| Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly CG Evans, J O’Brien, E Winfree, A Murugan Nature 625 (7995), 500-507, 2024 | 32 | 2024 |
| Learning and Inference in a Lattice Model of Multicomponent Condensates C Chalk, S Buse, K Shrinivas, A Murugan, E Winfree 30th International Conference on DNA Computing and Molecular Programming …, 2024 | | 2024 |
| Predicting DNA kinetics with a truncated continuous-time Markov chain method S Zolaktaf, F Dannenberg, M Schmidt, A Condon, E Winfree Computational Biology and Chemistry 104, 107837, 2023 | 5* | 2023 |
| The Tall Thin Molecular Programmer E Winfree 2023 IEEE International Solid-State Circuits Conference (ISSCC), 1-3, 2023 | | 2023 |
| Two-dimensional tile displacement can simulate cellular automata E Winfree, L Qian arXiv preprint arXiv:2301.01929, 2023 | 3 | 2023 |
| 29th International Conference on DNA Computing and Molecular Programming (DNA 29) A Shalaby, C Thachuk, D Woods, F Becker, S Heydarshahi, A Condon, ... Schloss Dagstuhl-Leibniz-Zentrum für Informatik GmbH, 2023 | 1 | 2023 |
| Revisiting Hybridization Kinetics with Improved Elementary Step Simulation J Lovrod, B Beronov, C Zhang, E Winfree, A Condon 29th International Conference on DNA Computing and Molecular Programming …, 2023 | 1 | 2023 |
| Visions of DNA Nanotechnology at 40 for the next 40: A Tribute to Nadrian C. Seeman N Jonoska, E Winfree Springer Nature, 2023 | 6 | 2023 |
| Detailed balanced chemical reaction networks as generalized Boltzmann machines W Poole, T Ouldridge, M Gopalkrishnan, E Winfree arXiv preprint arXiv:2205.06313, 2022 | 5 | 2022 |
| Winner-take-all dynamics in self-assembly J O'Brien, C Evans, E Winfree, A Murugan APS March Meeting Abstracts 2021, S07. 008, 2021 | 1 | 2021 |
| Verifying polymer reaction networks using bisimulation RF Johnson, E Winfree Theoretical Computer Science 843, 84-114, 2020 | 4 | 2020 |
| A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures S Badelt, C Grun, KV Sarma, B Wolfe, SW Shin, E Winfree Journal of the Royal Society Interface 17 (167), 20190866, 2020 | 53 | 2020 |
| Programming and simulating chemical reaction networks on a surface S Clamons, L Qian, E Winfree Journal of the Royal Society Interface 17 (166), 20190790, 2020 | 46 | 2020 |
| Pattern recognition through molecular self-assembly C Evans, J O'Brien, E Winfree, A Murugan Bulletin of the American Physical Society 65, 2020 | | 2020 |
| Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions D Cappelletti, A Ortiz-Muñoz, DF Anderson, E Winfree Theoretical Computer Science 801, 64-95, 2020 | 24 | 2020 |
| Verifying chemical reaction network implementations: a bisimulation approach R Johnson, Q Dong, E Winfree Theoretical Computer Science 765, 3-46, 2019 | 32 | 2019 |
| Verifying chemical reaction network implementations: A pathway decomposition approach SW Shin, C Thachuk, E Winfree Theoretical Computer Science 765, 67-96, 2019 | 28 | 2019 |
| Diverse and robust molecular algorithms using reprogrammable DNA self-assembly D Woods, D Doty, C Myhrvold, J Hui, F Zhou, P Yin, E Winfree Nature 567 (7748), 366-372, 2019 | 281 | 2019 |
| Chemical reaction networks and stochastic local search E Winfree DNA Computing and Molecular Programming: 25th International Conference, DNA …, 2019 | 15 | 2019 |
| Reversible computation using swap reactions on a surface T Brailovskaya, G Gowri, S Yu, E Winfree DNA Computing and Molecular Programming: 25th International Conference, DNA …, 2019 | 12 | 2019 |
