Winfree, Erik

Combined from CaltechAUTHORS

• Evans, Constantine Glen and O'Brien, Jackson, et el. (2024) Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly; Nature; Vol. 625; No. 7995; 500-507; 10.1038/s41586-023-06890-z
• Zolaktaf, Sedigheh and Dannenberg, Frits, et el. (2023) Predicting DNA kinetics with a truncated continuous-time Markov chain method; Computational Biology and Chemistry; Vol. 104; Art. No. 107837; 10.1016/j.compbiolchem.2023.107837
• Evans, Constantine Glen and O'Brien, Jackson, et el. (2022) Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly; 10.48550/arXiv.2207.06399
• 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
• Clamons, Samuel and Qian, Lulu, et el. (2020) Programming and simulating chemical reaction networks on a surface; Journal of the Royal Society Interface; Vol. 17; No. 166; Art. No. 20190790; PMCID PMC7276541; 10.1098/rsif.2019.0790
• Cappelletti, Daniele and Ortiz-Muñoz, Andrés, et el. (2020) Stochastic Chemical Reaction Networks for Robustly Approximating Arbitrary Probability Distributions; Theoretical Computer Science; Vol. 801; 64-95; 10.1016/j.tcs.2019.08.013
• 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
• Brailovskaya, Tatiana and Gowri, Gokul, et el. (2019) Reversible Computation Using Swap Reactions on a Surface; ISBN 978-3-030-26806-0; DNA Computing and Molecular Programming; 174-196; 10.1007/978-3-030-26807-7_10
• Johnson, Robert and Dong, Qing, et el. (2019) Verifying chemical reaction network implementations: A bisimulation approach; Theoretical Computer Science; Vol. 765; 3-46; 10.1016/j.tcs.2018.01.002
• Shin, Seung Woo and Thachuk, Chris, et el. (2019) Verifying chemical reaction network implementations: A pathway decomposition approach; Theoretical Computer Science; Vol. 765; 67-96; 10.1016/j.tcs.2017.10.011
• Woods, Damien and Doty, David, et el. (2019) Diverse and robust molecular algorithms using reprogrammable DNA self-assembly; Nature; Vol. 567; No. 3; 366-372; 10.1038/s41586-019-1014-9
• Wang, Boya and Thachuk, Chris, et el. (2018) Effective design principles for leakless strand displacement systems; Proceedings of the National Academy of Sciences of the United States of America; Vol. 115; No. 52; E12182-E12191; PMCID PMC6310779; 10.1073/pnas.1806859115
• Berleant, Joseph and Berlind, Christopher, et el. (2018) Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems; Journal of the Royal Society Interface; Vol. 15; No. 149; Art. No. 20180107; 10.1098/rsif.2018.0107
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Evans, Constantine G. and Hariadi, Rizal F., et el. (2012) Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level; Journal of the American Chemical Society; Vol. 134; No. 25; 10485-10492; 10.1021/ja301026z
• 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
• Franco, Elisa and Friedrichs, Eike, et el. (2011) Timing molecular motion and production with a synthetic transcriptional clock; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 40; E784-E793; PMCID PMC3189071; 10.1073/pnas.1100060108
• 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
• Soloveichik, David and Seelig, Georg, et el. (2010) DNA as a universal substrate for chemical kinetics; Proceedings of the National Academy of Sciences of the United States of America; Vol. 107; No. 12; 5393-5398; PMCID PMC2851759; 10.1073/pnas.0909380107
• Maune, Hareem T. and Han, Si-ping, et el. (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates; Nature Nanotechnology; Vol. 5; No. 1; 61-66; 10.1038/nnano.2009.311
• 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
• Barish, Robert D. and Schulman, Rebecca, et el. (2009) An information-bearing seed for nucleating algorithmic self-assembly; Proceedings of the National Academy of Sciences of the United States of America; Vol. 106; No. 15; 6054-6059; PMCID PMC2660060; 10.1073/pnas.0808736106
• 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
• 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
• 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 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
• Seelig, Georg and Soloveichik, David, et el. (2006) Enzyme-free nucleic acid logic circuits; Science; Vol. 314; No. 5805; 1585-1588; 10.1126/science.1132493
• 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) Self-Healing Tile Sets; ISBN 9783540302964; Nanotechnology: Science and Computation; 55-78; 10.1007/3-540-30296-4_4
• 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
• 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
• 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
• 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
• 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) Programmable Control of Nucleation for Algorithmic Self-assembly; ISBN 978-3-540-26174-2; DNA Computing; 319-328; 10.1007/11493785_28
• 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
• 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
• 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
• 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
• 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 (2003) DNA Computing by Self-Assembly; The Bridge; Vol. 33; No. 4; 31-38
• Winfree, Erik (2003) Whiplash PCR for O(1) Computing; 10.7907/Z94M92KH
• Winfree, Erik (2003) Simulations of Computing by Self-Assembly; 10.7907/Z9TB14X7
• 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
• 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 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
• 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
• 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
• 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
• 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
• 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
• Chen, Kevin and Winfree, Erik (2000) Error Correction in DNA Computing: Misclassification and Strand Loss; ISBN 9780821820537; DNA Based Computers V; 49-63
• 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
• 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
• 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
• Winfree, Erik and Liu, Furong, et el. (1998) Design and self-assembly of two-dimensional DNA crystals; Nature; Vol. 394; No. 6693; 539-544; 10.1038/28998
• 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) Complexity of Restricted and Unrestricted Models of Molecular Computation; ISBN 0821805185; DNA based computers; 187-198
• Winfree, Erik (1996) On the Computational Power of DNA Annealing and Ligation; ISBN 0821805185; DNA Based Computers; 199-221
• Winfree, A. T. and Winfree, E. M., et el. (1985) Organizing centers in a cellular excitable medium; Physica D; Vol. 17; No. 1; 109-115; 10.1016/0167-2789(85)90138-1