R. Deaton and M. Garzon, ``Fuzzy logic with biomolecules,'' Soft Computing, vol. 5, pp. 2-9, 2001. (pdf)
M. H. Garzon and R. J. Deaton, ``Biomolecular computing and programming: A definition,'' Kunstliche Intelligenz, vol. 1, pp. 63-72, 2000.
M. H. Garzon and R. J. Deaton, ``Biomolecular computing and programming,'' IEEE Transactions on Evolutionary Computation, vol. 3, pp. 236-250, 1999. (pdf)
R. Deaton, M. Garzon, J. A. Rose, D. R. Franceschetti, R. C. Murphy, and S. E. Stevens Jr., ``Reliability and efficiency of a DNA based computation,'' Phys. Rev. Lett., vol. 80, pp. 417-420, 1998. (pdf)
R. Deaton, M. Garzon, J. A. Rose, D. R. Franceschetti, and S. E. Stevens Jr., ``DNA computing: A review,'' Fundamenta Informaticae, vol. 35, pp. 231-245, 1998. (pdf)
R. Deaton and M. Garzon, ``Thermodynamic constraints on DNA-based computing,'' in Computing with Bio-Molecules: Theory and Experiments (G. Paun, ed.), Springer-Verlag. (pdf)
J. A. Rose, A. Suyama, M. Hagiya, and R. J. Deaton, ``PNA-Mediated whiplash PCR,'' in Preliminary Proceedings of the Seventh International Meeting on DNA Based Computers (N. Jonoska and N. C. Seeman, eds.), (Tampa, FL), pp. 311-320, University of South Florida, 2001. June 10-13, 2001.
J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama, ``The fidelity of the tag-antitag system,'' in Preliminary Proceedings of the Seventh International Meeting on DNA Based Computers (N. Jonoska and N. C. Seeman, eds.), (Tampa, FL), pp. 302-310, University of South Florida, 2001. June 10-13, 2001.
R. Deaton and J. A. Rose, ``Simulations of statistical mechanical estimates of hybridization error,'' in Preliminary Proceedings of the Sixth International Meeting on DNA Based Computers (A. Condon and G. Rozenberg, eds.), (Leiden, NE), pp. 251-252, Leiden University, Leiden Center for Natural Computing, 2000. DIMACS Workshop, Leiden, NE, June 13-17, 2000. (pdf)
J. Rose and R. J. Deaton, ``A bound on ligation error for the n-ary DNA mixture,'' in Preliminary Proceedings of the Sixth International Meeting on DNA Based Computers (A. Condon and G. Rozenberg, eds.), (Leiden, NE), pp. 201-221, Leiden University, Leiden Center for Natural Computing, 2000. DIMACS Workshop, Leiden, NE, June 13-17, 2000.
M. Garzon, E. Drumwright, R. Deaton, and D. Renault, ``Virtual test tubes: A new methodology for computing,'' in SPIRE-2000 4th Int. Meeting on String Processing and Information Retrieval, Sep 2000. A Coruna, Spain, pp. 116-121, IEEE Computer Society Press, 2000. (pdf)
J. A. Rose, R. J. Deaton, D. R. Franceschetti, M. Garzon, and S. E. Stevens, Jr., ``A statistical mechanical treatment of error in the annealing biostep of DNA computation,'' in Proceedings of the Genetic and Evolutionary Computation Conference, Volume 2, pp. 1829-1834, AAAI, Morgan Kaufmann, San Francisco, 1999. Orlando, FL, July 1999. (pdf)
M. Garzon, R. Deaton, and K. Barnes, ``Self-assembling graphs in vitro,'' in Proceedings of the Genetic and Evolutionary Computation Conference, Volume 2, pp. 1805-1809, AAAI, Morgan Kaufmann, San Francisco, 1999. Orlando, FL, July 1999. (pdf)
R. J. Deaton, ``Reaction temperature constraints in DNA computing,'' in Proceedings of the Genetic and Evolutionary Computation Conference, Volume 2, pp. -, AAAI, Morgan Kaufmann, San Francisco, 1999. Orlando, FL, July 1999. (pdf)
M. H. Garzon and R. J. Deaton, ``Biomolecular computing and programming,'' in Lecture Notes in Computer Science 1725: Proc. Theory and Practice of Informatics SOFSEM-1999 (G. Pavelka, G. Tel, and M. Bartosek, eds.), pp. 181-188, Springer-Verlag, 1999.