| Efficient parameter estimation for DNA kinetics modeled as continuous-time Markov chains S Zolaktaf, F Dannenberg, E Winfree, A Bouchard-Côté, M Schmidt, ... DNA Computing and Molecular Programming: 25th International Conference, DNA …, 2019 | 6 | 2019 |
| Effective design principles for leakless strand displacement systems B Wang, C Thachuk, AD Ellington, E Winfree, D Soloveichik Proceedings of the National Academy of Sciences 115 (52), E12182-E12191, 2018 | 138 | 2018 |
| Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems J Berleant, C Berlind, S Badelt, F Dannenberg, J Schaeffer, E Winfree Journal of the Royal Society Interface 15 (149), 20180107, 2018 | 21 | 2018 |
| Optimizing tile set size while preserving proofreading with a DNA self-assembly compiler CG Evans, E Winfree DNA Computing and Molecular Programming: 24th International Conference, DNA …, 2018 | 3 | 2018 |
| Enzyme-free nucleic acid dynamical systems N Srinivas, J Parkin, G Seelig, E Winfree, D Soloveichik Science 358 (6369), eaal2052, 2017 | 348 | 2017 |
| Chemical Boltzmann machines W Poole, A Ortiz-Munoz, A Behera, NS Jones, TE Ouldridge, E Winfree, ... International Conference on DNA-Based Computers, 210-231, 2017 | 40 | 2017 |
| A cargo-sorting DNA robot AJ Thubagere, W Li, RF Johnson, Z Chen, S Doroudi, YL Lee, G Izatt, ... Science 357 (6356), eaan6558, 2017 | 546 | 2017 |
| Inferring parameters for an elementary step model of DNA structure kinetics with locally context-dependent Arrhenius rates S Zolaktaf, F Dannenberg, X Rudelis, A Condon, JM Schaeffer, M Schmidt, ... International Conference on DNA-Based Computers, 172-187, 2017 | 11 | 2017 |
| Programming Molecules Using Biology, Chemistry, and Computer Science E Winfree 2017 AAAS Annual Meeting (February 16-20, 2017), 2017 | | 2017 |
| A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities S Badelt, SW Shin, RF Johnson, Q Dong, C Thachuk, E Winfree DNA Computing and Molecular Programming: 23rd International Conference, DNA …, 2017 | 49 | 2017 |
| Physical principles for DNA tile self-assembly CG Evans, E Winfree Chemical Society Reviews 46 (12), 3808-3829, 2017 | 101 | 2017 |
| Time complexity of computation and construction in the chemical reaction network-controlled tile assembly model N Schiefer, E Winfree International Conference on DNA-Based Computers, 165-182, 2016 | 9 | 2016 |
| Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics RF Hariadi, E Winfree, B Yurke Proceedings of the National Academy of Sciences 112 (45), E6086-E6095, 2015 | 28 | 2015 |
| Increasing redundancy exponentially reduces error rates during algorithmic self-assembly R Schulman, C Wright, E Winfree ACS nano 9 (6), 5760-5771, 2015 | 18 | 2015 |
| Stochastic simulation of the kinetics of multiple interacting nucleic acid strands JM Schaeffer, C Thachuk, E Winfree DNA Computing and Molecular Programming: 21st International Conference, DNA …, 2015 | 60 | 2015 |
| Leakless DNA strand displacement systems C Thachuk, E Winfree, D Soloveichik DNA Computing and Molecular Programming: 21st International Conference, DNA …, 2015 | 93 | 2015 |
| Universal computation and optimal construction in the chemical reaction network-controlled tile assembly model N Schiefer, E Winfree DNA Computing and Molecular Programming: 21st International Conference, DNA …, 2015 | 26 | 2015 |
| Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements RF Hariadi, B Yurke, E Winfree Chemical science 6 (4), 2252-2267, 2015 | 47 | 2015 |
| Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface L Qian, E Winfree International Workshop on DNA-Based Computers, 114-131, 2014 | 73 | 2014 |
| Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator M Weitz, J Kim, K Kapsner, E Winfree, E Franco, FC Simmel Nature chemistry 6 (4), 295-302, 2014 | 234 | 2014 |
| On the biophysics and kinetics of toehold-mediated DNA strand displacement N Srinivas, TE Ouldridge, P Šulc, JM Schaeffer, B Yurke, AA Louis, ... Nucleic acids research 41 (22), 10641-10658, 2013 | 541 | 2013 |
| Integrating DNA strand-displacement circuitry with DNA tile self-assembly DY Zhang, RF Hariadi, HMT Choi, E Winfree Nature communications 4 (1), 1965, 2013 | 217 | 2013 |
| Correction to “Design and Characterization of Programmable DNA Nanotubes” PWK Rothemund, A Ekani-Nkodo, N Papadakis, A Kumar, ... Journal of the American Chemical Society 135 (7), 2864-2864, 2013 | | 2013 |
| Active self-assembly of algorithmic shapes and patterns in polylogarithmic time D Woods, HL Chen, S Goodfriend, N Dabby, E Winfree, P Yin Proceedings of the 4th conference on Innovations in Theoretical Computer …, 2013 | 124 | 2013 |
| Design and Characterization of Programmable DNA Nanotubes (vol 126, pg 16344, 2004) PWK Rothemund, A Ekani-Nkodo, N Papadakis, A Kumar, DK Fygenson, ... Journal of the American Chemical Society 135 (7), 2864-2864, 2013 | | 2013 |
| DNA sticky end design and assignment for robust algorithmic self-assembly CG Evans, E Winfree DNA Computing and Molecular Programming: 19th International Conference, DNA …, 2013 | 22 | 2013 |
| Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch P Subsoontorn, J Kim, E Winfree ACS synthetic biology 1 (8), 299-316, 2012 | 72* | 2012 |
| Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level CG Evans, RF Hariadi, E Winfree Journal of the American Chemical Society 134 (25), 10485-10492, 2012 | 37 | 2012 |
| Simple evolution of complex crystal species R Schulman, E Winfree Natural Computing 11, 187-197, 2012 | 8 | 2012 |
| Robust self-replication of combinatorial information via crystal growth and scission R Schulman, B Yurke, E Winfree Proceedings of the national academy of sciences 109 (17), 6405-6410, 2012 | 136 | 2012 |
| Engineered toehold reactions and networks D Zhang, AJ Turberfield, E Winfree US Patent 8,110,353, 2012 | 20 | 2012 |
| Timing molecular motion and production with a synthetic transcriptional clock E Franco, E Friedrichs, J Kim, R Jungmann, R Murray, E Winfree, ... Proceedings of the National Academy of Sciences 108 (40), E784-E793, 2011 | 265 | 2011 |
| A simple DNA gate motif for synthesizing large-scale circuits L Qian, E Winfree Journal of The Royal Society Interface 8 (62), 1281-1297, 2011 | 400 | 2011 |
| Neural network computation with DNA strand displacement cascades L Qian, E Winfree, J Bruck nature 475 (7356), 368-372, 2011 | 1172 | 2011 |
| Scaling up digital circuit computation with DNA strand displacement cascades L Qian, E Winfree science 332 (6034), 1196-1201, 2011 | 1640 | 2011 |
| Using Biological Networks to Perform Bayesian Inference DT Lee, S Hsieh, D Koller, E Winfree | | 2011 |
| Synthetic in vitro transcriptional oscillators J Kim, E Winfree Molecular systems biology 7 (1), 465, 2011 | 384 | 2011 |
