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Johnson, Robert F. and Winfree, Erik (2020) Verifying polymer reaction networks using bisimulation ; Theoretical Computer Science; Vol. 843; 84-114; 10.1016/j.tcs.2020.08.007
Badelt, Stefan and Grun, Casey, et el. (2020) A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures ; Journal of the Royal Society Interface; Vol. 17; No. 167; Art. No. 20190866; 10.1098/rsif.2019.0866
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Winfree, Erik (2019) Chemical Reaction Networks and Stochastic Local Search ; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 1-20; 10.1007/978-3-030-26807-7_1
Zolaktaf, Sedigheh and Dannenberg, Frits, et el. (2019) Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains ; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 80-99; 10.1007/978-3-030-26807-7_5
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Evans, Constantine G. and Winfree, Erik (2018) Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler ; ISBN 978-3-030-00029-5; DNA Computing and Molecular Programming; 37-54; 10.1007/978-3-030-00030-1_3
Srinivas, Niranjan and Parkin, James, et el. (2017) Enzyme-Free Nucleic Acid Dynamical Systems ; Science; Vol. 358; No. 6369; Art. No. eaal2052; 10.1126/science.aal2052
Thubagere, Anupama J. and Li, Wei, et el. (2017) A cargo-sorting DNA robot ; Science; Vol. 357; No. 6356; Art. No. eaan6558; 10.1126/science.aan6558
Poole, William and Ortiz-Muñoz, Andrés, et el. (2017) Chemical Boltzmann Machines ; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 210-231; 10.1007/978-3-319-66799-7_14
Zolaktaf, Sedigheh and Dannenberg, Frits, et el. (2017) Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates ; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 172-187; 10.1007/978-3-319-66799-7_12
Badelt, Stefan and Shin, Seung Woo, et el. (2017) A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities ; ISBN 978-3-319-66798-0; DNA Computing and Molecular Programming; 232-248; 10.1007/978-3-319-66799-7_15
Evans, Constantine G. and Winfree, Erik (2017) Physical principles for DNA tile self-assembly ; Chemical Society Reviews; Vol. 46; No. 12; 3808-3829; 10.1039/c6cs00745g
Schiefer, Nicholas and Winfree, Erik (2016) Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model ; ISBN 978-3-319-43993-8; DNA Computing and Molecular Programming; 165-182; 10.1007/978-3-319-43994-5_11
Johnson, Robert F. and Dong, Qing, et el. (2016) Verifying Chemical Reaction Network Implementations: A Bisimulation Approach ; ISBN 9783319439938; DNA Computing and Molecular Programming; 114-134; 10.1007/978-3-319-43994-5_8
Hariadi, Rizal F. and Winfree, Erik, et el. (2015) Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 112; No. 45; E6086-E6095; PMCID PMC4653207; 10.1073/pnas.1424673112
Schaeffer, Joseph Malcolm and Thachuk, Chris, et el. (2015) Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands ; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming; 194-211; 10.1007/978-3-319-21999-8_13
Thachuk, Chris and Winfree, Erik, et el. (2015) Leakless DNA Strand Displacement Systems ; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming; 133-153; 10.1007/978-3-319-21999-8_9
Schulman, Rebecca and Wright, Christina, et el. (2015) Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly ; ACS Nano; Vol. 9; No. 6; 5760-5771; 10.1021/nn507493s
Hariadi, Rizal F. and Yurke, Bernard, et el. (2015) Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements ; Chemical Science; Vol. 6; No. 4; 2252-2267; PMCID PMC5645730; 10.1039/c3sc53331j
