Erik Winfree - Publications

Affiliations: 
Computer Science California Institute of Technology, Pasadena, CA 
Area:
biomolecular computation
Website:
http://www.dna.caltech.edu/~winfree/

99 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Woods D, Doty D, Myhrvold C, Hui J, Zhou F, Yin P, Winfree E. Author Correction: Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature. PMID 31375786 DOI: 10.1038/s41586-019-1378-x  0.68
2019 Woods D, Doty D, Myhrvold C, Hui J, Zhou F, Yin P, Winfree E. Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature. 567: 366-372. PMID 30894725 DOI: 10.1038/s41586-019-1014-9  0.68
2018 Wang B, Thachuk C, Ellington AD, Winfree E, Soloveichik D. Effective design principles for leakless strand displacement systems. Proceedings of the National Academy of Sciences of the United States of America. 115: E12182-E12191. PMID 30545914 DOI: 10.1073/pnas.1806859115  1
2017 Srinivas N, Parkin J, Seelig G, Winfree E, Soloveichik D. Enzyme-free nucleic acid dynamical systems. Science (New York, N.Y.). 358. PMID 29242317 DOI: 10.1126/science.aal2052  1
2017 Thubagere AJ, Li W, Johnson RF, Chen Z, Doroudi S, Lee YL, Izatt G, Wittman S, Srinivas N, Woods D, Winfree E, Qian L. A cargo-sorting DNA robot. Science (New York, N.Y.). 357. PMID 28912216 DOI: 10.1126/science.aan6558  1
2017 Evans CG, Winfree E. Physical principles for DNA tile self-assembly. Chemical Society Reviews. PMID 28489096 DOI: 10.1039/c6cs00745g  1
2015 Hariadi RF, Yurke B, Winfree E. Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements. Chemical Science. 6: 2252-2267. PMID 29308139 DOI: 10.1039/c3sc53331j  1
2015 Hariadi RF, Winfree E, Yurke B. Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics. Proceedings of the National Academy of Sciences of the United States of America. 112: E6086-95. PMID 26504222 DOI: 10.1073/pnas.1424673112  1
2015 Schulman R, Wright C, Winfree E. Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly. Acs Nano. 9: 5760-71. PMID 25965580 DOI: 10.1021/nn507493s  1
2015 Hariadi RF, Yurke B, Winfree E. Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements Chemical Science. 6: 2252-2267. DOI: 10.1039/c3sc53331j  1
2015 Schulman R, Wright C, Winfree E. Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly Acs Nano. 9: 5760-5771. DOI: 10.1021/nn507493s  1
2015 Thachuk C, Winfree E, Soloveichik D. Leakless DNA strand displacement systems Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9211: 133-153. DOI: 10.1007/978-3-319-21999-8_9  1
2015 Schiefer N, Winfree E. Universal computation and optimal construction in the chemical reaction network-controlled tile assembly model Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9211: 34-54. DOI: 10.1007/978-3-319-21999-8_3  1
2015 Schaeffer JM, Thachuk C, Winfree E. Stochastic simulation of the kinetics of multiple interacting nucleic acid strands Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9211: 194-211. DOI: 10.1007/978-3-319-21999-8_13  1
2014 Weitz M, Kim J, Kapsner K, Winfree E, Franco E, Simmel FC. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator Nature Chemistry. 6: 295-302. PMID 24651195 DOI: 10.1038/nchem.1869  1
2014 Qian L, Winfree E. Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8727: 114-131.  1
2013 Srinivas N, Ouldridge TE, Sulc P, Schaeffer JM, Yurke B, Louis AA, Doye JP, Winfree E. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Research. 41: 10641-58. PMID 24019238 DOI: 10.1093/nar/gkt801  1
2013 Zhang DY, Hariadi RF, Choi HMT, Winfree E. Integrating DNA strand-displacement circuitry with DNA tile self-assembly Nature Communications. 4. PMID 23756381 DOI: 10.1038/ncomms2965  1