| Efficient Turing-universal computation with DNA polymers L Qian, D Soloveichik, E Winfree DNA computing and molecular programming, 123-140, 2011 | 160 | 2011 |
| Robustness and modularity properties of a non-covalent DNA catalytic reaction DY Zhang, E Winfree Nucleic acids research 38 (12), 4182-4197, 2010 | 120 | 2010 |
| Nucleic acid-based logic circuits G Seelig, D Soloveichik, E Winfree, D Zhang US Patent 7,745,594, 2010 | 37 | 2010 |
| Molecular robots guided by prescriptive landscapes K Lund, AJ Manzo, N Dabby, N Michelotti, A Johnson-Buck, J Nangreave, ... Nature 465 (7295), 206-210, 2010 | 1062 | 2010 |
| DNA as a universal substrate for chemical kinetics D Soloveichik, G Seelig, E Winfree Proceedings of the National Academy of Sciences 107 (12), 5393, 2010 | 822 | 2010 |
| Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates HT Maune, S Han, RD Barish, M Bockrath, WAG Iii, PWK Rothemund, ... Nature nanotechnology 5 (1), 61-66, 2010 | 705 | 2010 |
| Control of DNA strand displacement kinetics using toehold exchange DY Zhang, E Winfree Journal of the American Chemical Society 131 (47), 17303-17314, 2009 | 1542 | 2009 |
| Error suppression mechanisms for DNA tile self-assembly and their simulation K Fujibayashi, DY Zhang, E Winfree, S Murata Natural Computing 8 (3), 589-612, 2009 | 52 | 2009 |
| Programmability of chemical reaction networks M Cook, D Soloveichik, E Winfree, J Bruck Algorithmic bioprocesses, 543-584, 2009 | 162 | 2009 |
| POLYNUCLEOTIDES AND RELATED NANOASSEMBLIES, STRUCTURES, ARRANGEMENTS, METHODS AND SYSTEMS HT Maune, S Han, RD Barish, MW Bockrath, WA Goddard, ... US Patent App. 20,100/069,621, 2009 | 33* | 2009 |
| Enzyme-free isothermal exponential amplification of nucleic acids and nucleic acid analog signals D Zhang, B Yurke, E Winfree US Patent 7,538,202, 2009 | 13 | 2009 |
| An information-bearing seed for nucleating algorithmic self-assembly RD Barish, R Schulman, PWK Rothemund, E Winfree Proceedings of the National Academy of Sciences 106 (15), 6054-6059, 2009 | 301 | 2009 |
| S1. Quasi-steady state (QSS) derivation of the BM rate constant DY Zhang, E Winfree J. Am. Chem. Soc. 131, 1-16, 2009 | 1 | 2009 |
| Algorithmic bioprocesses A Salomaa, E Winfree, D Harel, JN Kok Springer-Verlag Berlin Heidelberg, 2009 | 2 | 2009 |
| Programmable control of nucleation for algorithmic self-assembly R Schulman, E Winfree SIAM Journal on Computing 39 (4), 1581-1616, 2009 | 136* | 2009 |
| Computation with finite stochastic chemical reaction networks D Soloveichik, M Cook, E Winfree, J Bruck natural computing 7, 615-633, 2008 | 299 | 2008 |
| Dynamic allosteric control of noncovalent DNA catalysis reactions DY Zhang, E Winfree Journal of the American Chemical Society 130 (42), 13921-13926, 2008 | 88 | 2008 |
| How crystals that sense and respond to their environments could evolve R Schulman, E Winfree Natural Computing 7, 219-237, 2008 | 21 | 2008 |
| Combining self-healing and proofreading in self-assembly D Soloveichik, M Cook, E Winfree Natural Computing 7, 203-218, 2008 | 37 | 2008 |
| DNA Nanoscaffold Directed Self-Assembly of Carbon Nanotube Devices S Han, HT Maune, R Barish, P Rothemund, M Bockrath, E Winfree, ... ECS Meeting Abstracts, 55, 2008 | | 2008 |
| Toward molecular programming with DNA E Winfree Proceedings of the 13th international conference on Architectural support …, 2008 | 9 | 2008 |
