Erik Winfree

发表

A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits

Lulu Qian, Erik Winfree, 2008, DNA.

A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

Erik Winfree, Stefan Badelt, Casey Grun, 2015, Journal of the Royal Society Interface.

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

Erik Winfree, Constantine G. Evans, 2018, DNA.

Design and Characterization of Programmable DNA Nanotubes Correction to Supporting Information

Erik Winfree, Paul W. K. Rothemund, Axel Ekani-Nkodo, 2013 .

The computational power of Benenson automata pdf

Erik Winfree, David Soloveichik, 2005, Theor. Comput. Sci..

The Computer Science of Molecular Programming

Erik Winfree, E. Winfree, 2011 .

Toward molecular programming with DNA

Erik Winfree, 2008, ASPLOS.

Programming and simulating chemical reaction networks on a surface

Lulu Qian, Erik Winfree, Samuel Clamons, 2020, Journal of the Royal Society Interface.

On the Reduction of Errors in DNA Computation

Erik Winfree, Sam T. Roweis, S. Roweis, 1999, J. Comput. Biol..

Joint DAC/IWBDA special session design and synthesis of biological circuits

Mark Horowitz, Erik Winfree, Adam P. Arkin, 2011, 2011 48th ACM/EDAC/IEEE Design Automation Conference (DAC).

Chemical Boltzmann Machines

Nick S. Jones, Erik Winfree, Abhishek Behera, 2017, DNA.

A sticker based model for DNA computation

Erik Winfree, Leonard M. Adleman, Sam T. Roweis, 1996, DNA Based Computers.

Verifying polymer reaction networks using bisimulation

Erik Winfree, Robert Johnson, E. Winfree, 2020, Theor. Comput. Sci..

Complexity of Self-assembled Shapes

Erik Winfree, David Soloveichik, 2004, DNA.

Biomolecular Computing by In Vitro Transcriptional Networks

Erik Winfree, Jongmin Kim, Shaun Lee, 2004 .

Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates

Mark W. Schmidt, Mark Schmidt, Erik Winfree, 2017, DNA.

Enzyme-free nucleic acid dynamical systems

Erik Winfree, David Soloveichik, Georg Seelig, 2017 .

Experimental progress in computation by self-assembly of DNA tilings

Erik Winfree, John H. Reif, Thomas H. LaBean, 1999, DNA Based Computers.

Fault-Tolerance in Biochemical Systems

Erik Winfree, 2006, UC.

Programmable Control of Nucleation for Algorithmic Self-Assembly

Erik Winfree, Rebecca Schulman, 2009, SIAM J. Comput..

On the computational power of DNA annealing and ligation

Erik Winfree, E. Winfree, 1995, DNA Based Computers.

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

Erik Winfree, David Soloveichik, 2011, Theor. Comput. Sci..

Reversible Computation Using Swap Reactions on a Surface

Erik Winfree, Sean Yu, Tatiana Brailovskaya, 2019, DNA.

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

Mark W. Schmidt, Erik Winfree, Anne Condon, 2019, DNA.

Programming a DNA World

Erik Winfree, E. Winfree, 2007 .

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

Erik Winfree, Paul W. K. Rothemund, E. Winfree, 2000, STOC '00.

Self-healing Tile Sets

Erik Winfree, E. Winfree, 2006, Nanotechnology: Science and Computation.

Neural Network Computation by In Vitro Transcriptional Circuits

Erik Winfree, Jongmin Kim, John J. Hopfield, 2004, NIPS.

Efficient Turing-Universal Computation with DNA Polymers

Lulu Qian, Erik Winfree, David Soloveichik, 2010, DNA.

Molecular robots guided by prescriptive landscapes

Erik Winfree, Hao Yan, Milan N. Stojanovic, 2010, Nature.

A cargo-sorting DNA robot

Wei Li, Lulu Qian, Erik Winfree, 2017, Science.

An information-bearing seed for nucleating algorithmic self-assembly

Erik Winfree, Rebecca Schulman, Robert D. Barish, 2009, Proceedings of the National Academy of Sciences.

A Sticker-Based Model for DNA Computation

Erik Winfree, Leonard M. Adleman, Sam T. Roweis, 1998, J. Comput. Biol..

On applying molecular computation to the data encryption standard

Erik Winfree, Leonard M. Adleman, Sam T. Roweis, 1999, DNA Based Computers.

Evolution as Computation

Erik Winfree, Laura F. Landweber, E. Winfree, 2002, Natural Computing Series.

Simple evolution of complex crystal species

Erik Winfree, Rebecca Schulman, 2011, Natural Computing.

Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades

Lulu Qian, Erik Winfree, M. DePristo, 2022 .