Schiefer, Nicholas and Winfree, Erik (2015) Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model ; ISBN 978-3-319-21998-1; DNA Computing and Molecular Programming: 21st International Conference, DNA 21, Boston and Cambridge, MA, USA, August 17-21, 2015. Proceedings; 34-54; 10.1007/978-3-319-21999-8_3
Qian, Lulu and Winfree, Erik (2014) Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface ; ISBN 978-3-319-11294-7; DNA Computing and Molecular Programming; 114-131; 10.1007/978-3-319-11295-4_8
Weitz, Maximilian and Kim, Jongmin, et el. (2014) Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator ; Nature Chemistry; Vol. 6; No. 4; 295-302; 10.1038/NCHEM.1869
Srinivas, Niranjan and Ouldridge, Thomas E., et el. (2013) On the biophysics and kinetics of toehold-mediated DNA strand displacement ; Nucleic Acids Research; Vol. 41; No. 22; 10641-10658; PMCID PMC3905871; 10.1093/nar/gkt801
Zhang, David Yu and Hariadi, Rizal F., et el. (2013) Integrating DNA strand-displacement circuitry with DNA tile self-assembly ; Nature Communications; Vol. 4; No. 6; Art. No. 1965; PMCID PMC3709499; 10.1038/ncomms2965
Woods, Damien and Chen, Ho-Lin, et el. (2013) Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time ; ISBN 978-1-4503-1859-4; Proceedings of the 4th conference on Innovations in Theoretical Computer Science; 353-354; 10.1145/2422436.2422476
Evans, Constantine G. and Winfree, Erik (2013) DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly ; ISBN 978-3-319-01927-7; DNA Computing and Molecular Programming; 61-75; 10.1007/978-3-319-01928-4_5
Subsoontorn, Pakpoom and Kim, Jongmin, et el. (2012) Ensemble Bayesian Analysis of Bistability in a Synthetic Transcriptional Switch ; ACS Synthetic Biology; Vol. 1; No. 8; 299-316; 10.1021/sb300018h
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Schulman, Rebecca and Winfree, Erik (2012) Simple evolution of complex crystal species ; Natural Computing; Vol. 11; No. 2; 187-197; 10.1007/s11047-011-9302-9
Schulman, Rebecca and Yurke, Bernard, et el. (2012) Robust self-replication of combinatorial information via crystal growth and scission ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 109; No. 17; 6405-6410; PMCID PMC3340064; 10.1073/pnas.1117813109
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Qian, Lulu and Winfree, Erik (2011) A simple DNA gate motif for synthesizing large-scale circuits ; Journal of the Royal Society Interface; Vol. 8; No. 62; 1281-1297; 10.1098/rsif.2010.0729
Qian, Lulu and Winfree, Erik, et el. (2011) Neural network computation with DNA strand displacement cascades ; Nature; Vol. 475; No. 7356; 368-372; 10.1038/nature10262
Qian, Lulu and Winfree, Erik (2011) Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades ; Science; Vol. 332; No. 6034; 1196-1201; 10.1126/science.1200520
Densmore, Douglas and Horowitz, Mark, et el. (2011) Joint DAC/IWBDA special session design and synthesis of biological circuits ; ISBN 978-1-4503-0636-2; Proceedings of the 48th Design Automation Conference; 114-115; 10.1145/2024724.2024750
Kim, Jongmin and Winfree, Erik (2011) Synthetic in vitro transcriptional oscillators ; Molecular Systems Biology; Vol. 7; Art. No. 465; PMCID PMC3063688; 10.1038/msb.2010.119
Subsoontorn, Pakpoom and Kim, Jongmin, et el. (2011) Bistability of an In Vitro Synthetic Autoregulatory Switch ; 10.48550/arXiv.1101.0723
Qian, Lulu and Soloveichik, David, et el. (2011) Efficient Turing-Universal Computation with DNA Polymers ; ISBN 978-3-642-18304-1; DNA computing and molecular programming; 123-140; 10.1007/978-3-642-18305-8_12
Schulman, Rebecca and Winfree, Erik (2011) Simple Evolution of Complex Crystal Species ; ISBN 978-3-642-18304-1; DNA Computing and Molecular Programming; 147-161; 10.1007/978-3-642-18305-8_14
