Papers
by Reif on Biomolecular Computing and Self Assembly of DNA Nanostructures (105
papers)
1. John H.
Reif, Parallel Biomolecular Computation: Models and Simulations. Proceedings:
7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'95)
Santa Barbara, CA, July 1995, pp. 213-223. Published in Algorithmica, special
issue on Computational Biology, Vol. 25, No. 2, 142-176, 1999. [PDF] [PostScript] and [PostScriptFigures]
2. John H.
Reif, Local Parallel Biomolecular Computation, Proc. DNA-Based Computers, III:
University of Pennsylvania, June 23-26, 1997. DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, H. Rubin and D. H. Wood, editors.
American Mathematical Society, Providence, RI, vol. 48, 1999, pp. 217-254. [PDF] Revised as
invited paper of special issue "Biomolecular Computing - From Theory to
Practical Applications" of International Journal of
Unconventional Computing, Vol. 8, pp. 459-507 (2014). [PDF] or [PDF]
3. John H.
Reif, Paradigms for Biomolecular Computation, First International Conference on Unconventional Models of Computation,
Auckland, New Zealand, January 5-9, 1998, Unconventional Models of Computation, (edited
by C.S. Calude, J. Casti, and M.J. Dinneen), DMTCS Series, Springer-Verlag,
Singapore,
January 1998, pp. 72-93. [PostScript] [PDF]
4. A. Gehani
and John H. Reif, Micro Flow Bio-Molecular Computation, 4th DIMACS Workshop on
DNA Based Computers, University of Pennsylvania, June 15-19, 1998. DNA Based Computers, IV, DIMACS Series in
Discrete Mathematics and Theoretical Computer Science, (ed. H. Rubin),
American Mathematical Society, 1999. Also in a special issue of Biosystems,
Journal of Biological and Informational Processing Sciences, Vol. 52, Nos. 1-3,
(Edited By L. Kari, H. Rubin, and D. H. Wood), pp. 197-216, (October 1999). [PostScript] [PDF] or [PDF] Talk: [PDF]
5. John H.
Reif, Alternative Computational Models: A Comparison of Biomolecular and
Quantum Computation, Invited paper, 18th International
Conference on Foundations of Software Technology and Theoretical Computer
Science (FSTTCS1998), Chennai, India (December, 17-19, 1998). [PDF]
6. Thomas H.
LaBean, Hao Yan, Jens Kopatsch, Furong Liu, Erik Winfree, John H. Reif and
Nadrian C. Seeman, The construction, analysis, ligation and self-assembly of
DNA triple crossover complexes, Journal
of American Chemistry Society (JACS) 122, pp. 1848-1860 (2000). [PDF]
7. Ashish Gehani, Thomas H. LaBean, and John H.
Reif, DNA-based Cryptography, Proc. DNA Based Computers V: Cambridge, MA, June
14-16, 1999. Published in DIMACS Series in Discrete Mathematics and Theoretical
Computer Science, Volume 54, edited by Erik Winfree and D.K. Gifford, American
Mathematical Society, Providence, RI, pp. 233-249, (2000). [PDF] Talk: [PDF]. Published
as an invited chapter in "Aspects of Molecular
Computing - Essays dedicated to Tom Head on the occasion of his 70th
Birthday", Springer Verlag
series in Natural Computing (edited
by N. Jonoska, G. Paun and G. Rozenberg) LNCS 2950 Festschrift,
Springer, pp. 167-188, (2004). [PDF]
8. Thomas H. LaBean, Erik Winfree, and John H. Reif,
Experimental Progress in Computation by Self-Assembly of DNA Tilings,
Proceeding of DNA Based Computers V: Cambridge, MA, June 14-16, 1999. Published
in DIMACS Series in Discrete Mathematics and Theoretical Computer Science,
Volume 54, edited by Erik Winfree and D.K. Gifford, American Mathematical
Society, Providence, RI, pp. 123-140, (2000). [PostScript] [PDF] Talk: [HTML Lecture]
9. John H. Reif
and Thomas H. LaBean, and Nadrian C. Seeman. Programmable Assembly at the
Molecular Scale: Self-Assembly of DNA Lattices, Invited paper, 2001 IEEE
International Conference on Robotics and Automation (ICRA2001), Seoul, Korea, ed. Lee Beom (May,
2001). [PDF]
10.
John H. Reif and Thomas H.
LaBean, Computationally Inspired Biotechnologies: Improved DNA Synthesis and
Associative Search Using Error-Correcting Codes and Vector-Quantization, Sixth
International Meeting on DNA Based Computers (DNA6), Leiden, The Netherlands (June 2000). DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, Edited by A. Condon and G.
Rozenberg. Lecture Notes in Computer Science, Springer-Verlag, Berlin
Heidelberg, vol. 2054, pp. 145-172 (2001) [PostScript] [PDF] Talk: [PDF]
11.
John H. Reif, Thomas H. LaBean, and Nadrian C. Seeman,
Challenges and Applications for Self-Assembled DNA Nanostructures, Proc. Sixth
International Workshop on DNA-Based Computers, Leiden, The Netherlands, June
13-17, 2000. Published in DIMACS Series in Discrete Mathematics and Theoretical
Computer Science, Edited by A. Condon and G. Rozenberg. Lecture Notes in
Computer Science, Springer-Verlag, Berlin Heidelberg, vol. 2054, 2001, pp. 173-198. [PostScript] [PDF] Talk: [PDF] [PPT]
12.
Chengde Mao, Thomas H. LaBean,
John H. Reif, Nadrian C. Seeman, Logical Computation Using Algorithmic
Self-Assembly of DNA Triple-Crossover Molecules, Nature, vol. 407, pp. 493-495
(Sept. 28 2000); C. Erratum: Nature 408, 750-750 (2000). [PDF] or [PDF]
13.
John H. Reif, Thomas H. LaBean, M. Pirrung, V. Rana, B. Guo,
K. Kingsford, and G. Wickham, Experimental Construction of Very Large Scale DNA
Databases with Associative Search Capability, Seventh International Meeting on
DNA Based Computers (DNA7), Tampa,
FL, June 11-13, 2001. Lecture Notes in Computer
Science, Springer-Verlag, New York, Volume 2340, pp. 231-247, (2002). [PostScript] [PDF] Talk: [PDF] [PPT]. Also
published as John H. Reif, Michael Hauser, Michael
Pirrung, and Thomas LaBean, Application of Biomolecular Computing to Medical
Science: A Biomedical Database System for Storage and Retrieval of Genetic
Information and Material, Chapter 3 of Complex
Systems Science in Biomedicine (Edited by Thomas S.
