Winfree, Erik

Article from CaltechAUTHORS

Evans, Constantine Glen and O'Brien, Jackson, el al. (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, el al. (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
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, el al. (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, el al. (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, el al. (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
Johnson, Robert and Dong, Qing, el al. (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, el al. (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, el al. (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, el al. (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, el al. (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
Srinivas, Niranjan and Parkin, James, el al. (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, el al. (2017) A cargo-sorting DNA robot; Science; Vol. 357; No. 6356; Art. No. eaan6558; 10.1126/science.aan6558
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
Hariadi, Rizal F. and Winfree, Erik, el al. (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
Schulman, Rebecca and Wright, Christina, el al. (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, el al. (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
Weitz, Maximilian and Kim, Jongmin, el al. (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., el al. (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., el al. (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
Subsoontorn, Pakpoom and Kim, Jongmin, el al. (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., el al. (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, el al. (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, el al. (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, el al. (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
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
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., el al. (2010) Molecular robots guided by prescriptive landscapes; Nature; Vol. 465; No. 7295; 206-210; 10.1038/nature09012
Soloveichik, David and Seelig, Georg, el al. (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, el al. (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, el al. (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
Barish, Robert D. and Schulman, Rebecca, el al. (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
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, el al. (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
Fujibayashi, Kenichi and Hariadi, Rizal, el al. (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, el al. (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
Zhang, David Yu and Turberfield, Andrew J., el al. (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
Chen, Ho-Lin and Schulman, Rebecca, el al. (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., el al. (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., el al. (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., el al. (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, el al. (2006) Enzyme-free nucleic acid logic circuits; Science; Vol. 314; No. 5805; 1585-1588; 10.1126/science.1132493
Seelig, Georg and Yurke, Bernard, el al. (2006) Catalyzed relaxation of a metastable DNA fuel; Journal of the American Chemical Society; Vol. 128; No. 37; 12211-12220; 10.1021/ja0635635
Barish, Robert D. and Rothemund, Paul W. K., el al. (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
Rothemund, Paul W. K. and Ekani-Nkodo, Axel, el al. (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, el al. (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, el al. (2004) Paradigms for computational nucleic acid design; Nucleic Acids Research; Vol. 32; No. 4; 1392-1403; PMCID PMC390280; 10.1093/nar/gkh291
Kim, Jongmin and Hopfield, John J., el al. (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
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 (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, el al. (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
Seeman, Nadrian C. and Liu, Furong, el al. (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., el al. (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 Liu, Furong, el al. (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, el al. (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, A. T. and Winfree, E. M., el al. (1985) Organizing centers in a cellular excitable medium; Physica D; Vol. 17; No. 1; 109-115; 10.1016/0167-2789(85)90138-1