Zhang, David Yu and Winfree, Erik (2010) Robustness and modularity properties of a non-covalent DNA catalytic reaction ; Nucleic Acids Research; Vol. 38; No. 12; 4182-4197; 10.1093/nar/gkq088
Lund, Kyle and Manzo, Anthony J., et el. (2010) Molecular robots guided by prescriptive landscapes ; Nature; Vol. 465; No. 7295; 206-210; 10.1038/nature09012
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Zhang, David Yu and Winfree, Erik (2009) Control of DNA Strand Displacement Kinetics Using Toehold Exchange ; Journal of the American Chemical Society; Vol. 131; No. 47; 17303-17314; 10.1021/ja906987s
Fujibayashi, Kenichi and Zhang, David Yu, et el. (2009) Error suppression mechanisms for DNA tile self-assembly and their simulation ; Natural Computing; Vol. 8; No. 3; 589-612; 10.1007/s11047-008-9093-9
Cook, Matthew and Soloveichik, David, et el. (2009) Programmability of Chemical Reaction Networks ; ISBN 978-3-540-88868-0; Algorithmic Bioprocesses; 543-584; 10.1007/978-3-540-88869-7_27
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Qian, Lulu and Winfree, Erik (2009) A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits ; ISBN 978-3-642-03075-8; DNA computing : 14th International Meeting on DNA Computing, DNA 14, Prague, Czech Republic, June 2-9, 2008 : revised selected papers; 70-89; 10.1007/978-3-642-03076-5
Schulman, Rebecca and Winfree, Erik (2009) Programmable Control of Nucleation for Algorithmic Self-Assembly ; SIAM Journal on Computing; Vol. 39; No. 4; 1581-1616; 10.1137/070680266
Soloveichik, David and Seelig, Georg, et el. (2009) DNA as a Universal Substrate for Chemical Kinetics ; ISBN 978-3-642-03075-8; DNA Computing; 57-69; 10.1007/978-3-642-03076-5_6
Soloveichik, David and Cook, Matthew, et el. (2008) Computation with finite stochastic chemical reaction networks ; Natural Computing; Vol. 7; No. 4; 615-633; 10.1007/s11047-008-9067-y
Zhang, David Yu and Winfree, Erik (2008) Dynamic allosteric control of noncovalent DNA catalysis reactions ; Journal of the American Chemical Society; Vol. 130; No. 42; 13921-13926; 10.1021/ja803318t
Cook, Matthew and Soloveichik, David, et el. (2008) Programmability of Chemical Reaction Networks
Fujibayashi, Kenichi and Hariadi, Rizal, et el. (2008) Toward reliable algorithmic self-assembly of DNA tiles: A fixed-width cellular automaton pattern ; Nano Letters; Vol. 8; No. 7; 1791-1797; 10.1021/nl0722830
Soloveichik, David and Cook, Matthew, et el. (2008) Combining self-healing and proofreading in self-assembly ; Natural Computing; Vol. 7; No. 2; 203-218; 10.1007/s11047-007-9036-x
Schulman, Rebecca and Winfree, Erik (2008) How crystals that sense and respond to their environments could evolve ; Natural Computing; Vol. 7; No. 2; 219-237; 10.1007/s11047-007-9046-8
Winfree, Erik (2008) Toward molecular programming with DNA ; ISBN 978-1-59593-958-6; ASPLOS XIII Proceedings of the 13th international conference on Architectural support for programming languages and operating systems; 10.1145/1346281.1346282
Zhang, David Yu and Turberfield, Andrew J., et el. (2007) Engineering entropy-driven reactions and networks catalyzed by DNA ; Science; Vol. 318; No. 5853; 1121-1125; 10.1126/science.1148532
Schulman, Rebecca and Winfree, Erik (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 104; No. 39; 15236-15241; PMCID PMC1986573; 10.1073/pnas.0701467104
Soloveichik, David and Cook, Matthew, et el. (2007) Computation with Finite Stochastic Chemical Reaction Networks
Chen, Ho-Lin and Schulman, Rebecca, et el. (2007) Reducing facet nucleation during algorithmic self-assembly ; Nano Letters; Vol. 7; No. 9; 2913-2919; 10.1021/nl070793o