Deisboeck and J. Yasha Kresh),
International Topics in Biomedical Engineering Series,
Springer Publishers, New York, Chapter 3,
pp. 701-735, (2005). ISBN: 0-387-30241-7.
[PDF] or [PDF]. Talk: [PDF][PPT]
14.
John H. Reif, DNA Lattices: A
Method for Molecular Scale Patterning and Computation, special issue on
Bio-Computation, Computer and Scientific Engineering Magazine, IEEE Computer
Society, Vol. 4, No. 1, February 2002, pp. 32-41. [PostScript][PDF]
15.
John H. Reif, The Emerging Discipline of Biomolecular
Computation in the US, invited paper to the special
issue on Biomolecular Computing, New Generation Computing, edited by
Masami Hagiya, Masayuki Yamamura, and Tom Head, Vol. 20, No. 3, pp. 217-236,
(2002). [PostScript][PDF] or [PDF]
16.
John H. Reif,
Molecular Assembly and Computation: From Theory to Experimental Demonstrations,
plenary paper, Twenty Ninth International Colloquium on Automata, Languages,
and Programming(ICALP), Málaga, Spain (July 8, 2002). Lecture Notes in Computer
Science, New York, Volume 2380, pp. 1-21, (2002). [PostScript][PDF] Talk: [PDF] [PPT]
17.
John H. Reif, The Design of Autonomous DNA
Nanomechanical Devices: Walking and Rolling DNA. DNA Based Computers (DNA8),
Sapporo, Japan, June 10-13, 2002, (Edited by Masami Hagiya and Azuma Ohuchi),
Lecture Notes in Computer Science, No. 2568, Springer-Verlag, New York, (2003),
pp. 22-37. Published in Natural Computing, DNA8 special issue, Vol. 2, p
439-461, (2003). [PDF]
or [PostScript][PDF]
Talk: [PDF]
18.
Dage Liu, John H.
Reif, Thomas H. LaBean, DNA Nanotubes, Construction and Characterization of
Filaments Composed of TX-tile Lattice. DNA Based Computers (DNA8), Sapporo, Japan, June 10-13, 2002,
(Edited by Masami Hagiya and Azuma Ohuchi), Lecture Notes in Computer Science,
No. 2568, Springer-Verlag, New York, (2003), pp. 10-21. Published
as DNA nanotubes self-assembled from
triple-crossover tiles as templates for conductive nanowires, Proceedings
of the National Academy of Science(PNAS),
Vol. 101, No. 3, pp. 717-722, (January
20, 2004).
PubMed PMID: 14709674. [PDF]
19.
John H. Reif, DNA Computation - Perspectives:
Successes and Challenges, Science, 296: 478-479, April 19, 2002. PubMed
PMID: 11964464. [PostScript][PDF]
20.
Hao Yan, Thomas H. LaBean, Liping Feng, and John H. Reif,
Directed Nucleation Assembly of Barcode Patterned DNA Lattices, Proceedings of the National Academy of Science(PNAS), Volume
100, No. 14, pp. 8103-8108, July 8, (2003). PubMed
PMID: 12821776. [PostScript] [PDF]
21.
Hao Yan, Liping Feng, Thomas H.
LaBean, and John Reif, DNA Nanotubes, Parallel Molecular Computation of Pair-Wise XOR Using DNA
String Tile, Ninth International Meeting
on DNA Based Computers (DNA9), Madison, Wisconsin, June 2-4, 2003,
(Edited by Junghuei Chen and John Reif),
Abstract in Lecture Notes in Computer Science, Springer-Verlag, New York,
(2003). Published as Parallel Molecular Computations of Pairwise
Exclusive-Or (XOR) Using DNA "String Tile" Self-Assembly in Journal of American Chemistry Society (JACS), Vol. 125, No. 47, pp. 14246-14247, 2003. PubMed
PMID: 14624551. [PDF] or [PDF]; Supporting Information: [PDF]
22.
Hao Yan, Sung Ha Park, Liping Feng, John Reif, and Thomas H.
LaBean, 4x4 DNA
Tile and Lattices: Characterization, Self-Assembly and Metallization of a Novel
DNA Nanostructure Motif, Ninth
International Meeting on DNA
Based Computers (DNA9), Madison, Wisconsin, June 2-4, 2003, (Edited by Junghuei
Chen and John Reif), Lecture Notes in Computer
Science, Springer-Verlag, New York, (2003). Published as Hao Yan, Sung Ha Park,
Gleb Finkelstein, John H. Reif, and Thomas H. LaBean, DNA-Templated Self-Assembly of Protein
Arrays and Highly Conductive Nanowires, Science, Vol. 301, pp. 1882-1884, Sep 26 2003. PubMed
PMID: 14512621. [PDF]
Supplemental Information: [PDF]
23.
Liping Feng, Sung Ha Park, John H. Reif, and Hao Yan, A
Two-State DNA Lattice Switched by DNA Nanoactuator, Angewandte Chemie
[International Edition], Vol. 42, pp. 4342-4346, Sept. 2003. PubMed
PMID: 14502706. [PDF]
Supplemental Information: [PDF]
24.
H. Li, S.H. Park,
John H. Reif, Thomas H. LaBean, Hao Yan, DNA-Templated Self-Assembly of Protein
and Nanoparticle Linear Arrays,
Journal of American Chemistry Society (JACS), Vol.
126, No. 2, pp. 418-419, 2004. PubMed PMID:
14719910. [PDF]. Supporting Information: [PDF]
25.
John H. Reif, Sudheer Sahu, Peng Yin, Compact
Error-Resilient Computational DNA Tiling Assemblies, Tenth
International Meeting on DNA
Based Computers (DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science (Edited by C Ferretti, G. Mauri and C.
Zandron), Vol. 3384, Springer-Verlag, New York, (2005), pp. 293-307. Published as an invited chapter in text "Nanotechnology: Science and Computation”, Springer Verlag series in Natural
Computing (edited by
J. Chen; N. Jonoska and G. Rozenberg),
Springer-Verlag Berlin, Germany, pp. 79-104, 2006. [PDF] Talk: [PDF] [PPT]
26.
Peng Yin, Andrew J.
Turberfield, Sudheer Sahu, John H. Reif, Designs for Autonomous Unidirectional
Walking DNA Devices, Tenth International Meeting on DNA Based Computers (DNA10), Milano,
Italy, June 7-10, 2004. Lecture Notes in Computer
Science (Edited by C Ferretti, G. Mauri and C.