2013 Woods D, Chen HL, Goodfriend S, Dabby N, Winfree E, Yin P. Active self-assembly of algorithmic shapes and patterns in polylogarithmic time Itcs 2013 - Proceedings of the 2013 Acm Conference On Innovations in Theoretical Computer Science. 353-354. DOI: 10.1145/2422436.2422476  1
2013 Evans CG, Winfree E. DNA sticky end design and assignment for robust algorithmic self-assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8141: 61-75. DOI: 10.1007/978-3-319-01928-4_5  1
2012 Subsoontorn P, Kim J, Winfree E. Ensemble bayesian analysis of bistability in a synthetic transcriptional switch Acs Synthetic Biology. 1: 299-316. PMID 23651285 DOI: 10.1021/sb300018h  1
2012 Evans CG, Hariadi RF, Winfree E. Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level Journal of the American Chemical Society. 134: 10485-10492. PMID 22694312 DOI: 10.1021/ja301026z  1
2012 Schulman R, Yurke B, Winfree E. Robust self-replication of combinatorial information via crystal growth and scission Proceedings of the National Academy of Sciences of the United States of America. 109: 6405-6410. PMID 22493232 DOI: 10.1073/pnas.1117813109  1
2012 Schulman R, Winfree E. Simple evolution of complex crystal species Natural Computing. 11: 187-197. DOI: 10.1007/s11047-011-9302-9  1
2011 Franco E, Friedrichs E, Kim J, Jungmann R, Murray R, Winfree E, Simmel FC. Timing molecular motion and production with a synthetic transcriptional clock Proceedings of the National Academy of Sciences of the United States of America. 108: E784-E793. PMID 21921236 DOI: 10.1073/pnas.1100060108  1
2011 Qian L, Winfree E, Bruck J. Neural network computation with DNA strand displacement cascades Nature. 475: 368-372. PMID 21776082 DOI: 10.1038/nature10262  1
2011 Qian L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades Science. 332: 1196-1201. PMID 21636773 DOI: 10.1126/science.1200520  1
2011 Qian L, Winfree E. A simple DNA gate motif for synthesizing large-scale circuits Journal of the Royal Society Interface. 8: 1281-1287. PMID 21296792 DOI: 10.1098/rsif.2010.0729  1
2011 Kim J, Winfree E. Synthetic in vitro transcriptional oscillators Molecular Systems Biology. 7. PMID 21283141 DOI: 10.1038/msb.2010.119  1
2011 Qian L, Soloveichik D, Winfree E. Efficient turing-universal computation with DNA polymers Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6518: 123-140. DOI: 10.1007/978-3-642-18305-8_12  1
2011 Densmore D, Horowitz M, Krishnaswamy S, Shen X, Arkin A, Winfree E, Voigt C. Joint DAC/IWBDA special session design and synthesis of biological circuits Proceedings - Design Automation Conference. 114-115.  1
2010 Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J, Taylor S, Pei R, Stojanovic MN, Walter NG, Winfree E, Yan H. Molecular robots guided by prescriptive landscapes. Nature. 465: 206-10. PMID 20463735 DOI: 10.1038/nature09012  1
2010 Soloveichik D, Seelig G, Winfree E. DNA as a universal substrate for chemical kinetics Proceedings of the National Academy of Sciences of the United States of America. 107: 5393-5398. PMID 20203007 DOI: 10.1073/pnas.0909380107  1
2010 Zhang DY, Winfree E. Robustness and modularity properties of a non-covalent DNA catalytic reaction Nucleic Acids Research. 38: 4182-4197. PMID 20194118 DOI: 10.1093/nar/gkq088  1
2010 Maune HT, Han SP, Barish RD, Bockrath M, Iii WAG, Rothemund PWK, Winfree E. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates Nature Nanotechnology. 5: 61-66. PMID 19898497 DOI: 10.1038/nnano.2009.311  1
2009 Zhang DY, Winfree E. Control of DNA strand displacement kinetics using toehold exchange Journal of the American Chemical Society. 131: 17303-17314. PMID 19894722 DOI: 10.1021/ja906987s  1