M. Garzon, R. Deaton, J. A. Rose, and D. R. Franceschetti, ``Soft molecular computing,'' in DNA Based Computers V (E. Winfree and D. K. Gifford, eds.), (Providence, RI), pp. 91-100, DIMACS, American Mathematical Society, 1999. DIMACS Workshop, Massachusetts Institute of Technology, Cambridge, MA, June 14-16, 1999. (pdf)
M. Garzon, P. Neathery, R. Deaton, D. Franceschetti, and S. E. Stevens Jr., ``Encoding genomes for DNA computing,'' in Genetic Programming 1998: Proceedings of the Third Annual Conference, pp. -, AAAI, 1998. University of Wisconsin - Madison, July 13-16, 1998. (pdf)
R. Deaton, R. C. Murphy, J. A. Rose, M. Garzon, D. R. Franceschetti, and S. E. Stevens Jr., ``A DNA based implementation of an evolutionary search for good encodings for DNA computation,'' in Proceedings of the 1997 IEEE International Conference on Evolutionary Computation, pp. 267-272, IEEE, 1997. Indianapolis, IN, April 13-16. (pdf)
R. C. Murphy, R. Deaton, D. R. Franceschetti, S. E. Stevens Jr., and M. Garzon, ``A new algorithm for DNA based computation,'' in Proceedings of the 1997 IEEE International Conference on Evolutionary Computation, pp. 207-212, IEEE, 1997. Indianapolis, IN, April 13-16.
M. Garzon, R. Deaton, P. Neathery, R. C. Murphy, S. E. Stevens Jr., and D. R. Franceschetti, ``A new metric for DNA computing,'' in Genetic Programming 1997: Proceedings of the Second Annual Conference, pp. 479-490, AAAI, 1997. Stanford University, July 13-16, 1997. (pdf)
J. A. Rose, R. Deaton, M. Garzon, R. C. Murphy, D. R. Franceschetti, and S. E. Stevens Jr., ``The effect of uniform melting temperatures on the efficiency of DNA computing,'' in Preliminary Proceedings of the 3rd DIMACS Workshop on DNA Based Computers (H. Rubin and D. H. Wood, eds.), (Providence, RI), pp. 35-42, DIMACS, American Mathematical Society, 1999. DIMACS Workshop, Philadelphia, PA, June 23-27, 1997.
M. Garzon, R. Deaton, P. Neathery, R. C. Murphy, D. R. Franceschetti, and S. E. Stevens Jr., ``On the encoding problem for DNA computing,'' in Preliminary Proceedings of the 3rd DIMACS Workshop on DNA Based Computers (H. Rubin and D. H. Wood, eds.), (Providence, RI), DIMACS, American Mathematical Society, 1999. DIMACS Workshop, Philadelphia, PA, June 23-27, 1997.
R. Deaton, D. R. Franceschetti, M. Garzon, J. A. Rose, R. C. Murphy, and S. E. Stevens Jr., ``Information transfer through hybridization reactions in DNA based computing,'' in Genetic Programming 1997: Proceedings of the Second Annual Conference, pp. 463-471, AAAI, 1997. Stanford University, July 13-16, 1997. (pdf)
R. Deaton, M. Garzon, J. A. Rose, D. R. Franceschetti, R. C. Murphy, and S. E. S. Jr., ``DNA based artificial immune system for self-nonself discrimination,'' in The Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, IEEE, 1997. Orlando, FL, Oct. 12-15. (pdf)
M. Garzon, Y. Gao, J. A. Rose, R. C. Murphy, R. Deaton, D. R. Franceschetti, and S. E. Stevens Jr., ``In-vitro implementation of finite-state machines,'' in Proc. 2nd Intl. Workshop on Implementing Automata WIA'97, (Berlin), Springer-Verlag, 1998. Lecture Notes in Computer Science. (pdf)
M. Garzon, J. A. Rose, Y. Gao, and R. Deaton, ``DNA implementation of finite-state machine,'' in Genetic Programming 1997: Proceedings of the Second Annual Conference, pp. 472-478, AAAI, 1997. Stanford University, July 13-16, 1997. (pdf)
Y. Gao, M. Garzon, R. C. Murphy, J. A. Rose, R. Deaton, D. R. Franceschetti, and S. E. Stevens Jr., ``DNA implementation of nondeterminism,'' in DNA Based Computers III (H. Rubin and D. H. Wood, eds.), (Providence, RI), pp. 137-148, DIMACS, American Mathematical Society, 1999. DIMACS Workshop, Philadelphia, PA, June 23-27, 1997.
R. Deaton, R. C. Murphy, M. Garzon, D. R. Franceschetti, and S. E. Stevens Jr., ``Genetic search of reliable encodings for dna-based computation,'' in Late Breaking Papers, (Stanford University), First Genetic Programming Conference, 1996. (pdf)
R. Deaton, R. C. Murphy, M. Garzon, D. R. Franceschetti, and S. E. Stevens Jr., ``Good encodings for DNA-based solutions to combinatorial problems,'' in DNA Based Computers II (L. F. Landweber and E. B. Baum, eds.), vol. 44, (Providence, RI), pp. 247-258, DIMACS, American Mathematical Society, 1998. DIMACS Workshop, Princeton, NJ, June 10-12, 1996. (pdf)