Zandron), Vol. 3384, Springer-Verlag, New York, (2005), pp. 410-425. [PDF] Talk: [PDF] [PPT]
27.
Peng Yin, Hao Yan, Xiaoju G. Daniel, Andrew J.
Turberfield, John H. Reif, A Unidirectional DNA Walker Moving Autonomously
Along a Linear Track, Angewandte
Chemie [International Edition],
Volume 43, Number 37, Sept. 20, 2004, pp. 4906-4911.
PubMed PMID: 15372637. [PDF] or [PDF] Supplemental Information: [PDF] Abstract: [PDF] Talk: [PDF] [PPT]
28.
Peng Yin, Andrew J. Turberfield, John H. Reif, Design of an
Autonomous DNA Nanomechanical Device Capable of Universal Computation and
Universal Translational Motion, Tenth International
Meeting on DNA Based Computers
(DNA10), (Edited by C Ferretti, G. Mauri and C. Zandron), Milano,
Italy, June 7-10, 2004. Lecture Notes in Computer
Science(LNCS), Number 3384, Springer-Verlag, New York, (2005), pp. 426-444. [PDF] Talk: [PDF] [PPT]
29.
Peng Yin, Bo Guo, Christina Belmore, Will Palmeri, Erik
Winfree, Thomas H. LaBean, John H. Reif, TileSoft: Sequence Optimization
Software For Designing DNA Secondary Structures, Duke University Computer Science Department Technical Report
TR-CS-2004-09.
Poster Abstract, Preliminary Proceedings,
Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy,
(June 7-10, 2004). [PDF] Talk: [PDF] [PPT]
30.
John H. Reif,
DNA-Based Nano-Engineering: DNA and its Enzymes as the Engines of Creation at
the Molecular Scale, Invited Talk, Abstract,
Preliminary Proceedings, Tenth International Meeting on DNA Based Computers
(DNA10), Milano, Italy, (June 7-10, 2004).
Abstract: [PDF] Talk: [PDF] [PPT]
31.
John H. Reif, Thomas LaBean, Sudheer Sahu, Hao Yan, Peng Yin,
Design, Simulation, and Experimental Demonstration of Self-Assembled DNA
Nanostructures and DNA Motors, Unconventional Programming
Paradigms: International Workshop UPP 2004, Le Mont Saint Michel, France,
September 15-17, 2004. Published
by Springer-Verlag Berlin Heidelberg, edited by Jean-Pierre
Banâtre, Pascal Fradet, Jean-Louis Giavitto, Olivier Michel, Lecture Notes for
Computer Science (LNCS) 3566, pp. 173-187, (2005). [PDF] Talk: [PDF] [PPT]
32.
Sung Ha Park, Hao Yan, John H. Reif, Thomas H
LaBean, and Gleb Finkelstein, Electronic nanostructures templated on
self-assembled DNA scaffolds, Nanotechnology 15 pp. S525–S527 (2004). [PDF]
33.
Hao Yan, Peng Yin, Sung Ha Park, Hanying Li,
Liping Feng, Xiaoju Guan, Dage Liu, John H. Reif, & Thomas H. LaBean (2004)
Self-Assembled DNA Structures for
Nanoconstruction. International Symposium on DNA-Based Molecular
Electronics, Jena, Germany, May, 2004. Fritzsche, W. eds. AIP Conference
Proceedings, 725, American
Institute of Physics. pp. 43-52. [PDF]
34.
Sung Ha Park, Peng Yin, Yan Liu,
John H. Reif, Thomas LaBean, and Hao Yan, Programmable DNA Self-assemblies for
Nanoscale Organization of Ligands and Proteins, Nano Letters (Communication),
Volume 5, Number 4, pp. 729-733, (2005). PubMed PMID:15826117.
[PDF]; Supplemental Information: [PDF]
35.
Sung Ha Park, Robert Barish, Hanying
Li, John Reif, Gleb Finkelstein, Hao Yan and Thomas LaBean, Three-Helix Bundle
DNA Tiles Self-Assemble into 2D Lattice or 1D Templates for Silver Nanowires,
Nano Letters (Communication), Volume 5, Number 4, pp. 693-696 (2005). PubMed
PMID:15826110. [PDF] Supplemental Information: [PDF]
36.
Sung Ha Park, Constantin Pistol, Sang Jung Ahn, John H.
Reif, Alvin R. Lebeck, Chris Dwyer, and Thomas H. LaBean, Finite-Size, Fully Addressable DNA Tile
Lattices Formed by Hierarchical Assembly Procedures,
Angewandte Chemie
[International Edition], Volume 45, Issue 5, pp. 735-739, January 23, 2006.
DOI: 10.1002/anie.200503797. [PDF]
37.
John H. Reif, Sudheer Sahu, and Peng Yin, Complexity
of Graph Self-Assembly in Accretive Systems and Self-Destructible Systems, Eleventh International Meeting on DNA Based
Computers (DNA11), London, Ontario, Canada
(June, 2005). Springer-Verlag Lecture Notes for Computer Science (LNCS), NYC,
NY, (edited by Alessandra Carbone and Niles Pierce),
Vol. 3892, Springer-Verlag, New York, (2006), pp. 257-274 [PDF]. Talk: [PPT]. Published
in Theoretical Computer Science, Volume 412, pp 1592-1605, (2011). DOI
information: 10.1016/j.tcs.2010.10.034 [PDF].
38.
Peng Yin, Andrew J. Turberfield, John H. Reif, Design of
Autonomous DNA Cellular Automata,
Eleventh International Meeting on DNA
Based Computers (DNA11), London, Ontario, Canada (June, 2005). Springer-Verlag
Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Alessandra
Carbone and Niles Pierce), Vol. 3892,
Springer-Verlag, New York, (2006), pp. 399-416 [PDF].
39.
Sudheer Sahu, Peng Yin and John H. Reif, A
Self-Assembly Model of Time-Dependent Glue Strength, Eleventh International
Meeting on DNA Based Computers
(DNA11), London, Ontario, Canada (June, 2005). Springer-Verlag Lecture Notes
for Computer Science (LNCS), NYC, NY, (edited by Alessandra Carbone
and Niles Pierce), Vol. 3892,
Springer-Verlag, New York, pp. 290-304
(2006). Invited Chapter in "Algorithmic
Bioprocesses" (edited by A.Condon, D.Harel, J.N.Kok, A.Salomaa, and
E.Winfree), Published by Springer-Verlag, ISBN:
978-3-540-88868-0, pp. 185-204
(2009). [PDF] [PDF] Talk: [PPT]
40.
