Publications Software Laboratory Conferences

Journal Publications

• J. Rose, R. J. Deaton, M. Hagiya, and A. Suyama, "A Coupled Equilibrium Model for Hybridization Error Estimation for the DNA Microarray and Tag-Antitag Systems", IEEE Transactions in NanoBioscience, Special Issue on Computational NanoBioscience, 6(1), 18-27 (2007).
• J. Rose, "Analysis and re-engineering of Whiplash PCR: simulations of fidelity and efficiency, and an improved architecture based on a targeted strand displacement strategy", Journal of the Japan Society of Simulation Technology (Journal of the JSST), Special Issue on Application and Simulation Technology of DNA Computing 24, 289-99 (2006).
• J. Rose, "The Fidelity of the Tag Antitag System: Characterization of the Stringent Temperature for Robustness in the Excess Limit," Int'l Journal of Knowledge-Based & Intelligent Engineering Systems (KES Journal) 9, 282-292 (2005).　　　　　　　　　　
• J. Rose and A. Suyama, "Physical Modeling of Biomolecular Computers: Models, limitations, and experimental validation," Int'l Journal of Natural Computing 3, 411-426 (2004).
• J. Rose, R. J. Deaton, and A. Suyama, "Statistical Thermodynamic Analysis and Design of DNA-based Computers," Int'l Journal of Natural Computing 3, 443-59 (2004). 　　　　　　　　　　
• M. Hagiya, J. Rose, K. Komiya, and K. Sakamoto, ``Complexity Analysis of the SAT Engine: DNA Algorithms as Probabilistic Algorithms", invited paper: Theoretical Computer Science, 287, pp. 59-71 (2002).
• J. Rose, R. J. Deaton, M. Hagiya, A. Suyama, ``An Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer" , Physical Review E 65, Article 02910, pp. 1-13 (2002). Also invited to Virt. J. Biol. Phys.
• J. Rose, R. J. Deaton, M. Hagiya, A. Suyama, ``An Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer", invited for publication in Virtual Journal of Biological Physics 3, (2002).

Books and Book Chapters

• J. Rose, 陶山明、DNA解析科学入門バイオインフォマティクス概論（高木利久編）羊土社、（２００４、編集中）.
• J. Rose, , ``The Fidelity of DNA Computation", Doctoral Dissertation, Major Advisor, R. J. Deaton, PhD, The University of Memphis, December, 1999.
• ``A Study on the Photoproduction of Psi-prime Mesons", Masters Thesis, Major Advisor, D. W. Jones, PhD, Memphis State University, August, 1990.

LNCS Monograph and Refereed Conference Publications (Full Papers)

• Z. Ibrahim, M. Saaid, A. Paramita, J. Rose, and A. Suyama, “Analysis of a DNA Computing Readout Method based on Real-Time PCR with TaqMan Probes”, International Conference on Control, Instrumentation, and Mechatronics Engineering, May 28-29, 2007, pp. 22-28 (Best Instrumentation Award).
　　　　　　　　　　
• K. Komiya, S. Yaegashi, M. Hagiya, A. Suyama and J. Rose*, "Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation", DNA Computing, 12^th Int'l Conference on DNA-based Computers, Seoul Korea, Springer Lecture Notes in Computer Science (LNCS Vol. 4287, Springer-Verlag, Berlin, 2006), pp. 428-438.
• J. Rose, "The Fidelity of the Tag-Antitag System III: Robustness in the Excess Limit: the Stringent Temperature", in M. Negoita, et al. Eds., 8th Int’l Conference, KES 2004 (Wellington, New Zealand), Proceedings, Part I, Lecture Notes in Artificial Intelligence 3212, (Springer, Berlin, 2004), pp. 40-49; Best Conference Paper Award. Invited for publication in KES Journal.
• J. Rose, M. Hagiya, and A. Suyama, ``The Fidelity of the Tag-Antitag System 2: Reconciliation with the Stringency Picture", in Proceedings of the 2003 Congress on Evolutionary Computation (CEC'03), Dec. 8-12 2003, Canberra, Australia, pp. 2740-47.
• R. Deaton, J. Chen, H. Bi, and J. Rose, ``A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides", in DNA Computing, 8th International Workshop on DNA Based Computers (DNA8), June 10-13 2002, Hokkaido University, Springer LNCS Vol. 2568, (Springer-Verlag, Berlin, 2003) pp. 252-261.
• J. Rose, R. J. Deaton, M. Hagiya, and A. Suyama, ``The Fidelity of the Tag-Antitag System", in DNA Computing, 7th International Meeting on DNA Based Computers), Springer LNCS Vol. 2340 June 2001, University of South Florida, 302-310.
• J. Rose, R. J. Deaton, M. Hagiya, and A. Suyama,``PNA-mediated Whiplash PCR", in DNA Computing (7th International Meeting on DNA Based Computers), Springer Lecture Notes in Computer Science (LNCS) Vol. 2340 June 2001, University of South Florida, 104-116.
• J. Rose and R. J. Deaton, ``The Fidelity of Annealing-Ligation: A Theoretical Analysis", in DNA Computing, 7th International Meeting on DNA Based Computers, Springer Verlag Lecture Notes in Computer Science (LNCS) Vol. 2054 (Springer-Verlag, Berlin, 2001), 231-246.
• J. A. Rose, R. J. Deaton, D. R. Francescetti, M. Garzon, S. Edward Stevens, Jr., ``A Statistical Mechanical Treatment of Error in the Annealing Biostep of DNA Computation", in Proceedings of the Genetic and Evolutionary Computation Conference, (Morgan Kauffman, San Francisco, 1999), 1829-1834.
• M. Garzon, R. J. Deaton, J. A. Rose, D. R. Franceshcetti, ``Soft Molecular Computing", in DNA Computers V (Proc. DNA 5), Massachusetts Institute of Technology, (American Mathematical Society, Providence, Rhode Island, 1999), 91-100.
• R. J. Deaton, R. C. Murphy, J. 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, April 13-16, 1997, Indianapolis, IN, (Piscatay, NJ: IEEE Press, 1997), 267-272.
• R. Deaton, D. R. Franceschetti, M. Garzon, J. Rose, R. C. Murphy, S. E. Stevens, Jr., ``Information Transfer through Hybridization Reactions in DNA based Computing", in Genetic Programming 1997: Proceedings of the Second Annual Conference, July 13-16, 1997, Stanford University (Morgan Kaufman, San Francisco, 1997), 479-490.

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