Faculty Information - ROSE John A.

（Last updated : 2023-06-12 11:31:48）

ROSE John A.
Department Ritsumeikan Asia Pacific University College of Asia Pacific Studies

Position Professor

■ Education

1.	1999/12	〔Doctorial Course〕 Electrical Engineering; DNA Computing, Graduate School Division of Engineering, The University of Memphis Department of Electrical Engineering, Completed, Doctor of Philosophy
2.	1990/08	〔Master Course〕 Physics, Graduate School Division of Science, Memphis State University Department of Physics, Completed, Master of Science
3.	1990/05	Department of Physics, Rhodes College, Graduated, Bachelor of Arts

■ Academic and professional experience

1.	2006/04～2011/03	Ritsumeikan Asia Pacific University College of Asia Pacific Studies Associate Professor
2.	2002/04～2006/03	The University of Tokyo Department of Information Science Assistant Professor
3.	2001/04～2002/03	The University of Tokyo Department of Information Science J.S.P.S. Postdoctoral Fellow
4.	2000/01～2001/03	The University of Tokyo Department of Information Science and\nInstitute of Physics Postdoctoral Researcher

■ Message

I.T. competency has become a necessity for success in the modern workplace. My courses in Visual Basic provide students with the fundamentals for developing programs for Business and the Social Sciences.

■ Current specialized field

Nano Materials/Nano Bioscience, Sensitivity Informatics/Soft Computing, System Engineering, Biological/Living Body Informatics, Software