Peng Yin, Sudheer
Sahu, Rizal Hariadi, Harry M. T. Choi, Sung Ha Park, Bethany Walters, Thomas H.
LaBean, John H. Reif, On Constructing Tile-less DNA Ribbons and Tubes, Abstract,
Preliminary Proceedings, 12th International Meeting on DNA Computing (DNA12),
Seoul, Korea (June 5-9, 2006).
[PDF] Published as: Peng Yin, Rizal F.
Hariadi, Sudheer Sahu, Harry M.T.Choi, Sung Ha Park, Thomas H. LaBean, John H.
Reif, Programming DNA Tube Circumferences, Science, Vol. 321. no. 5890, pp.
824–826 (August 8, 2008). DOI: 10.1126/science.1157312. [PDF] Supplemental Information: [PDF]
41.
Sudheer Sahu and John H. Reif, Capabilities and Limits of
Compact Error Resilience Methods for Algorithmic Self-Assembly in Two and Three
Dimensions, 12th International Meeting on DNA Computing (DNA 12), Seoul, Korea,
June 5-9, 2006. Published in DNA Computing: DNA12, Springer-Verlag Lecture
Notes for Computer Science (LNCS), Volume 4287 (edited by Chengde Mao and
Takashi Yokomori), Springer, Berlin Heidelberg, pp. 223-238 (2006). DNA12
Version: [PDF]. Talk: [PPT]. Published in
Algorithmica, Volume 56, Issue 4, pp. 480-504, Springer New York (April
2010), Full Paper: [PDF] [Error! Hyperlink reference not valid.].
42.
Sudheer Sahu, Bei
Wang, Peng Yin, John H. Reif, A Framework for Modeling
DNA based Molecular Systems, 12th
International Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006.
Published in DNA Computing: DNA12,
Springer-Verlag Lecture Notes for
Computer Science (LNCS), Volume 4287 (edited by Chengde
Mao and Takashi Yokomori), Springer,
Berlin Heidelberg, pp.
250-265 (2006).
DNA12 Version: [PDF]. Sudheer Sahu, Bei Wang, John H. Reif, A
Framework for Modeling DNA based Molecular Systems. Published as Sudheer
Sahu, Bei Wang, John H. Reif, A Framework for Modeling DNA based Molecular
Systems. Computational and Theoretical Nanoscience, Volume 5, Number 11, pp. 2124-2134(11) (November 2008). Full Paper: [PDF] Presentation: [PPT]
43.
Urmi Majumder, Sudheer Sahu, Thomas LaBean, and John H.
Reif, Design and Simulation of Self-Repairing DNA Lattices, 12th International
Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006, DNA Computing:
DNA12, Springer-Verlag Lecture Notes for Computer Science (LNCS), Volume 4287
(edited by Chengde Mao and Takashi Yokomori),
Springer, Berlin Heidelberg, pp. 195–214,
(2006). DNA12 Version: [PDF]
Poster: [PDF].
Revised paper: Urmi Majumder, Sudheer Sahu, Thomas LaBean, and John H.
Reif, Toward Compact Inherently Self-Repairing DNA Lattices Using
Reversibility, submitted for journal publication (2012). [PDF]
44.
Thomas H. LaBean, Kurt V. Gothelf, and John H. Reif,
Self-assembling DNA Nanostructures for Patterned Molecular Assembly, invited
chapter 5 in Nanobiotechnology II:
More Concepts and Applications, (edited by Chad A. Mirkin and
Christof M. Niemeyer), John Wiley & Sons Publishers, pp. 79-97, (2007). [PDF]
DOI:
10.1002/9783527610389.ch5
45.
John H. Reif and Thomas H.
LaBean, Autonomous Programmable
Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited paper, Fourteenth
Workshop on Logic, Language, Information and Computation (WoLLIC'2007), Rio de
Janeiro, Brazil, July 2-5, 2007, Springer-Verlag
Lecture Notes for Computer Science (LNCS), Volume
4576 - 0297, pp. 297-306. Published
in Communications of the ACM (CACM), Special
Section entitled “New Computing Paradigms (edited by Toshinori Munakata), Volume
50, Issue 9, pp. 46-53 (Sept 2007). Short version [PDF] Extended version [PDF] Talk: [PPT] [PDF]
46.
John H. Reif and
Thomas
H. LaBean, DNA
Nanotechnology and its Biological Applications. In
book “Bio-inspired
and Nanoscale Integrated Computing”, Chapter
13, pp. 349-375 (edited by Mary Mehrnoosh
Eshaghian-Wilner), Publisher:
Wiley, Hoboken, NJ, USA,
(February 2009). [PDF]
47.
John H. Reif and Sudheer Sahu, Autonomous
Programmable DNA Nanorobotic Devices Using DNAzymes, 13th
International Meeting on DNA Computing (DNA 13), Memphis, Tennessee,
June 4-8, 2007. In DNA Computing: DNA13
(edited by Max
Garzon and Hao Yan), Springer-Verlag Lecture Notes for
Computer Science (LNCS), Springer, Berlin
Heidelberg, Volume 4848, pp. 66-78
(2008). DNA13
Version: [PDF] Talk: [PDF]. Published in Special
Journal Issue on Self-Assembly, Theoretical
Computer Science (TCS), Vol 410, Issue 15, pp. 1428-1439 (April 2009). Full Paper: [PDF] [PDF].
48. Urmi Majumder, Thomas H
LaBean, and John H. Reif, Activatable Tiles for Compact Error-Resilient
Directional Assembly. 13th International Meeting on DNA Computing (DNA 13),
Memphis, Tennessee, June 4-8, 2007. Conference Version: Activatable Tiles:
Compact, Robust Programmable Assembly and Other Applications, in DNA Computing:
DNA13 (edited by Max Garzon and Hao Yan), Springer-Verlag Lecture Notes for
Computer Science (LNCS), Springer, Berlin Heidelberg, Volume 4848, pp. 15-25,
(2008). [PDF] Talk: [PPT]. Published as: Urmi
Majumder, Sudhanshu Garg, Thomas H LaBean, and John H. Reif, Activatable Tiles for
Compact Robust Programmable Molecular Assembly and Other Applications, Natural Computing, Volume 15, Issue
4, pp 611–634 (December 2016). DOI
10.1007/s11047-015-9532-3 [PDF] [PDF]
49. Urmi
Majumder, John H. Reif, and Sudheer Sahu, Stochastic Analysis of Reversible
Self-Assembly. Journal of
Computational and Theoretical Nanoscience, Volume 5, Number 7, pp. 1289-1305,
July 2008. Full Paper: [PDF] [PDF].