| Self-stabilizing synchronization in 3 dimensions M Cook, P Gacs, E Winfree Preprint, 2008 | 3* | 2008 |
| Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern K Fujibayashi, R Hariadi, SH Park, E Winfree, S Murata Nano letters 8 (7), 1791-1797, 2007 | 231 | 2007 |
| Engineering entropy-driven reactions and networks catalyzed by DNA DY Zhang, AJ Turberfield, B Yurke, E Winfree Science 318 (5853), 1121-1125, 2007 | 1214 | 2007 |
| Synthesis of crystals with a programmable kinetic barrier to nucleation R Schulman, E Winfree Proceedings of the National Academy of Sciences 104 (39), 15236-15241, 2007 | 210 | 2007 |
| Programming a DNA World E Winfree Colloquia Videos from Princeton Plasma Physics Laboratory (PPPL), 2007 | | 2007 |
| Reducing facet nucleation during algorithmic self-assembly HL Chen, R Schulman, A Goel, E Winfree Nano letters 7 (9), 2913-2919, 2007 | 86 | 2007 |
| An autonomous polymerization motor powered by DNA hybridization S Venkataraman, RM Dirks, PWK Rothemund, E Winfree, NA Pierce Nature Nanotechnology 2 (8), 490-494, 2007 | 359 | 2007 |
| Self-assembling tile systems that heal from small fragments H Chen, A Goel, C Luhrs, E Winfree Preliminary Proceedings of DNA Computing 13, 30-46, 2007 | 12 | 2007 |
| Complexity of self-assembled shapes D Soloveichik, E Winfree SIAM Journal on Computing 36 (6), 1544-1569, 2007 | 296 | 2007 |
| Research Note-Biochemical Logic: Submerged Circuits of Floating DNA E Winfree ENGenious, 52-54, 2007 | 1 | 2007 |
| Thermodynamic analysis of interacting nucleic acid strands RM Dirks, JS Bois, JM Schaeffer, E Winfree, NA Pierce SIAM review 49 (1), 65-88, 2007 | 435 | 2007 |
| Construction of an in vitro bistable circuit from synthetic transcriptional switches J Kim, KS White, E Winfree Molecular systems biology 2 (1), 68, 2006 | 384 | 2006 |
| Enzyme-free nucleic acid logic circuits G Seelig, D Soloveichik, DY Zhang, E Winfree Science 314 (5805), 1585-1588, 2006 | 1692 | 2006 |
| Catalyzed relaxation of a metastable DNA fuel G Seelig, B Yurke, E Winfree Journal of the American Chemical Society 128 (37), 12211-12220, 2006 | 216 | 2006 |
| Self-healing tile sets E Winfree Nanotechnology: science and computation, 55-78, 2006 | 111 | 2006 |
| Complexity of compact proofreading for self-assembled patterns D Soloveichik, E Winfree DNA Computing: 11th International Workshop on DNA Computing, DNA11, London …, 2006 | 73 | 2006 |
| Two computational primitives for algorithmic self-assembly: Copying and counting RD Barish, PWK Rothemund, E Winfree Nano letters 5 (12), 2586-2592, 2005 | 303 | 2005 |
| The computational power of Benenson automata D Soloveichik, E Winfree Theoretical Computer Science 344 (2-3), 279-297, 2005 | 38 | 2005 |
| Self-replication and evolution of DNA crystals R Schulman, E Winfree European Conference on Artificial Life, 734-743, 2005 | 37 | 2005 |
| Self-assembled circuits and circuit patterns M Cook, P Rothemund, E Winfree US Patent App. 10/848,513, 2005 | 32 | 2005 |
| DNA hybridization catalysts and catalyst circuits G Seelig, B Yurke, E Winfree DNA Computing: 10th International Workshop on DNA Computing, DNA10, Milan …, 2005 | 28 | 2005 |
| Design and characterization of programmable DNA nanotubes PWK Rothemund, A Ekani-Nkodo, N Papadakis, A Kumar, DK Fygenson, ... Journal of the American Chemical Society 126 (50), 16344-16352, 2004 | 584 | 2004 |
Paul W.K. RothemundCalifornia Institute of TechnologyVerified email at dna.caltech.edu