■ Books and theses

1.	2023/01/11	Article	Reputation-based Decentralized Autonomous Organization for the non-profit sector: Leveraging blockchain to enhance good governance Frontiers in Blockchain 5,pp.1-17 (Collaboration)
2.	2016/08	Article	Engineering multistate DNA molecules: a tunable thermal band-pass filter Micro & Nano Letters 10,pp.595-601 (Collaboration)
3.	2016/04	Article	Analysis and Design of a Single-Molecule DNA Nanodevice for Thermal Band-Pass Filters The 11th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems (IEEE-NEMS 2016; Proceedings) pp.78-89 (Collaboration)
4.	2010/11	Article	Autonomous DNA Molecule Computing - towards construction of in vitro intelligence T. SICE pp.700-705 (Collaboration)
5.	2010/04	Article	Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states Nucleic Acids Research 38(13),pp.4539-4546 (Collaboration)
6.	2010/03	Article	Experimental Validation and Optimization of Signal Dependent Operation in Whiplash PCR Natural Computing 9(1),pp.207-218 (Collaboration)
7.	2009/10	Article	Experimental Validation of Signal-Dependent Operation in Whiplash PCR Springer-Verlag LNCS 5347,pp.1-10 (Collaboration)
8.	2008/08	Article	Fuzzy C-Means Clustering for DNA Computing Readout Method Implemented on LightCycler System SICE International Conference 2008 (Proceedings) pp.676-681 (Collaboration)
9.	2007/05	Article	Analysis of a DNA Computing Readout Method based on Real-Time PCR with TaqMan Probes Int'l Conference on Control, Instrumentation, and Mechatronics Engineering (Proceedings) pp.22-28 (Collaboration)
10.	2007/05	Article	Experimental Implementation and Analysis of a DNA Computing Readout Method based on Real-Time PCR with TaqMan Probes Natural Computing 7,pp.277-286 (Collaboration)
11.	2007/05	Article	Rapid Modulation of Long-term Depression and Spinogenesis via Synaptic Estrogen Receptors in Hippocampal Principal Neurons Journal of Neurochemistry (Wiley/Blackwell) 100,pp.950-967 (Collaboration)
12.	2007/03	Article	A Coupled Equilibrium Model for Hybridization Error Estimation for the DNA Microarray and Tag-Antitag Systems IEEE Transactions in NanoBioscience 6(1),pp.18-27 (Collaboration)
13.	2007/03	Article	An Improved Readout Method of Molecular Computation based on Real-Time PCR Implemented on DNA Engine Opticon 2 System 2007 IEEE Congress on Evolutionary Computation (Proceedings) pp.1829-34 (Collaboration)
14.	2007/03	Other	Developed the Java Software Package 'NucleicPark on the Web' (on the APU web-site of J. Rose). (Collaboration)
15.	2007	Other	Z. Ibrahim, J. Rose, A. Suyama, and M. Khalid, "Experimental Implementation and Analysis of a DNA Computing Readout Method based on Real-Time PCR with TaqMan Probes", invited paper: International Journal of Natural Computing (in press; Published Online: 15 May 2007 ).
16.	2006/12	Article	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 24,pp.289-99 (Collaboration)
17.	2006/10	Article	Enhancement of NO production by association of nitric oxide synthase with NMDA receptors via PSD-95 in genetically engineered CHO cells: real-time fluorescence imaging using NO sensitive dye J. Neurochem. 96,pp.1531-39 (Collaboration)
18.	2006/09	Article	A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes Springer-Verlag LNCS 4287,pp.350-359 (Collaboration)
19.	2006/09	Article	Displacement Whiplash PCR: Optimized Architecture and Experimental Validation Springer-Verlag LNCS pp.393-403 (Collaboration)
20.	2006/09	Article	Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation Springer-Verlag LNCS 4287,pp.428-438 (Collaboration)
21.	2006/04	Other	Kiban B (J. Rose, PI) DWPCRを用いた高性能試験管内遺伝的プログラミングによるタンパク質の創製’ (Collaboration)
22.	2005/06	Article	Spatiotemporal analysis of NO production upon NMDA- and tetanic stimulation of the hippocampus, N. Takata, T. Harada, J. Rose, and S. Kawato Hippocampus 15(4), 427-40 (Wiley, 2005). 15(4),pp.427-40 (Collaboration)
23.	2005/04	Article	The Fidelity of the Tag Antitag System: Characterization of the Stringent Temperature for Robustness in the Excess Limit KES Journal 9,pp.282-292 (Single)
24.	2004/12	Article	Physical Modeling of Biomolecular Computers: Models, limitations, and experimental validation Natural Computing 3,pp.411-426 (Collaboration)
25.	2004/12	Article	Statistical Thermodynamic Analysis and Design of DNA-based Computers Natural Computing 3,pp.443-59 (Collaboration)
26.	2004/12	Article	The Fidelity of the Tag-Antitag System III: Robustness in the Excess Limit: the Stringent Temperature Springer-Verlag LNAI 3212,pp.40-49 (Single)
27.	2003/12	Article	A DNA Computing-based Genetic Program for in vitro Protein Evolution via Constrained Pseudomodule Shuffling Journal of Genetic Programming and Evolvable machines 4,pp.139-152 (Collaboration)
28.	2003/12	Article	The Fidelity of the Tag-Antitag System 2: Reconciliation with the Stringency Picture Proc. 2003 Congress on Evolutionary Computation pp.2740-47 (Collaboration)
29.	2002/10	Article	A DNA-based in vitro Genetic Program Journal of Biological Physics 28,pp.493-498 (Collaboration)
30.	2002/10	Article	An Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer Physical Review E 65,pp.1-13 (Collaboration)
31.	2002/09	Article	An Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer Virtual Journal of Biological Physics 3 (Collaboration)
32.	2002/08	Article	Complexity Analysis of the SAT Engine: DNA Algorithms as Probabilistic Algorithms Theoretical Computer Science 287,pp.59-71 (Collaboration)
33.	2002/06	Article	A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides Springer-Verlag LNCS 2568,pp.252-261 (Collaboration)
34.	2001/10	Article	The Fidelity of Annealing-Ligation: A Theoretical Analysis Springer-Verlag LNCS 2054,pp.231-246 (Collaboration)
35.	2001/06	Article	PNA-mediated Whiplash PCR Springer-Verlag LNCS pp.104-116 (Collaboration)
36.	2001/06	Article	The Fidelity of the Tag-Antitag System Springer-Verlag LNCS 2340,pp.302-310 (Collaboration)
37.	2000/07	Article	An Equilibrium Analysis of the Efficiency of Whiplash PCR Late Breaking Papers, GECCO 2000 (Las Vegas, Nevada) pp.338-345 (Collaboration)
38.	1999/12	Book	The Fidelity of DNA Computation no. (Single)
39.	1999/12	Article	DNA Implementation of Nondeterminism DNA Computers III pp.137-148 (Collaboration)
40.	1999/12	Article	Soft Molecular Computing DNA Computers V pp.91-100 (Collaboration)
41.	1999/08	Article	A Statistical Mechanical Treatment of Error in the Annealing Biostep of DNA Computation GECCO'99 (Proceedings) pp.1829-1834 (Collaboration)
42.	1998/06	Article	DNA Computing: A Review Fundamenta Informaticae 35,pp.231-245 (Collaboration)
43.	1998/06	Article	In-vitro Implementation of Finite State Machines Springer-Verlag LNCS 1436,pp.56-74 (Collaboration)
44.	1998/06	Article	The Reliability of DNA-based Computing Physical Review Letters 80,pp.417-420 (Collaboration)
45.	1997/10	Article	A DNA Based Artificial Immune System for Self-Nonself Discrimination IEEE International Conference on Systems, Man, and Cybernetics (Proceedings) pp.369-374 (Collaboration)
46.	1997/07	Article	DNA Implementation of a Finite-State Machine GP'97 (Proceedings) pp.479-490 (Collaboration)
47.	1997/07	Article	Information Transfer through Hybridization Reactions in DNA based Computing GP'97 (Proceedings) pp.479-490 (Collaboration)
48.	1997/06	Article	The Effect of Uniform Melting Temperatures on the Efficiency of DNA Computing Preliminary Proceedings of the Third DIMACS Workshop on DNA Based Computers pp.35-42 (Collaboration)
49.	1997/04	Article	A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation 1997 IEEE C.E.C. (Proceedings) pp.267-272 (Collaboration)
50.	1996/07	Article	Genetic Search of Reliable Encodings for DNA-based Computation Late Breaking Papers, First Genetic Programming Conference(Stanford University, 1996) pp.267-271 (Collaboration)
51.	1990/08	Book	A Study on the Photoproduction of Psi-prime Mesons no. (Single)
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■ Academic or professional association memberships

2007/01～

IEEE

■ Awards and honors

2010/07

Ritsumeikan APU Outstanding Research Award (AY2009)

■ Committee and society

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