50.
John H. Reif and
Urmi Majumder, Isothermal Reactivating Whiplash PCR
for Locally Programmable Molecular Computation, Fourteenth
International Meeting on DNA Based Computers (DNA14),
Prague, Czech Republic (June, 2008). Lecture Notes for Computer Science
(LNCS), NYC, NY, (edited by Ashish Goel and Friedrich
C. Simmel), Springer-Verlag, New York, (2009). Conference
Version: [PDF] Talk: [PDF] [PPT]. Invited Paper, Special issue in
Natural Computing, Vol. 9, Number 1, pp. 183-206, (March 2010). Springer
Netherlands, ISSN: 1567-7818 (Online),
DOI: 10.1007/s11047-009-9148-6.
Full Paper: [PDF] [PDF]
51.
Sudheer Sahu,
Thomas H. LaBean and John H. Reif, A DNA Nanotransport Device Powered by
Polymerase ϕ29, Nano Letters, 2008, 8 (11), pp 3870–3878,
(October, 2008) DOI: 10.1021/nl802294d. [PDF] [PDF] supplementary material: [PDF]
52.
Thomas H. LaBean, Geetha Shetty, Peng Yin, Erik
A. Schultes, Harish
Chandran, John H. Reif, A Dendritic Nanostructure for
DNA Detection, abstract, Proceedings of the Sixth Conference on
Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO09),
Snowbird, Utah, Sciencetechnica, pp. 82-83 (April 2009). [PDF]
Thomas H. LaBean, Geetha Shetty, Hao Yan, Erik A. Schultes, Harish
Chandran, John H. Reif, Target DNA Detection by
Strand Displacement and Deoxyribozymogen Amplification, abstract,
Proceedings of the Sixth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO09),
Snowbird, Utah, Sciencetechnica, pp. 60-61 (April 2009). [PDF] Bishop Morgan A., Clare D.
Thiem, Thomas E. Renz, Erik A. Schultes, Harish Chandran, John H Reif,
Structural Optimization of Dendritic DNA Self-Assembly, abstract, Proceedings
of the Sixth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices (FNANO09), Snowbird, Utah, Sciencetechnica, pp.
147-148 (April 2009). [PDF]
Final Publication: Harish Chandran,
Abhijit Rangnekar, Geetha Shetty, Erik A Schultes, John H Reif, Thomas H
LaBean, An
Autonomously Self‐Assembling Dendritic DNA Nanostructure for Target DNA
Detection, Biotechnology Journal, Wiley-VCH
Verlag, Vol. 8, Number 2, pp. 221-227, (Feb,
2013). PMID: 22965937.
DOI: 10.1002/biot.201100499. [PDF]
(also published online Oct, 2012)
53.
Nikhil
Gopalkrishnan, Harish Chandran and John Reif, 2D and 3D DNA Lattices Via
Staggered Assembly of the Double-Decker Tile, abstract, Digital
Proceedings of the Ninth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO12), Snowbird, Utah, pp. 108
(April 2012).
54.
Harish Chandran, Nikhil
Gopalkrishnan, and John Reif, The Tile Complexity of Linear Assemblies, 36th
International Colloquium on Automata, Languages and Programming (ICALP 2009),
July 5 - 12, 2009, Rhodes, Greece, Proceedings Part I (edited by Susanne Albers,
Alberto Marchetti-Spaccamela, Yossi Matias, Sotiris Nikoletseas, and Wolfgang
Thomas), Lecture Notes in Computer Science, Springer-Verlag, Berlin, pp.
235-253 (2009). Published in SIAM Journal of Computation (SICOMP), Society for
Industrial Mathematics, Vol. 41, No, 4, pp. 1051-1073, (2012). [PDF] [PDF] Talk: [PPT] [PDF]
55.
John H. Reif and Thomas H. LaBean, Engineering Natural
Computation by Autonomous DNA-Based Biomolecular Devices,
Invited Chapter, Handbook of
Natural Computing, Chapter 39, Volume III, edited by Grzegor Rozenberg, Thomas Bäck, Joost Kok,
Springer-Verlag, Heidelberg, Germany, pp.1314-1354 (July, 2012), 3540929096
978-3-540-9-2909-3. [PDF] [PDF]
56.
John H. Reif and Urmi Majumder, Design of a Biomolecular Device that Executes Process
Algebra, Fifteenth International Meeting on DNA Computing and Molecular
Programming
(DNA15), Fayetteville, Arkansas (June 8-11,
2009). Lecture Notes for Computer Science (LNCS), Vol 5877, NYC, NY, (edited by
Russell Deaton and Jin-Woo Kim), Springer-Verlag,
New York, pp 107-105, (2010) [PDF]
[PDF]. Published in Natural
Computing, Vol 10, No. 1. pp 447-466 (2011). Talk:
[PDF]
[PPT]
[Keynote].
57.
John Reif, Harish Chandran,
Nikhil Gopalkrishnan, and Thomas LaBean, Self-assembled DNA Nanostructures and
DNA Devices. Invited Chapter 14, Nanofabrication Handbook (Edited by Stefano
Cabrini and Satoshi Kawata), pages 299-328, CRC
Press, Taylor and Francis Group, New York, NY, ISBN13:9781420090529,
ISBN10: 1420090526 (2012). [PDF][PDF]
58.
Nikhil Gopalkrishnan, Harish Chandran and John Reif, High-Fidelity DNA Hybridization using Programmable Molecular DNA
Devices, International
Conference on DNA Computing and Molecular Programming (DNA16),
Hong Kong University of Science and Technology. Hong Kong, China, June 14-17th, 2010. Lecture Notes
for Computer Science (LNCS), Vol. 6516, NYC, NY, (edited by Yasubumi Sakakibara and Mi Yongli),
Springer-Verlag, LNCS 6518, New York, (Feb 2011), pp 59-70. ISBN: 978-3-642-18304-1 [PDF]
[PDF]
Talk: [PDF]
[PPT]
59.
Harish Chandran, Nikhil Gopalkrishnan and John Reif, Tile
Complexity of Approximate Squares and Lower Bounds for Arbitrary Shapes,
Algorithmica, Volume 66, Issue 1 (2013), Page 1-17 (2013) (also published
online Feb 22,
2012). ISSN 0178-4617, DOI 10.1007/s00453-012-9620-z. [PDF]
[PDF]
60. Urmi
Majumder, Abhijit Rangnekar, Kurt V. Gothelf, John H Reif and Thomas H LaBean,
Design and Construction of Double-Decker Tile as a Route to Three-Dimensional
Periodic Assembly of DNA, Journal American Chemical Society (JACS),
Vol.