Protein design is NP-hard.

Niles A Pierce, Erik Winfree, E. Winfree, 2002, Protein engineering.

Self-replication and Evolution of DNA Crystals

Erik Winfree, Rebecca Schulman, E. Winfree, 2005, ECAL.

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

Satoshi Murata, Erik Winfree, David Yu Zhang, 2009, Natural Computing.

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

Erik Winfree, Nicholas Schiefer, E. Winfree, 2015, DNA.

Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly

Erik Winfree, Renat Bekbolatov, E. Winfree, 2003, DNA.

On applying molecular computation to the data encryption standard

Erik Winfree, Leonard M. Adleman, Sam T. Roweis, 1999, DNA Based Computers.

Complexity of restricted and unrestricted models of molecular computation

Erik Winfree, E. Winfree, 1995, DNA Based Computers.

Physical principles for DNA tile self-assembly.

Erik Winfree, Constantine G. Evans, Constantine G Evans, 2017, Chemical Society reviews.

Author Correction: Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

Erik Winfree, Cameron Myhrvold, David Doty, 2019, Nature.

DNA as a universal substrate for chemical kinetics

Erik Winfree, Georg Seelig, David Soloveichik, 2009, Proceedings of the National Academy of Sciences.

Complexity of Compact Proofreading for Self-assembled Patterns

Erik Winfree, David Soloveichik, 2005, DNA.

Verifying Chemical Reaction Network Implementations: A Bisimulation Approach

Erik Winfree, Qing Dong, Robert F. Johnson, 2016, DNA.

Reducing facet nucleation during algorithmic self-assembly.

Erik Winfree, Ho-Lin Chen, Rebecca Schulman, 2007, Nano letters.

One Dimensional Boundaries for DNA Tile Self-Assembly

Erik Winfree, Nick Papadakis, Rebecca Schulman, 2003, DNA.

In-vitro Transcriptional Circuits

Erik Winfree, 2000, UMC.

Molecular Programming with DNA

Erik Winfree, E. Winfree, 2009 .

TileSoft: Sequence Optimization Software for Designing DNA Secondary Structures

Erik Winfree, John H. Reif, Peng Yin, 2004 .

Complexity of Self-Assembled Shapes

Erik Winfree, David Soloveichik, D. Soloveichik, 2004, SIAM J. Comput..

Active self-assembly of algorithmic shapes and patterns in polylogarithmic time

Erik Winfree, Ho-Lin Chen, Peng Yin, 2013, ITCS '13.

Programmability of Chemical Reaction Networks

Jehoshua Bruck, Erik Winfree, David Soloveichik, 2009, Algorithmic Bioprocesses.

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

Erik Winfree, Xiaoping Yang, Nadrian C. Seeman, 1996, DNA Based Computers.

Combining self-healing and proofreading in self-assembly

Matthew Cook, Erik Winfree, David Soloveichik, 2008, Natural Computing.

How crystals that sense and respond to their environments could evolve

Erik Winfree, Rebecca Schulman, 2007, Natural Computing.

Proceedings Machines, Computations and Universality 2013: Ludicrously fast universal computation and construction with reconfigurable molecular robots

Erik Winfree, E. Winfree, 2013 .

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

Erik Winfree, Nicholas Schiefer, E. Winfree, 2016, DNA.

Thermodynamic Analysis of Interacting Nucleic Acid Strands

Erik Winfree, Niles A. Pierce, Robert M. Dirks, 2007, SIAM Rev..

Computation with finite stochastic chemical reaction networks

Matthew Cook, Jehoshua Bruck, Erik Winfree, 2008, Natural Computing.

Verifying chemical reaction network implementations: A bisimulation approach

Erik Winfree, Qing Dong, Robert F. Johnson, 2019, Theor. Comput. Sci..

Self-Assembled Circuit Patterns

Matthew Cook, Erik Winfree, Paul W. K. Rothemund, 2003, DNA.

Leakless DNA Strand Displacement Systems

Erik Winfree, David Soloveichik, Chris Thachuk, 2015, DNA.

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

Erik Winfree, Constantine G. Evans, 2013, DNA.

Molecules computing: self-assembled nanostructures, molecular automata, and chemical reaction networks

Erik Winfree, David Soloveichik, D. Soloveichik, 2008 .

Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions pdf

Erik Winfree, Daniele Cappelletti, David F. Anderson, 2018, Theor. Comput. Sci..

DNA Computing by Self-Assembly

Erik Winfree, 2003 .

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

Erik Winfree, Cameron Myhrvold, David Doty, 2019, Nature.

Algorithmic Bioprocesses

Arto Salomaa, Joost N. Kok, Erik Winfree, 2009, Natural Computing Series.

