Papers by Reif on Biomolecular Computing and Self Assembly of DNA Nanostructures (70 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 and accepted as invited paper of special issue "Biomolecular Computing - From Theory to Practical Applications" of International Journal of Unconventional Computing, (2013). [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 BanČtre, 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] [PDF].

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, Compact Self-Repairing DNA Lattices, submitted as 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]

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. Appears as: 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). Conference Version: [PDF] Talk: [PPT] Revised paper submitted as for journal publication (2012). [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]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]

55.        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].

56.        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]

57.        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]

58.        Harish Chandrann 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]

59.        Urmi Majumdar, 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]

60.        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]

61.        John H. Reif, Perspectives: Biochemistry: Scaling Up DNA Computation, Science, Vol. 332, pp. 1156-1157 (June 3, 2011). DOI: 10.1126/science.1208068 [PDF]

62.        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]

63.        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]

64.        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 in Systems and Synthetic Biology: A Systematic Approach, edited by K. Raman, G.B. Stan and V. Kulkarni, published by Springer, (2013). [PDF] [PDF] Talk: [PDF] [PPT]

65.        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.

66.        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), The Computer Science Handbook, Third Edition (Editor-In-Chief Allen B. Tucker), Taylor & Francis Group, (2013). [PDF]

67.        Sudhanshu Garg, Nikhil Gopalkrishnan, Harish Chandran, and John Reif, Self-Replicating DNA Nanostructures: Autocatalytic Nanodevices derived from Catalytic Nanodevices, Poster Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013.

68.        Reem Mokhtar, Hieu Bui, Harish Chandran, Sudhanshu Garg, 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. Poster Abstract, DNA19, Tempe, AZ Sept, 22-27, 2013.

69.        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.

70.        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.