133, no. 11, pp. 3843—3845 (Feb. 2011) [PDF]
Supplementary Info: [PDF]
61. Harish Chandran, Nikhil Gopalkrishnan, and John Reif, DNA NanoRobotics,
Chapter, Nanorobotics: Current Approaches and Techniques, (edited by
Constantinos Mavroidis and Antoine Ferreira), Springer-Verlag, New York, NY,
pp. 355-382 (Jan. 31, 2013). ISBN 13: 9781461421184, ISBN
10: 1461421187 [PDF] [PDF]
62. John
H. Reif, Perspectives: Biochemistry: Scaling Up DNA Computation, Science, Vol. 332, pp. 1156-1157
(June 3, 2011). DOI: 10.1126/science.1208068 [PDF]
63.
Harish Chandran, Nikhil Gopalkrishnan, Andrew Philips and
John Reif, Localized Hybridization Circuits, International Conference on DNA
Computing and Molecular Programming, (DNA17), California Institute of
Technology, Pasadena, California, Sept 19-23, 2011, pp. 64-83. Lecture Notes
for Computer Science (LNCS), NYC, NY, (edited by Luca Cardelli and William
Shih), Springer-Verlag, LNCS, Berlin,
Heidelberg, (2011). ISBN: 978-3-642-23637-2 [PDF] Revised as Neil
Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Philips and John Reif, Probabilistic
Analysis of Localized DNA Hybridization Circuits, ACS Synthetic Biology, Vol. 4, Issue 8, pp 898–913, (July, 2015). DOI:10.1021/acssynbio.5b00044 [PDF] [PDF] Supporting Info:
[PDF] https://dx.doi.org/10.1002/smll.201602983
64.
Harish Chandran, Nikhil
Gopalkrishnan, Sudhanshu Garg, and John Reif, Biomolecular Computing Systems -
From Logic Systems to Smart Sensors and Actuators, Invited Chapter 11, Molecular
and Biomolecular Information Processing (Editor: Evgeny Katz),
Published by Wiley-VCH, Verlag GmbH & Comp.
KGaA, Weinheim, Germany, pp. 199-224,
July 2012. ISBN 978-3-527-33228-1
Online ISBN: 9783527645480 DOI:
10.1002/9783527645480 [PDF] [PDF]
65.
Harish Chandran, Nikhil
Gopalkrishnan, Bernard
Yurke, John Reif, Meta-DNA: Synthetic Biology via DNA Nanostructures and
Hybridization Reactions, Journal
of the Royal Society Interface, (published
online Jan., 2012), pp. 1742-5662 doi: 10.1098/rsif.2011.0819 [PDF] [PDF] [Supplement].
An expanded version appears as Meta-DNA:
A DNA-Based Approach to Synthetic Biology,
Chapter 7 in Book: A Systems Theoretic Approach to Systems and Synthetic
Biology II: Analysis and Design of Cellular Systems, edited by Vishwesh V. Kulkarni, Guy-Bart
Stan, and Karthik
Raman, published by
Springer, New
York (2014).
ISBN:
978-94-017-9046-8 (Print) 978-94-017-9047-5 (Online)
DOI
10.1007/978-94-017-9047-5 [PDF]
[PDF]
Talk: [PDF]
[PPT]
66.
Harish
Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan and John H Reif, Activatable
Tiles: Demonstration of Linear and Directed Self Assembly, abstract, Digital
Proceedings of the Ninth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO12), Snowbird, Utah, pp. 109
(April 2012). Also, Sudhanshu Garg, Harish Chandran, Nikhil Gopalkrishnan, and
John Reif, One-Time, Directed and Catalytic Activation of 1-D DNA Tiles, Poster
Abstract DNA19, Tempe, AZ, Sept, 22-27, 2013. Journal publication: Sudhanshu
Garg, Harish Chandran, Nikhil Gopalkrishnan, Thomas H. LaBean, and John Reif,
Directed Enzymatic Activation of 1-D DNA Tiles, ACS Nano, Volume 9, Issue 2,
pages 1072-1079, January 27, 2015. [PDF] [PDF] Supplementary [PDF] DOI: 10.1021/nn504556v
67. Hieu Bui, Harish
Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan, Reem Mokhtar, Tianqi Song
and John H Reif, DNA Computing, Chapter in Section 3: Architecture
and Organization, Volume I: Computer Science and Software Engineering
(Edited by Teofilo F. Gonzalez, Jorge Diaz-Herrera, Allen Tucker), The Computer
Science Handbook, Third Edition (Editor-In-Chief Allen B. Tucker), Taylor
& Francis Group, (2013). ISBN 9781439898529 [PDF]
68. Sudhanshu Garg, Nikhil Gopalkrishnan, Harish Chandran,
and John Reif, Self-Replicating DNA Nanostructures: Autocatalytic Nanodevices
derived from Catalytic Nanodevices, FNANO 2013, Snowbird, Utah, April 15-18,
2013.
69. Reem Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu
Bui, Tianqi Song, and John Reif, Kinetic Digraph Rewrite Systems:
Coarse-Grained Models for Dynamic DNA Nanodevices, Poster Abstract, FNANO 2013,
Snowbird, Utah, April 15-18, 2013. Also, A Python Implementation
of a DNA Graph Rewriting System (DAGR), poster abstract, FNANO2015, p148, April
2015. Published as Reem
Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu Bui, Tianqi Song, and John Reif,
Modeling DNA Nanodevices Using Graph Rewriting Systems, invited Chapter, Advances in Unconventional Computing, Volume
2: Prototypes, Models and Algorithms (Edited by Andrew Adamatzky),
Springer, pp. 347-396 (2017). ISBN
978-3-319-33921-4 [PDF] [PDF]
70. Hieu Bui, Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Harish
Chandran, and John Reif, Local Hybridization Chain-Reactions on the Surface of
DNA Origami, Poster Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013.