2009 Barish RD, Schulman R, Rothemund PWK, Winfree E. An information-bearing seed for nucleating algorithmic self-assembly Proceedings of the National Academy of Sciences of the United States of America. 106: 6054-6059. PMID 19321429 DOI: 10.1073/pnas.0808736106  1
2009 Fujibayashi K, Zhang DY, Winfree E, Murata S. Error suppression mechanisms for DNA tile self-assembly and their simulation Natural Computing. 8: 589-612. DOI: 10.1007/s11047-008-9093-9  1
2009 Qian L, Winfree E. A simple DNA gate motif for synthesizing large-scale Circuits (Extended abstract) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5347: 70-89. DOI: 10.1007/978-3-642-03076-5_7  1
2009 Soloveichik D, Seelig G, Winfree E. DNA as a universal substrate for chemical kinetics (Extended Abstract) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5347: 57-69. DOI: 10.1007/978-3-642-03076-5_6  1
2008 Zhang DY, Winfree E. Dynamic allosteric control of noncovalent DNA catalysis reactions Journal of the American Chemical Society. 130: 13921-13926. PMID 18823118 DOI: 10.1021/ja803318t  1
2008 Fujibayashi K, Hariadi R, Park SH, Winfree E, Murata S. Toward reliable algorithmic self-assembly of DNA tiles: A fixed-width cellular automaton pattern Nano Letters. 8: 1791-1797. PMID 18162000 DOI: 10.1021/nl0722830  1
2008 Winfree E. Toward molecular programming with DNA Operating Systems Review (Acm). 42: 1. DOI: 10.1145/1346281.1346282  1
2008 Soloveichik D, Cook M, Winfree E, Bruck J. Computation with finite stochastic chemical reaction networks Natural Computing. 7: 615-633. DOI: 10.1007/s11047-008-9067-y  1
2008 Schulman R, Winfree E. How crystals that sense and respond to their environments could evolve Natural Computing. 7: 219-237. DOI: 10.1007/s11047-007-9046-8  1
2008 Soloveichik D, Cook M, Winfree E. Combining self-healing and proofreading in self-assembly Natural Computing. 7: 203-218. DOI: 10.1007/s11047-007-9036-x  1
2007 Venkataraman S, Dirks RM, Rothemund PW, Winfree E, Pierce NA. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnology. 2: 490-4. PMID 18654346 DOI: 10.1038/nnano.2007.225  1
2007 Zhang DY, Turberfield AJ, Yurke B, Winfree E. Engineering entropy-driven reactions and networks catalyzed by DNA Science. 318: 1121-1125. PMID 18006742 DOI: 10.1126/science.1148532  1
2007 Schulman R, Winfree E. Synthesis of crystals with a programmable kinetic barrier to nucleation Proceedings of the National Academy of Sciences of the United States of America. 104: 15236-15241. PMID 17881584 DOI: 10.1073/pnas.0701467104  1
2007 Chen HL, Schulman R, Goel A, Winfree E. Reducing facet nucleation during algorithmic self-assembly Nano Letters. 7: 2913-2919. PMID 17718529 DOI: 10.1021/nl070793o  1
2007 Soloveichik D, Winfree E. Complexity of self-assembled shapes Siam Journal On Computing. 36: 1544-1569. DOI: 10.1137/S0097539704446712  1
2007 Dirks RM, Bois JS, Schaeffer JM, Winfree E, Pierce NA. Thermodynamic analysis of interacting nucleic acid strands Siam Review. 49: 65-88. DOI: 10.1137/060651100  1
2006 Kim J, White KS, Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches Molecular Systems Biology. 2. PMID 17170763 DOI: 10.1038/msb4100099  1
2006 Seelig G, Soloveichik D, Zhang DY, Winfree E. Enzyme-free nucleic acid logic circuits Science. 314: 1585-1588. PMID 17158324 DOI: 10.1126/science.1132493  1
2006 Seelig G, Yurke B, Winfree E. Catalyzed relaxation of a metastable DNA fuel Journal of the American Chemical Society. 128: 12211-12220. PMID 16967972 DOI: 10.1021/ja0635635  1
2006 Winfree E. Algorithmic self-assembly of DNA Proceedings of 2006 International Conference On Microtechnologies in Medicine and Biology. 4. DOI: 10.1109/MMB.2006.251471  1
2006 Winfree E. Algorithmic self-assembly of DNA Proceedings of 2006 International Conference On Microtechnologies in Medicine and Biology. 4. DOI: 10.1109/MMB.2006.251471  1