Error Correction for DNA Self-Assembly : Preventing Facet Nucleation

Erik Winfree, Ho-Lin Chen, Rebecca Schulman, 2005 .

DNA Hybridization Catalysts and Catalyst Circuits

Erik Winfree, Georg Seelig, Bernard Yurke, 2004, DNA.

Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach

Erik Winfree, Chris Thachuk, Seung Woo Shin, 2014, Theor. Comput. Sci..

Two computational primitives for algorithmic self-assembly: copying and counting.

Erik Winfree, Robert D. Barish, Robert D Barish, 2005, Nano letters.

Chemical Reaction Networks and Stochastic Local Search

Erik Winfree, E. Winfree, 2019, DNA.

DNA based computers V : DIMACS Workshop DNA Based Computers V, June 14-15, 1999, Massachusetts Institute of Technology

Erik Winfree, David K. Gifford, 2000 .

String Tile Models for DNA Computing by Self-Assembly

Grzegorz Rozenberg, Erik Winfree, Tony Eng, 2000, DNA Computing.

Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands

Erik Winfree, Chris Thachuk, Joseph M. Schaeffer, 2015, DNA.

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

Lulu Qian, Erik Winfree, E. Winfree, 2014, DNA.

Programmable Control of Nucleation for Algorithmic Self-assembly

Erik Winfree, Rebecca Schulman, 2004, DNA.

Error correction in DNA computing: Misclassification and strand loss

Kevin Chen, Erik Winfree, E. Winfree, 1999, DNA Based Computers.

Enzyme-free nucleic acid dynamical systems

Erik Winfree, Georg Seelig, David Soloveichik, 2017, Science.

The computational power ofBenenson automata

Erik Winfree, David Soloveichik, 2005 .

Neural network computation with DNA strand displacement cascades

Jehoshua Bruck, Lulu Qian, Erik Winfree, 2011, Nature.

A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities

Erik Winfree, Chris Thachuk, Seung Woo Shin, 2017, DNA.

The pathway elaboration method for mean first passage time estimation in large continuous-time Markov chains with applications to nucleic acid kinetics

Mark W. Schmidt, Erik Winfree, Anne Condon, 2021, 2101.03657.

Effective design principles for leakless strand displacement systems

Erik Winfree, David Soloveichik, Chris Thachuk, 2018, Proceedings of the National Academy of Sciences.

Evolution as computation : DIMACS workshop, Princeton, January 1999

Erik Winfree, Laura F. Landweber, 2002 .

Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level.

Erik Winfree, Constantine G. Evans, Constantine G Evans, 2012, Journal of the American Chemical Society.

Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch.

Erik Winfree, Pakpoom Subsoontorn, E. Winfree, 2012, ACS synthetic biology.

Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems

Erik Winfree, Joseph Berleant, Frits Dannenberg, 2018, Journal of the Royal Society Interface.

Erratum: Toward reliable algorithmic self-assembly of DNA tiles: A fixed-width cellular automaton pattern (Nano Letters (2008) 8: 10 (1791))

Satoshi Murata, Erik Winfree, Kenichi Fujibayashi, 2008 .

Dynamic allosteric control of noncovalent DNA catalysis reactions.

Erik Winfree, E. Winfree, David Yu Zhang, 2008, Journal of the American Chemical Society.

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates.

Erik Winfree, Robert D. Barish, Robert D Barish, 2010, Nature nanotechnology.

Robustness and modularity properties of a non-covalent DNA catalytic reaction

Erik Winfree, E. Winfree, David Yu Zhang, 2010, Nucleic acids research.

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics

Erik Winfree, Bernard Yurke, Rizal F Hariadi, 2015, Proceedings of the National Academy of Sciences.

Complexity of Self-assembled Shapes ( Extended Abstract )

Erik Winfree, David Soloveichik, .

Catalyzed relaxation of a metastable DNA fuel.

Erik Winfree, Georg Seelig, Bernard Yurke, 2006, Journal of the American Chemical Society.

Whiplash Pcr for O1 Computing

Erik Winfree, 1998 .

Bistability of an In Vitro Synthetic Autoregulatory Switch

Erik Winfree, Pakpoom Subsoontorn, E. Winfree, 2011, 1101.0723.

DNA Based Computers V

Erik Winfree, David K. Gifford, D. Gifford, 2000 .

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator

Erik Winfree, Elisa Franco, Friedrich C. Simmel, 2014 .

Integrating DNA strand-displacement circuitry with DNA tile self-assembly

Erik Winfree, Rizal F. Hariadi, Harry M. T. Choi, 2013, Nature Communications.