Also Design DNA Hairpin Systems for Localized DNA Hybridization Reactions,
poster abstract, FNANO2015, p169, April 2015. Expanded paper rewritten for
journal publication as: Hieu Bui, Sudhanshu Garg, Reem Mokhtar, Harish
Chandran, Vincent Miao and John Reif, Design and
Analysis of Localized DNA Hybridization Chain Reactions, Small (2017), 1602983. [PDF]
[PDF]
71. John H. Reif and Tianqi Song, Complexity and
Computability of Temperature-1 Tilings, Poster Abstract, FNANO 2013, Snowbird,
Utah, April 15-18, 2013. Poster Abstract DNA19, Tempe, AZ, Sept, 22-27, 2013. Submitted
for journal publication, (2014). [PDF]
72. Tianqi
Song, Sudhanshu Garg, Hieu Bui, Reem Mokhtar, and John H. Reif, Analog Computation by DNA Strand Displacement Circuits, ACS
Synthetic Biology, 5, 898−912 (July, 2016). DOI: 10.1021/acssynbio.6b00144 [PDF] [PDF]
73. Hieu
Bui,
Sudhanshu Garg, Vincent Miao, Tianqi Song, Reem
Mokhtar, and John Reif, Design and Analysis of Linear Cascade DNA Hybridization
Chain Reactions Using DNA Hairpins, Special Issue, Journal of New Physics, Vol.
19, (2017) 015006. doi:10.1088/1367-2630/aa53d0 [PDF]
[PDF]
74. Sudhanshu Garg, Shalin Shah, Hieu Bui, Tianqi Song, Reem Mokhtar, and John Reif,
Renewable Time‐Responsive DNA Circuits, Small 14, 1801470(July 18, 2018). [PDF] [PDF] DOI:
10.1002/smll.201801470 https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201801470
75.
Hieu Bui, Shalin
Shah, Reem Mokhtar, Tianqi Song, Sudhanshu Garg, John Reif, Localized
DNA Hybridization Chain Reactions on DNA Origami,
ACS Nano, Volume 12, Num. 2, pp 1146–1155(January 22, 2018). DOI: 10.1021/acsnano.7b06699
76.
Daniel
Fu, Shalin Shah, Tianqi Song and John H Reif, DNA-based Analog
Computing, Chapter in book: Synthetic Biology:
Methods and Protocols, Edited by Jeffrey C. Braman), In Series Methods
in Molecular Biology, published by Springer, pp.
411-417 (2018). ISBN 978-1-4939-7795-6 [PDF] [PDF]
77.
Tianqi
Song, Sudhanshu
Garg, Hieu Bui, Reem Mokhtar, and John H Reif, Design
and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation
Using Autocatalytic Amplifiers, ACS Synthetic Biology (Dec
2017). DOI: 10.1021/acssynbio.6b00390
78.
Xin
Song, Abeer Eshra, Chris Dwyer, and John Reif, Renewable
DNA Seesaw Logic Circuits Enabled by Photoregulation of Toehold-Mediated Strand
Displacement, RSC Advances, Volume 7,
Issue 45, pp. 28130-28144 (March, 2017). DOI: 10.1039/C7RA02607B [PDF] (supplementary: [PDF])
79.
Sudhanshu Garg, Hieu Bui,
Abeer Eshra, Shalin Shah and John H Reif, Nucleic Acid Hairpins:
A Robust and Powerful Motif for Molecular Devices, Chapter 7 in book: “Soft
Nanomaterials” (Edited by Ye Zhang and Bing Xu), World Scientific Series in Nanoscience and Nanotechnology,
World Scientific, Volume 19, pp. 175-199 (2019). ISBN: 978-981-120-102-8, DOI:
10.1142/9789811201035_0007
80.
John H. Reif, DNA
robots sort as they walk, Prospective,
Science, Vol. 357, Issue 6356, pp. 1095-1096 (September, 2017). DOI:
10.1126/science.aao5125
81.
Hieu Bui and John H Reif, Localized DNA Computation,
Chapter 19 in book: “From Parallel to Emergent Computing” (Edited by Andrew Adamatzky, Selim Akl, and Georgios Ch.
Sirakoulis), CRC
Press (February 18, 2019). Taylor & Francis Group of CRC Press. ISBN: 9781138054011
82.
Shalin
Shah and John H. Reif, Temporal DNA Barcodes: A Time-Based Approach for
Single-Molecule Imaging, 24th International Conference, DNA 24,
Jinan, China, Also, Chapter 5 of DNA
Computing and Molecular Programming (DNA
2018), edited by D. Doty and H. Dietz, LNCS 11145, published by Springer Nature Switzerland AG, pp.71-86, (2018). DOI: 10.1007/978-3-030-00030-1_5 Also published as Shah,
Shalin, Abhishek Dubey, and John Reif. "Improved optical multiplexing with
temporal DNA barcodes." ACS Synthetic Biology 8.5 (2019): 1100-1111. DOI:
10.1021/acssynbio.9b00010
83.
Tianqi Song, Nikhil Gopalkrishnan, Abeer Eshra, Sudhanshu
Garg, Reem Mokhtar, Hieu Bui, Harish Chandran and John Reif, Improving the
Performance of DNA Strand Displacement Circuits by Shadow Cancellation, ACS Nano, (Oct 29, 2018). DOI: 10.1021/acsnano.8b07394 https://doi.org/10.1021/acsnano.8b07394
84.
Abeer
Eshra, Shalin Shah, Tianqi Song, John Reif, Renewable DNA hairpin-based logic circuits,
IEEE Transactions on Nanotechnology, Vol. 18, pp. 252-259, (2019). DOI: 10.1109/TNANO.2019.2896189
85.
Shalin Shah,
Dubey Abhishek and John H. Reif, Programming temporal DNA barcodes for single-molecule
fingerprinting, Nano letters, 19 (4), pp 2668–2673
(March 2019). DOI: 10.1021/acs.nanolett.9b00590
86. Xin Song and John H Reif, Nucleic Acid Databases and
Molecular-Scale Computing, ACS Nano, Vol 13, Issue
6, pp 6256-6268 (May 2019). DOI: 10.1021/acsnano.9b02562
87. Tianqi Song, Abeer Eshra, Shalin Shah, Hieu Bui, Daniel Fu, Ming
Yang, Reem Mokhtar, and John Reif, Fast and Compact DNA Logic Circuits Based on
Single-Stranded Gates Using Strand-Displacing Polymerase, Nature Nanotechnology
(Sept 2019). DOI: 10.1038/s41565-019-0544-5
88.
Tianqi Song, Shalin
Shah, Hieu Bui, Sudhanshu Garg, Abeer Eshra, Ming Yang, and John Reif,
Programming DNA-Based Biomolecular Reaction Networks on Cancer Cell Membranes,
Journal of the American Chemical Society (JACS), Vol. 141, No. 42, pp.
