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Items: 46

1.

Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems.

Berleant J, Berlind C, Badelt S, Dannenberg F, Schaeffer J, Winfree E.

J R Soc Interface. 2018 Dec 21;15(149):20180107. doi: 10.1098/rsif.2018.0107.

2.

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly.

Woods D, Doty D, Myhrvold C, Hui J, Zhou F, Yin P, Winfree E.

Nature. 2019 Mar;567(7748):366-372. doi: 10.1038/s41586-019-1014-9. Epub 2019 Mar 20.

PMID:
30894725
3.

Effective design principles for leakless strand displacement systems.

Wang B, Thachuk C, Ellington AD, Winfree E, Soloveichik D.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12182-E12191. doi: 10.1073/pnas.1806859115. Epub 2018 Dec 13.

PMID:
30545914
4.

Enzyme-free nucleic acid dynamical systems.

Srinivas N, Parkin J, Seelig G, Winfree E, Soloveichik D.

Science. 2017 Dec 15;358(6369). pii: eaal2052. doi: 10.1126/science.aal2052.

PMID:
29242317
5.

A cargo-sorting DNA robot.

Thubagere AJ, Li W, Johnson RF, Chen Z, Doroudi S, Lee YL, Izatt G, Wittman S, Srinivas N, Woods D, Winfree E, Qian L.

Science. 2017 Sep 15;357(6356). pii: eaan6558. doi: 10.1126/science.aan6558.

PMID:
28912216
6.

Physical principles for DNA tile self-assembly.

Evans CG, Winfree E.

Chem Soc Rev. 2017 Jun 19;46(12):3808-3829. doi: 10.1039/c6cs00745g. Review.

PMID:
28489096
7.

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics.

Hariadi RF, Winfree E, Yurke B.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):E6086-95. doi: 10.1073/pnas.1424673112. Epub 2015 Oct 26.

8.

Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly.

Schulman R, Wright C, Winfree E.

ACS Nano. 2015 Jun 23;9(6):5760-71. doi: 10.1021/nn507493s. Epub 2015 May 12.

PMID:
25965580
9.

Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements.

Hariadi RF, Yurke B, Winfree E.

Chem Sci. 2015 Apr 1;6(4):2252-2267. doi: 10.1039/c3sc53331j. Epub 2015 Feb 20.

10.

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator.

Weitz M, Kim J, Kapsner K, Winfree E, Franco E, Simmel FC.

Nat Chem. 2014 Apr;6(4):295-302. doi: 10.1038/nchem.1869. Epub 2014 Feb 16. Erratum in: Nat Chem. 2014 May;6(5):453.

PMID:
24651195
11.

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

Srinivas N, Ouldridge TE, Sulc P, Schaeffer JM, Yurke B, Louis AA, Doye JP, Winfree E.

Nucleic Acids Res. 2013 Dec;41(22):10641-58. doi: 10.1093/nar/gkt801. Epub 2013 Sep 9.

12.

Integrating DNA strand-displacement circuitry with DNA tile self-assembly.

Zhang DY, Hariadi RF, Choi HM, Winfree E.

Nat Commun. 2013;4:1965. doi: 10.1038/ncomms2965.

13.

Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch.

Subsoontorn P, Kim J, Winfree E.

ACS Synth Biol. 2012 Aug 17;1(8):299-316. doi: 10.1021/sb300018h. Epub 2012 Jun 26.

PMID:
23651285
14.

Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level.

Evans CG, Hariadi RF, Winfree E.

J Am Chem Soc. 2012 Jun 27;134(25):10485-92. doi: 10.1021/ja301026z. Epub 2012 Jun 13.

PMID:
22694312
15.

Robust self-replication of combinatorial information via crystal growth and scission.

Schulman R, Yurke B, Winfree E.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6405-10. doi: 10.1073/pnas.1117813109. Epub 2012 Apr 9.

16.

Timing molecular motion and production with a synthetic transcriptional clock.

Franco E, Friedrichs E, Kim J, Jungmann R, Murray R, Winfree E, Simmel FC.

Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):E784-93. doi: 10.1073/pnas.1100060108. Epub 2011 Sep 15.

17.

Neural network computation with DNA strand displacement cascades.

Qian L, Winfree E, Bruck J.

Nature. 2011 Jul 20;475(7356):368-72. doi: 10.1038/nature10262.

PMID:
21776082
18.

Scaling up digital circuit computation with DNA strand displacement cascades.

Qian L, Winfree E.

Science. 2011 Jun 3;332(6034):1196-201. doi: 10.1126/science.1200520.

19.

A simple DNA gate motif for synthesizing large-scale circuits.

Qian L, Winfree E.

J R Soc Interface. 2011 Sep 7;8(62):1281-97. doi: 10.1098/rsif.2010.0729. Epub 2011 Feb 4.

20.

Synthetic in vitro transcriptional oscillators.

Kim J, Winfree E.

Mol Syst Biol. 2011 Feb 1;7:465. doi: 10.1038/msb.2010.119.

21.

Molecular robots guided by prescriptive landscapes.

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.

Nature. 2010 May 13;465(7295):206-10. doi: 10.1038/nature09012.

22.

DNA as a universal substrate for chemical kinetics.

Soloveichik D, Seelig G, Winfree E.

Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5393-8. doi: 10.1073/pnas.0909380107. Epub 2010 Mar 4.