Venkataraman, Suvir and Dirks, Robert M., et el. (2007) An autonomous polymerization motor powered by DNA hybridization ; Nature Nanotechnology; Vol. 2; No. 8; 490-494; 10.1038/nnano.2007.225
Soloveichik, David and Winfree, Erik (2007) Complexity of Self-Assembled Shapes ; SIAM Journal on Computing; Vol. 36; No. 6; 1544-1569; 10.1137/S0097539704446712
Dirks, Robert M. and Bois, Justin S., et el. (2007) Thermodynamic Analysis of Interacting Nucleic Acid Strands ; SIAM Review; Vol. 49; No. 1; 65-88; 10.1137/060651100
Kim, Jongmin and White, Kristin S., et el. (2006) Construction of an in vitro bistable circuit from synthetic transcriptional switches ; Molecular Systems Biology; Vol. 2; Art. No. 68; PMCID PMC1762086; 10.1038/msb4100099
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Seelig, Georg and Yurke, Bernard, et el. (2006) Catalyzed relaxation of a metastable DNA fuel ; Journal of the American Chemical Society; Vol. 128; No. 37; 12211-12220; 10.1021/ja0635635
Winfree, Erik (2006) Algorithmic Self-Assembly of DNA ; ISBN 978-1-4244-0337-0; Proceedings of the 2006 International Conference on Microtechnologies in Medicine and Biology; 4-4
Winfree, Erik (2006) Fault-Tolerance in Biochemical Systems ; ISBN 978-3-540-38593-6; Unconventional Computation; 26; 10.1007/11839132_3
Winfree, Erik (2006) Self-Healing Tile Sets ; ISBN 9783540302964; Nanotechnology: Science and Computation; 55-78; 10.1007/3-540-30296-4_4
Soloveichik, David and Winfree, Erik (2006) Complexity of compact proofreading for self-assembled patterns ; ISBN 3-540-34161-7; DNA Computing; 305-324; 10.1007/11753681_24
Barish, Robert D. and Rothemund, Paul W. K., et el. (2005) Two computational primitives for algorithmic self-assembly: Copying and counting ; Nano Letters; Vol. 5; No. 12; 2586-2592; 10.1021/nl052038l
Soloveichik, David and Winfree, Erik (2005) The computational power of Benenson automata ; Theoretical Computer Science; Vol. 344; No. 2-3; 279-297; 10.1016/j.tcs.2005.07.027
Soloveichik, David and Winfree, Erik (2005) Complexity of Self-assembled Shapes (Extended Abstract) ; ISBN 978-3-540-26174-2; DNA Computing; 344-354; 10.1007/11493785_30
Schulman, Rebecca and Winfree, Erik (2005) Self-replication and evolution of DNA crystals ; ISBN 3-540-28848-1; Advances in Artificial Life; 734-743; 10.1007/11553090_74
Schulman, Rebecca and Winfree, Erik (2005) Programmable Control of Nucleation for Algorithmic Self-assembly ; ISBN 978-3-540-26174-2; DNA Computing; 319-328; 10.1007/11493785_28
Seelig, Georg and Yurke, Bernard, et el. (2005) DNA hybridization catalysts and catalyst circuits ; ISBN 3-540-26174-5; DNA Computing; 329-343; 10.1007/11493785_29
Rothemund, Paul W. K. and Ekani-Nkodo, Axel, et el. (2004) Design and characterization of programmable DNA nanotubes ; Journal of the American Chemical Society; Vol. 126; No. 50; 16344-16352; 10.1021/ja044319l
Rothemund, Paul W. K. and Papadakis, Nick, et el. (2004) Algorithmic Self-Assembly of DNA Sierpinski Triangles ; PLoS Biology; Vol. 2; No. 12; 2041-2053; PMCID PMC534809; 10.1371/journal.pbio.0020424
Dirks, Robert M. and Lin, Milo, et el. (2004) Paradigms for computational nucleic acid design ; Nucleic Acids Research; Vol. 32; No. 4; 1392-1403; PMCID PMC390280; 10.1093/nar/gkh291
Cook, Matthew and Rothemund, Paul W. K., et el. (2004) Self-assembled circuit patterns ; ISBN 3-540-20930-1; DNA Computing; 91-107; 10.1007/978-3-540-24628-2_11
Kim, Jongmin and Hopfield, John J., et el. (2004) Neural network computation by in vitro transcriptional circuits ; Advances in Neural Information Processing Systems; Vol. 17; 681-688
