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ORCIDErik Winfree
Person information
- affiliation: California Institute of Technology, Department of Computing and Mathematical Sciences
- award (2001): Presidential Early Career Award for Scientists and Engineers
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2020 – today
- 2024
[c46]Cameron T. Chalk, Salvador Buse, Krishna Shrinivas, Arvind Murugan, Erik Winfree:
Learning and Inference in a Lattice Model of Multicomponent Condensates. DNA 2024: 5:1-5:24- 2023
- [j20]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: 107837 (2023) - [c45]Jordan Lovrod, Boyan Beronov, Chenwei Zhang, Erik Winfree, Anne Condon:
Revisiting Hybridization Kinetics with Improved Elementary Step Simulation. DNA 2023: 5:1-5:24 - [c44]Erik Winfree:
The Tall Thin Molecular Programmer. ISSCC 2023: 392-393 - [i9]Erik Winfree, Lulu Qian:
Two-dimensional tile displacement can simulate cellular automata. CoRR abs/2301.01929 (2023) - 2022
- [i8]William Poole, Thomas E. Ouldridge, Manoj Gopalkrishnan, Erik Winfree:
Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines. CoRR abs/2205.06313 (2022) - [i7]Constantine Glen Evans, Jackson O'Brien, Erik Winfree, Arvind Murugan:
Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. CoRR abs/2207.06399 (2022) - 2020
- [j19]Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree:
Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions. Theor. Comput. Sci. 801: 64-95 (2020) - [j18]Robert F. Johnson, Erik Winfree:
Verifying polymer reaction networks using bisimulation. Theor. Comput. Sci. 843: 84-114 (2020)
2010 – 2019
- 2019
- [j17]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): 366-372 (2019) - [j16]Robert F. Johnson, Qing Dong, Erik Winfree:
Verifying chemical reaction network implementations: A bisimulation approach. Theor. Comput. Sci. 765: 3-46 (2019) - [j15]Seung Woo Shin, Chris Thachuk, Erik Winfree:
Verifying chemical reaction network implementations: A pathway decomposition approach. Theor. Comput. Sci. 765: 67-96 (2019) - [c43]Erik Winfree:
Chemical Reaction Networks and Stochastic Local Search. DNA 2019: 1-20 - [c42]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: 80-99 - [c41]Tatiana Brailovskaya, Gokul Gowri, Sean Yu, Erik Winfree:
Reversible Computation Using Swap Reactions on a Surface. DNA 2019: 174-196 - 2018
- [c40]Constantine G. Evans, Erik Winfree:
Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler. DNA 2018: 37-54 - [i6]Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree:
Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions. CoRR abs/1810.02854 (2018) - 2017
- [c39]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: 172-187 - [c38]William Poole, Andrés Ortiz-Muñoz, Abhishek Behera, Nick S. Jones, Thomas E. Ouldridge, Erik Winfree, Manoj Gopalkrishnan:
Chemical Boltzmann Machines. DNA 2017: 210-231 - [c37]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: 232-248 - 2016
- [c36]Robert F. Johnson, Qing Dong, Erik Winfree:
Verifying Chemical Reaction Network Implementations: A Bisimulation Approach. DNA 2016: 114-134 - [c35]Nicholas Schiefer, Erik Winfree:
Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. DNA 2016: 165-182 - 2015
- [c34]Nicholas Schiefer, Erik Winfree:
Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model. DNA 2015: 34-54 - [c33]Chris Thachuk, Erik Winfree, David Soloveichik:
Leakless DNA Strand Displacement Systems. DNA 2015: 133-153 - [c32]Joseph Malcolm Schaeffer, Chris Thachuk, Erik Winfree:
Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. DNA 2015: 194-211 - [i5]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 abs/1505.03738 (2015) - 2014
- [c31]Lulu Qian, Erik Winfree:
Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface. DNA 2014: 114-131 - [i4]Seung Woo Shin, Chris Thachuk, Erik Winfree:
Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach. CoRR abs/1411.0782 (2014) - 2013
- [c30]Constantine G. Evans, Erik Winfree:
DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly. DNA 2013: 61-75 - [c29]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: 353-354 - [i3]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 abs/1301.2626 (2013) - 2012
- [j14]Rebecca Schulman, Erik Winfree:
Simple evolution of complex crystal species. Nat. Comput. 11(2): 187-197 (2012) - 2011
- [j13]Lulu Qian, Erik Winfree, Jehoshua Bruck:
Neural network computation with DNA strand displacement cascades. Nat. 475(7356): 368-372 (2011) - [j12]David Soloveichik, Erik Winfree:
Erratum to "The computational power of Benenson automata" [Theoret. Comput. Sci. 344 (2005) 279-297]. Theor. Comput. Sci. 412(43): 6112-6113 (2011) - [c28]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: 114-115 - 2010
- [c27]Lulu Qian, David Soloveichik, Erik Winfree:
Efficient Turing-Universal Computation with DNA Polymers. DNA 2010: 123-140 - [c26]Rebecca Schulman, Erik Winfree:
Simple Evolution of Complex Crystal Species. DNA 2010: 147-161
2000 – 2009
- 2009
- [j11]Kenichi Fujibayashi, David Yu Zhang, Erik Winfree, Satoshi Murata:
Error suppression mechanisms for DNA tile self-assembly and their simulation. Nat. Comput. 8(3): 589-612 (2009) - [j10]Rebecca Schulman, Erik Winfree:
Programmable Control of Nucleation for Algorithmic Self-Assembly. SIAM J. Comput. 39(4): 1581-1616 (2009) - [c25]Matthew Cook, David Soloveichik, Erik Winfree, Jehoshua Bruck:
Programmability of Chemical Reaction Networks. Algorithmic Bioprocesses 2009: 543-584 - [e2]Anne Condon, David Harel, Joost N. Kok, Arto Salomaa, Erik Winfree:
Algorithmic Bioprocesses. Natural Computing Series, Springer 2009, ISBN 978-3-540-88868-0 [contents] - 2008
- [j9]David Soloveichik, Matthew Cook, Erik Winfree:
Combining self-healing and proofreading in self-assembly. Nat. Comput. 7(2): 203-218 (2008) - [j8]Rebecca Schulman, Erik Winfree:
How crystals that sense and respond to their environments could evolve. Nat. Comput. 7(2): 219-237 (2008) - [j7]David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck:
Computation with finite stochastic chemical reaction networks. Nat. Comput. 7(4): 615-633 (2008) - [c24]Erik Winfree:
Toward molecular programming with DNA. ASPLOS 2008: 1 - [c23]David Soloveichik, Georg Seelig, Erik Winfree:
DNA as a Universal Substrate for Chemical Kinetics. DNA 2008: 57-69 - [c22]Lulu Qian, Erik Winfree:
A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. DNA 2008: 70-89 - 2007
- [j6]David Soloveichik, Erik Winfree:
Complexity of Self-Assembled Shapes. SIAM J. Comput. 36(6): 1544-1569 (2007) - [j5]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): 65-88 (2007) - 2006
- [c21]Erik Winfree:
Self-healing Tile Sets. Nanotechnology: Science and Computation 2006: 55-78 - [c20]Erik Winfree:
Fault-Tolerance in Biochemical Systems. UC 2006: 26 - 2005
- [j4]David Soloveichik, Erik Winfree:
The computational power of Benenson automata. Theor. Comput. Sci. 344(2-3): 279-297 (2005) - [c19]David Soloveichik, Erik Winfree:
Complexity of Compact Proofreading for Self-assembled Patterns. DNA 2005: 305-324 - [c18]Rebecca Schulman, Erik Winfree:
Self-replication and Evolution of DNA Crystals. ECAL 2005: 734-743 - 2004
- [c17]Rebecca Schulman, Erik Winfree:
Programmable Control of Nucleation for Algorithmic Self-assembly. DNA 2004: 319-328 - [c16]Georg Seelig, Bernard Yurke, Erik Winfree:
DNA Hybridization Catalysts and Catalyst Circuits. DNA 2004: 329-343 - [c15]David Soloveichik, Erik Winfree:
Complexity of Self-assembled Shapes. DNA 2004: 344-354 - [c14]Jongmin Kim, John J. Hopfield, Erik Winfree:
Neural Network Computation by In Vitro Transcriptional Circuits. NIPS 2004: 681-688 - [i2]David Soloveichik, Erik Winfree:
Complexity of Self-Assembled Shapes. CoRR abs/cs/0412096 (2004) - [i1]David Soloveichik, Erik Winfree:
The Computational Power of Benenson Automata. CoRR abs/cs/0412097 (2004) - 2003
- [c13]Matthew Cook, Paul W. K. Rothemund, Erik Winfree:
Self-Assembled Circuit Patterns. DNA 2003: 91-107 - [c12]Rebecca Schulman, Shaun Lee, Nick Papadakis, Erik Winfree:
One Dimensional Boundaries for DNA Tile Self-Assembly. DNA 2003: 108-126 - [c11]Erik Winfree, Renat Bekbolatov:
Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. DNA 2003: 126-144 - 2000
- [c10]Erik Winfree, Tony Eng, Grzegorz Rozenberg:
String Tile Models for DNA Computing by Self-Assembly. DNA Computing 2000: 63-88 - [c9]Paul W. K. Rothemund, Erik Winfree:
The program-size complexity of self-assembled squares (extended abstract). STOC 2000: 459-468 - [c8]Erik Winfree:
In-vitro Transcriptional Circuits. UMC 2000: 121-122 - [e1]Erik Winfree, David K. Gifford:
DNA Based Computers, Proceedings of a DIMACS Workshop, New Brunswick, New Jersey, USA, June 14-15, 1999. DIMACS Series in Discrete Mathematics and Theoretical Computer Science 54, DIMACS/AMS 2000, ISBN 978-0-8218-2053-7 [contents]
1990 – 1999
- 1999
- [j3]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): 53-63 (1999) - [j2]Sam T. Roweis, Erik Winfree:
On the Reduction of Errors in DNA Computation. J. Comput. Biol. 6(1): 65-75 (1999) - [c7]Kevin Chen, Erik Winfree:
Error correction in DNA computing: Misclassification and strand loss. DNA Based Computers 1999: 49-63 - [c6]Thomas H. LaBean, Erik Winfree, John H. Reif:
Experimental progress in computation by self-assembly of DNA tilings. DNA Based Computers 1999: 123-140 - 1998
- [j1]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): 615-629 (1998) - 1996
- [c5]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: 1-29 - [c4]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: 31-44 - [c3]Erik Winfree, Xiaoping Yang, Nadrian C. Seeman:
Universal computation via self-assembly of DNA: Some theory and experiments. DNA Based Computers 1996: 191-213 - 1995
- [c2]Erik Winfree:
Complexity of restricted and unrestricted models of molecular computation. DNA Based Computers 1995: 187-198 - [c1]Erik Winfree:
On the computational power of DNA annealing and ligation. DNA Based Computers 1995: 199-221
Coauthor Index
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last updated on 2024-10-07 22:15 CEST by the dblp team
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