2006 Soloveichik D, Winfree E. Complexity of compact proofreading for self-assembled patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3892: 305-324. DOI: 10.1007/11753681_24  1
2006 Soloveichik D, Winfree E. Complexity of compact proofreading for self-assembled patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3892: 305-324. DOI: 10.1007/11753681_24  1
2006 Schulman R, Winfree E. Engineering an adjustible kinetic barrier to 1-dimensional crystal nucleation 3rd Conference On Foundations of Nanoscience: Self-Assembled Architectures and Devices, Fnano 2006. 155-156.  1
2006 Schulman R, Winfree E. Engineering an adjustible kinetic barrier to 1-dimensional crystal nucleation 3rd Conference On Foundations of Nanoscience: Self-Assembled Architectures and Devices, Fnano 2006. 155-156.  1
2006 Winfree E. Fault-tolerance in biochemical systems Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4135: 26.  1
2005 Barish RD, Rothemund PWK, Winfree E. Two computational primitives for algorithmic self-assembly: Copying and counting Nano Letters. 5: 2586-2592. PMID 16351220 DOI: 10.1021/nl052038l  1
2005 Barish RD, Rothemund PWK, Winfree E. Two computational primitives for algorithmic self-assembly: Copying and counting Nano Letters. 5: 2586-2592. PMID 16351220 DOI: 10.1021/nl052038l  0.6
2005 Soloveichik D, Winfree E. The computational power of Benenson automata Theoretical Computer Science. 344: 279-297. DOI: 10.1016/j.tcs.2005.07.027  1
2005 Schulman R, Winfree E. Self-replication and evolution of DNA crystals Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3630: 734-743. DOI: 10.1007/11553090_74  1
2005 Schulman R, Winfree E. Self-replication and evolution of DNA crystals Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3630: 734-743. DOI: 10.1007/11553090_74  1
2005 Schulman R, Winfree E. Programmable control of nucleation for algorithmic self-assembly Lecture Notes in Computer Science. 3384: 319-328.  1
2005 Seelig G, Yurke B, Winfree E. DNA hybridization catalysts and catalyst circuits Lecture Notes in Computer Science. 3384: 329-343.  1
2005 Seelig G, Yurke B, Winfree E. DNA hybridization catalysts and catalyst circuits Lecture Notes in Computer Science. 3384: 329-343.  1
2005 Kim J, Hopfield JJ, Winfree E. Neural network computation by in vitro transcriptional circuits Advances in Neural Information Processing Systems 1
2005 Kim J, Hopfield JJ, Winfree E. Neural network computation by in vitro transcriptional circuits Advances in Neural Information Processing Systems 1
2004 Rothemund PWK, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E. Design and characterization of programmable DNA nanotubes Journal of the American Chemical Society. 126: 16344-16352. PMID 15600335 DOI: 10.1021/ja044319l  1
2004 Rothemund PWK, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E. Design and characterization of programmable DNA nanotubes Journal of the American Chemical Society. 126: 16344-16352. PMID 15600335 DOI: 10.1021/ja044319l  0.6
2004 Rothemund PWK, Papadakis N, Winfree E. Algorithmic self-assembly of DNA Sierpinski triangles Plos Biology. 2. PMID 15583715 DOI: 10.1371/journal.pbio.0020424  1
2004 Dirks RM, Lin M, Winfree E, Pierce NA. Paradigms for computational nucleic acid design. Nucleic Acids Research. 32: 1392-403. PMID 14990744 DOI: 10.1093/nar/gkh291  1
2004 Schulman R, Lee S, Papadakis N, Winfree E. One Dimensional Boundaries for DNA Tile Self-Assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2943: 108-125.  1
2004 Schulman R, Lee S, Papadakis N, Winfree E. One Dimensional Boundaries for DNA Tile Self-Assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2943: 108-125.  1