Winfree, Erik and Bekbolatov, Renat (2004) Proofreading tile sets: Error correction for algorithmic self-assembly ; ISBN 3-540-20930-1; DNA Computing; 126-144; 10.1007/978-3-540-24628-2_13
Schulman, Rebecca and Lee, Shaun, et el. (2004) One dimensional boundaries for DNA tile self-assembly ; ISBN 3-540-20930-1; DNA Computing; 108-125; 10.1007/978-3-540-24628-2_12
Winfree, Erik (2003) DNA Computing by Self-Assembly ; The Bridge; Vol. 33; No. 4; 31-38
Winfree, Erik (2003) Simulations of Computing by Self-Assembly ; 10.7907/Z9TB14X7
Winfree, Erik (2003) Whiplash PCR for O(1) Computing ; 10.7907/Z94M92KH
Pierce, Niles A. and Winfree, Erik (2002) Protein Design is NP-hard ; Protein Engineering; Vol. 15; No. 10; 779-782; 10.1093/protein/15.10.779
Winfree, Erik and Landweber, Laura F. (2002) Introduction: Evolution and Computation: Where Do They Meet? ; ISBN 978-3-642-63081-1; Evolution as Computation: DIMACS Workshop, Princeton, January 1999; v-ix
Landweber, Laura F. and Winfree, Erik (2002) Evolution as Computation ; ISBN 978-3-642-63081-1; Evolution as Computation; 10.1007/978-3-642-55606-7
Winfree, Erik (2001) In Vitro Transcriptional Circuits ; ISBN 978-1-85233-415-4; Unconventional Models of Computation, UMC'2K; 121-122; 10.1007/978-1-4471-0313-4_10
Winfree, Erik and Eng, Tony, et el. (2001) String tile models for DNA computing by self-assembly ; ISBN 978-3-540-42076-7; DNA Computing; 63-88; 10.1007/3-540-44992-2_6
Rothemund, Paul W. K. and Winfree, Erik (2000) The program-size complexity of self-assembled squares ; ISBN 1-58113-184-4; STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing; 459-468; 10.1145/335305.335358
Winfree, Erik (2000) Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments ; Journal of Biomolecular Structure and Dynamics; Vol. 11; No. 2; 263-270
LaBean, Thomas H. and Yan, Hao, et el. (2000) Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes ; Journal of the American Chemical Society; Vol. 122; No. 9; 1848-1860; 10.1021/ja993393e
LaBean, Thomas H. and Winfree, Erik, et el. (2000) Experimental Progress in Computation by Self-Assembly of DNA Tilings ; ISBN 9780821820537; DNA Based Computers V; 123-40
Chen, Kevin and Winfree, Erik (2000) Error Correction in DNA Computing: Misclassification and
Strand Loss ; ISBN 9780821820537; DNA Based Computers V; 49-63
Seeman, Nadrian C. and Liu, Furong, et el. (2000) Two Dimensions and Two States in DNA Nanotechnology ; Journal of Biomolecular Structure and Dynamics; Vol. 11; No. S2; 253-262
Roweis, Sam and Winfree, Erik (1999) On the Reduction of Errors in DNA Computation ; Journal of Computational Biology; Vol. 6; No. 1; 65-75; 10.1089/cmb.1999.6.65
Adleman, Leonard M. and Rothemund, Paul W. K., et el. (1999) On Applying Molecular Computation to the Data Encryption Standard ; Journal of Computational Biology; Vol. 6; No. 1; 53-63; 10.1089/cmb.1999.6.53
Winfree, Erik and Yang, Xiaoping, et el. (1999) Universal Computation via Self-assembly of DNA: Some Theory and Experiments ; ISBN 0821807560; DNA Based Computers II; 191-213
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Roweis, Sam and Winfree, Erik, et el. (1998) A sticker-based model for DNA computation ; Journal of Computational Biology; Vol. 5; No. 4; 615-629; 10.1089/cmb.1998.5.615
Winfree, Erik (1996) On the Computational Power of DNA Annealing and Ligation ; ISBN 0821805185; DNA Based Computers; 199-221
Winfree, Erik (1996) Complexity of Restricted and Unrestricted Models of Molecular Computation ; ISBN 0821805185; DNA based computers; 187-198
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