
Programmable Control of Nucleation for Algorithmic Self-Assembly. SIAM J. Comput. 39 (4) (2009)
Matthew Cook, David Soloveichik, Erik Winfree, Jehoshua Bruck
Programmability of Chemical Reaction Networks. Algorithmic Bioprocesses (2009)
Kenichi Fujibayashi, David Yu Zhang, Erik Winfree, Satoshi Murata
Error suppression mechanisms for DNA tile self-assembly and their simulation. Nat. Comput. 8 (3) (2009)
Lulu Qian, Erik Winfree
A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. DNA (2008)
David Soloveichik, Georg Seelig, Erik Winfree
DNA as a Universal Substrate for Chemical Kinetics. DNA (2008)
David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck
Computation with finite stochastic chemical reaction networks. Nat. Comput. 7 (4) (2008)
Erik Winfree
Toward molecular programming with DNA. ASPLOS (2008)
Rebecca Schulman, Erik Winfree
How crystals that sense and respond to their environments could evolve. Nat. Comput. 7 (2) (2008)
David Soloveichik, Matthew Cook, Erik Winfree
Combining self-healing and proofreading in self-assembly. Nat. Comput. 7 (2) (2008)
Robert M. Dirks, Justin S. Bois, Joseph M. Schaeffer, Erik Winfree, Niles A. Pierce
Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM Rev. 49 (1) (2007)
David Soloveichik, Erik Winfree
Complexity of Self-Assembled Shapes. SIAM J. Comput. 36 (6) (2007)
Erik Winfree
Self-healing Tile Sets. Nanotechnology: Science and Computation (2006)
Erik Winfree
Fault-Tolerance in Biochemical Systems. UC (2006)
David Soloveichik, Erik Winfree
Complexity of Compact Proofreading for Self-assembled Patterns. DNA (2005)
David Soloveichik, Erik Winfree
The computational power of Benenson automata. Theor. Comput. Sci. 344 (2-3) (2005)
Rebecca Schulman, Erik Winfree
Self-replication and Evolution of DNA Crystals. ECAL (2005)
David Soloveichik, Erik Winfree
The Computational Power of Benenson Automata CoRR (2004)
Jongmin Kim, John J. Hopfield, Erik Winfree
Neural Network Computation by In Vitro Transcriptional Circuits. NIPS (2004)
Georg Seelig, Bernard Yurke, Erik Winfree
DNA Hybridization Catalysts and Catalyst Circuits. DNA (2004)
Rebecca Schulman, Erik Winfree
Programmable Control of Nucleation for Algorithmic Self-assembly. DNA (2004)
David Soloveichik, Erik Winfree
Complexity of Self-assembled Shapes. DNA (2004)
David Soloveichik, Erik Winfree
Complexity of Self-Assembled Shapes CoRR (2004)
Matthew Cook, Paul W. K. Rothemund, Erik Winfree
Self-Assembled Circuit Patterns. DNA (2003)
Erik Winfree, Renat Bekbolatov
Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. DNA (2003)
Rebecca Schulman, Shaun Lee, Nick Papadakis, Erik Winfree
One Dimensional Boundaries for DNA Tile Self-Assembly. DNA (2003)
Erik Winfree, Tony Eng, Grzegorz Rozenberg
String Tile Models for DNA Computing by Self-Assembly. DNA Computing (2000)
Paul W. K. Rothemund, Erik Winfree
The program-size complexity of self-assembled squares (extended abstract). STOC (2000)
Erik Winfree
In-vitro Transcriptional Circuits. UMC (2000)
Kevin Chen, Erik Winfree
Error correction in DNA computing: Misclassification and strand loss. DNA Based Computers (1999)
Thomas H. LaBean, Erik Winfree, John H. Reif
Experimental progress in computation by self-assembly of DNA tilings. DNA Based Computers (1999)
Sam T. Roweis, Erik Winfree
On the Reduction of Errors in DNA Computation. J. Comput. Biol. 6 (1) (1999)
Leonard M. Adleman, Paul W. K. Rothemund, Sam T. Roweis, Erik Winfree
On Applying Molecular Computation to the Data Encryption Standard. J. Comput. Biol. 6 (1) (1999)
Sam T. Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman
A Sticker-Based Model for DNA Computation. J. Comput. Biol. 5 (4) (1998)
Erik Winfree, Xiaoping Yang, Nadrian C. Seeman
Universal computation via self-assembly of DNA: Some theory and experiments. DNA Based Computers (1996)
Sam T. Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman
A sticker based model for DNA computation. DNA Based Computers (1996)
Leonard M. Adleman, Paul W. K. Rothemund, Sam T. Roweis, Erik Winfree
On applying molecular computation to the data encryption standard. DNA Based Computers (1996)
Erik Winfree
On the computational power of DNA annealing and ligation. DNA Based Computers (1995)
Erik Winfree
Complexity of restricted and unrestricted models of molecular computation. DNA Based Computers (1995)