23.

Robustness and modularity properties of a non-covalent DNA catalytic reaction.

Zhang DY, Winfree E.

Nucleic Acids Res. 2010 Jul;38(12):4182-97. doi: 10.1093/nar/gkq088. Epub 2010 Mar 1.

24.

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates.

Maune HT, Han SP, Barish RD, Bockrath M, Goddard WA III, Rothemund PW, Winfree E.

Nat Nanotechnol. 2010 Jan;5(1):61-6. doi: 10.1038/nnano.2009.311. Epub 2009 Nov 8.

PMID:
19898497
25.

Control of DNA strand displacement kinetics using toehold exchange.

Zhang DY, Winfree E.

J Am Chem Soc. 2009 Dec 2;131(47):17303-14. doi: 10.1021/ja906987s.

PMID:
19894722
26.

An information-bearing seed for nucleating algorithmic self-assembly.

Barish RD, Schulman R, Rothemund PW, Winfree E.

Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6054-9. doi: 10.1073/pnas.0808736106. Epub 2009 Mar 24.

27.

Dynamic allosteric control of noncovalent DNA catalysis reactions.

Zhang DY, Winfree E.

J Am Chem Soc. 2008 Oct 22;130(42):13921-6. doi: 10.1021/ja803318t. Epub 2008 Sep 20.

PMID:
18823118
28.

An autonomous polymerization motor powered by DNA hybridization.

Venkataraman S, Dirks RM, Rothemund PW, Winfree E, Pierce NA.

Nat Nanotechnol. 2007 Aug;2(8):490-4. doi: 10.1038/nnano.2007.225. Epub 2007 Jul 29.

PMID:
18654346
29.

Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern.

Fujibayashi K, Hariadi R, Park SH, Winfree E, Murata S.

Nano Lett. 2008 Jul;8(7):1791-7. Epub 2007 Dec 28. Erratum in: Nano Lett. 2008 Oct;8(10):3554.

PMID:
18162000
30.

Engineering entropy-driven reactions and networks catalyzed by DNA.

Zhang DY, Turberfield AJ, Yurke B, Winfree E.

Science. 2007 Nov 16;318(5853):1121-5. Erratum in: Science. 2009 Dec 18;326(5960):1633.

31.

Synthesis of crystals with a programmable kinetic barrier to nucleation.

Schulman R, Winfree E.

Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15236-41. Epub 2007 Sep 19.

32.

Reducing facet nucleation during algorithmic self-assembly.

Chen HL, Schulman R, Goel A, Winfree E.

Nano Lett. 2007 Sep;7(9):2913-9. Epub 2007 Aug 24.

PMID:
17718529
33.

Construction of an in vitro bistable circuit from synthetic transcriptional switches.

Kim J, White KS, Winfree E.

Mol Syst Biol. 2006;2:68. Epub 2006 Dec 12.

34.

Enzyme-free nucleic acid logic circuits.

Seelig G, Soloveichik D, Zhang DY, Winfree E.

Science. 2006 Dec 8;314(5805):1585-8.

35.

Catalyzed relaxation of a metastable DNA fuel.

Seelig G, Yurke B, Winfree E.

J Am Chem Soc. 2006 Sep 20;128(37):12211-20.

PMID:
16967972
36.

Two computational primitives for algorithmic self-assembly: copying and counting.

Barish RD, Rothemund PW, Winfree E.

Nano Lett. 2005 Dec;5(12):2586-92.

PMID:
16351220
37.

Design and characterization of programmable DNA nanotubes.

Rothemund PW, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E.

J Am Chem Soc. 2004 Dec 22;126(50):16344-52. Erratum in: J Am Chem Soc. 2013 Feb 20;135(7):2864.

PMID:
15600335
38.

Algorithmic self-assembly of DNA Sierpinski triangles.

Rothemund PW, Papadakis N, Winfree E.

PLoS Biol. 2004 Dec;2(12):e424. Epub 2004 Dec 7.

39.

Paradigms for computational nucleic acid design.

Dirks RM, Lin M, Winfree E, Pierce NA.

Nucleic Acids Res. 2004 Feb 27;32(4):1392-403. Print 2004.

40.

Protein design is NP-hard.

Pierce NA, Winfree E.

Protein Eng. 2002 Oct;15(10):779-82.

PMID:
12468711
41.

Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments.

Winfree E.

J Biomol Struct Dyn. 2000;17 Suppl 1:263-70.

PMID:
22607433
42.

Two dimensions and two States in DNA nanotechnology.

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.

J Biomol Struct Dyn. 2000;17 Suppl 1:253-62.

PMID:
22607432
43.

On the reduction of errors in DNA computation.

Roweis S, Winfree E.

J Comput Biol. 1999 Spring;6(1):65-75.

PMID:
10223665
44.

On applying molecular computation to the data encryption standard.

Adleman LM, Rothemund PW, Roweis S, Winfree E.

J Comput Biol. 1999 Spring;6(1):53-63.

PMID:
10223664
45.

A sticker-based model for DNA computation.

Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PW, Adleman LM.

J Comput Biol. 1998 Winter;5(4):615-29.

PMID:
10072080
46.

Design and self-assembly of two-dimensional DNA crystals.

Winfree E, Liu F, Wenzler LA, Seeman NC.

Nature. 1998 Aug 6;394(6693):539-44.

PMID:
9707114

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