16539-16543. (Oct 2019). DOI: 10.1021/jacs.9b05598
https://doi.org/10.1021/jacs.9b05598
89.
Shalin Shah., Tianqi Song, Xin Song, Ming Yang, John H. Reif, Implementing Arbitrary CRNs
Using Strand Displacing Polymerase. In: Thachuk C., Liu Y. (eds) DNA Computing
and Molecular Programming. International
Conference on DNA Computing and Molecular Programming (DNA 2019). Lecture Notes in Computer Science, vol 11648.
Springer, Cham, pp 21-36 (2019). DOI: 10.1007/978-3-030-26807-7_2. Published as Chapter
in: DNA Computing and Molecular Programming (edited by Chris Thachuk and Yan
Liu), Volume 11648, Springer, Switzerland AG, pp 21-36, (2019). ISBN:
978-3-030-26807-7. [PDF]
90.
Xin Song, Shalin Shah, and John Reif, An Overview of DNA-Based Digital
Data Storage, Chapter 18, DNA- and RNA-Based Computing Systems (Evgeny Katz,
editor), Wiley-VCH Verlag GmbH Publishers, Weinheim, Germany, pp. 345-350
(Dec., 2020). ISBN: 978-3-527-82541-7
91.
Reem Mokhtar,
Tianqi Song, Daniel Fu, Shalin Shah, Xin Song, Ming Yang, and
John Reif, DNA Origami Transformers, Chapter 16, DNA- and RNA-Based Computing
Systems (Evgeny Katz, editor), Wiley-VCH Verlag GmbH Publishers, Weinheim,
Germany, pp. 307-322 (Dec., 2020). ISBN:
978-3-527-82541-7 [PDF]
92.
Xin
Song, Daniel Fu, Shalin Shah, John Reif, UV-Micropatterned Miniaturization:
Rapid In-Situ Photopatterning and Miniaturization of Microscale Features on
Shrinkable Thermoplastics, Advanced Materials, Vol. 5, Issue 6 (May 4,2020). DOI: 10.1002/admt.202000146 https://doi.org/10.1002/admt.202000146
93.
Shalin
Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin Strauss, Yuan-Jyue Chen, John
Reif, Using strand displacing polymerase to program chemical reaction networks,
Journal of the American Chemical Society (JACS), Vol.
142, Issue. 21, pp. 9587–9593 (May 4, 2020). DOI: 10.1021/jacs.0c02240
https://pubs.acs.org/doi/10.1021/jacs.0c02240
(Supporting Information https://pubs.acs.org/doi/10.1021/jacs.0c02240).
94.
Xin Song and John Reif, Optics-Free Imaging with
DNA Microscopy: An Overview, Chapter 6. Handbook of Unconventional Computing:
Volume 2: Implementations (edited by Andrew Adamatzky), WSPC Book Series in
Unconventional Computing, World Scientific Publishers (WSPC), pp. 181-191
(2021). DOI: 10.1142/12232 DOI: 10.1142/9789811235740_0006. [PDF] ISBN: 978-981-123-527-6 (ebook),
978-981-123-503-0 (hardcover).
95.
Shalin Shah, Ming Yang, Tianqi Song, and John
Reif, Molecular computation via polymerase strand displacement reactions,
Chapter 5. Handbook of Unconventional Computing: Volume 2: Implementations (edited
by Andrew Adamatzky), WSPC Book Series in Unconventional Computing, World
Scientific Publishers, pp. 165-197 (2021) [PDF] DOI: 10.1142/9789811235740_0005. ISBN:
978-981-123-527-6 (ebook), 978-981-123-503-0 (hardcover).
96.
Daniel Fu, Raghu Narayanan Pradeep, Fei Zhang,
John Schreck, Hao Yan and John Reif, Automated Design of Curved DNA Origami
Nano-Capsules with Specific Shape and Variable Multilayer-Reinforced Rigidity,
International Conference on DNA Computing and Molecular Programming (DNA 2019),
Seattle, WA (Aug, 2019).
97.
Daniel Fu and
John H Reif, 3D DNA Nanostructures: The Nanoscale
Architect. special issue (Mechanical Design in DNA Nanotechnology)
of Applied Sciences, Volume 11, No. 6, eLocator-ID
2624, (2021). DIO: https://doi.org/10.3390/app11062624
98.
Xin Song, Shalin Shah, John Reif,
Multidimensional Data Organization and Random Access in Large-Scale DNA Storage
Systems, special issue of Natural Computing (Theoretical Computer Science –
track C), Vol. 894, pp. 190–202 (2021). DIO: https://doi.org/10.1016/j.tcs.2021.09.021
99. Xin Song, Felicity Coulter, Ming Yang, Fikadu
Tafesse, William Messer, John Reif, Lyophilized
Colorimetric RT-LAMP Test Kit for Rapid, Low-Cost, At-Home Molecular Testing of SARS-CoV-2 and Other
Pathogens, Scientific Reports,12: 7043 (April 2022). DOI:
10.1038/s41598-022-11144-5.
100. Ming Yang, and John H. Reif, Social DNA
Nanorobots, pp 371-396, Invited
Chapter for Book on DNA Nanotechnology at 40 for the next 40 - A Tribute to
Nadrian C. Seeman, (edited by Natasha Jonoska and Erik Winfree, book series
Natural Computing, Springer (2023).
101. Daniel Fu, Raghu Pradeep Narayanan, Abhay
Prasad, Fei Zhang, Dewight Williams, John S. Schreck, Hao Yan, John Reif, Automated
Design of 3D DNA Origami with Non-Rasterized 2D Curvature, Science
Advances, Volume 8, Issue 51, (2022). DOI: 10.1126/sciadv.ade4455
102. Rajiv Teja Nagipogu Daniel Fu and John
Reif, Molecular scale learning using DNA circuits” Nanoscale (2022). A
survey on molecular-scale learning systems with relevance to DNA computing,
Nanoscale, Royal Society of Chemistry,(2023), DOI: 10.1039/d2nr06202j
103. Daniel Fu and John Reif,
A Biomimetic Branching Signal-Passing Tiling Model with Dynamic Assembly and
Disassembly. Submitted for publication, Dec 2023.
104. Rajiv Teja Nagipogu and
John H. Reif, Leak-resilient Nucleic Acid Dynamical Systems through Shadow
Cancellation. Submitted for publication, Dec 2023.
105. Grayson York and John
Reif, Nondeterministic Temperature 1 Self Assembly in 2 Dimensions is
Undecidable. Submitted for publication, Dec 2023.