2004 Winfree E, Bekbolatov R. Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2943: 126-144.  1
2004 Cook M, Rothemund PWK, Winfree E. Self-Assembled Circuit Patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2943: 91-107.  1
2004 Cook M, Rothemund PWK, Winfree E. Self-Assembled Circuit Patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2943: 91-107.  0.8
2002 Pierce NA, Winfree E. Protein design is NP-hard. Protein Engineering. 15: 779-82. PMID 12468711  1
2002 Pierce NA, Winfree E. Protein design is NP-hard. Protein Engineering. 15: 779-82. PMID 12468711  1
2001 Winfree E, Eng T, Rozenberg G. String tile models for DNA computing by self-assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2054: 63-88. DOI: 10.1007/3-540-44992-2_6  1
2000 Seeman NC, Liu F, Mao C, Yang X, Wenzler LA, Sha R, Sun W, Shen Z, Li X, Qi J, Zhang Y, Fu TJ, Chen J, Winfree E. Two dimensions and two States in DNA nanotechnology. Journal of Biomolecular Structure & Dynamics. 17: 253-62. PMID 22607432 DOI: 10.1080/07391102.2000.10506629  1
2000 Seeman NC, Liu F, Mao C, Yang X, Wenzler LA, Sha R, Sun W, Shen Z, Li X, Qi J, Zhang Y, Fu TJ, Chen J, Winfree E. Two dimensions and two States in DNA nanotechnology. Journal of Biomolecular Structure & Dynamics. 17: 253-62. PMID 22607432 DOI: 10.1080/07391102.2000.10506629  1
2000 Winfree E. Algorithmic self-assembly of DNA: Theoretical motivations and 2D assembly experiments Journal of Biomolecular Structure and Dynamics. 17: 263-270. DOI: 10.1080/07391102.2000.10506630  1
2000 LaBean TH, Yan H, Kopatsch J, Liu F, Winfree E, Reif JH, Seeman NC. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes Journal of the American Chemical Society. 122: 1848-1860. DOI: 10.1021/ja993393e  1
2000 LaBean TH, Yan H, Kopatsch J, Liu F, Winfree E, Reif JH, Seeman NC. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes Journal of the American Chemical Society. 122: 1848-1860. DOI: 10.1021/ja993393e  1
2000 Rothemund PWK, Winfree E. Program-size complexity of self-assembled squares Conference Proceedings of the Annual Acm Symposium On Theory of Computing. 459-468.  1
2000 Rothemund PWK, Winfree E. Program-size complexity of self-assembled squares Conference Proceedings of the Annual Acm Symposium On Theory of Computing. 459-468.  0.8
1999 Roweis S, Winfree E. On the reduction of errors in DNA computation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 65-75. PMID 10223665  1
1999 Roweis S, Winfree E. On the reduction of errors in DNA computation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 65-75. PMID 10223665  1
1999 Adleman LM, Rothemund PW, Roweis S, Winfree E. On applying molecular computation to the data encryption standard. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 53-63. PMID 10223664  1
1999 Adleman LM, Rothemund PW, Roweis S, Winfree E. On applying molecular computation to the data encryption standard. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 53-63. PMID 10223664  1
1998 Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PW, Adleman LM. A sticker-based model for DNA computation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 5: 615-29. PMID 10072080  1
1998 Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PW, Adleman LM. A sticker-based model for DNA computation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 5: 615-29. PMID 10072080  1
1998 Winfree E, Liu F, Wenzler LA, Seeman NC. Design and self-assembly of two-dimensional DNA crystals. Nature. 394: 539-44. PMID 9707114 DOI: 10.1038/28998  1
1998 Winfree E, Liu F, Wenzler LA, Seeman NC. Design and self-assembly of two-dimensional DNA crystals. Nature. 394: 539-44. PMID 9707114 DOI: 10.1038/28998  1
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