| 2008 | DNA | Experimental Validation of Signal Dependent Operation in Whiplash PCR. | Ken Komiya, Masayuki Yamamura, John A. Rose |
| 2007 | CEC | An improved readout method of molecular computation based on real-time PCR implemented on DNA Engine Opticon 2 System. | Zuwairie Ibrahim, Muhammad Faiz Mohamed Saaid, Ali S. Paramita, Akira Suyama, John A. Rose |
| 2006 | DNA | A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes. | Zuwairie Ibrahim, John A. Rose, Yusei Tsuboi, Osamu Ono, Marzuki Khalid |
| 2006 | DNA | Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation. | Ken Komiya, Satsuki Yaegashi, Masami Hagiya, Akira Suyama, John A. Rose |
| 2006 | DNA | Displacement Whiplash PCR: Optimized Architecture and Experimental Validation. | John A. Rose, Ken Komiya, Satsuki Yaegashi, Masami Hagiya |
| 2004 | KES | Equilibrium Modelling of Oligonucleotide Hybridization, Error, and Efficiency for DNA-Based Computational Systems. | John A. Rose |
| 2004 | KES | The Fidelity of the Tag-Antitag System III. Robustness in the Excess Limit: The Stringent Temperature. | John A. Rose |
| 2003 | CEC | The fidelity of the tag-antitag system II: reconciliation with the stringency picture. | John A. Rose, Masami Hagiya, Akira Suyama |
| 2002 | DNA | A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides. | Russell J. Deaton, Junghuei Chen, Hong Bi, John A. Rose |
| 2002 | DNA | A PNA-mediated Whiplash PCR-based Program for In Vitro Protein Evolution. | John A. Rose, Mitsunori Takano, Akira Suyama |
| 2001 | DNA | PNA-mediated Whiplash PCR. | John A. Rose, Russell J. Deaton, Masami Hagiya, Akira Suyama |
| 2001 | DNA | The Fidelity of the Tag-Antitag System. | John A. Rose, Russell J. Deaton, Masami Hagiya, Akira Suyama |
| 2000 | DNA | The Fidelity of Annealing-Ligation: A Theoretical Analysis. | John A. Rose, Russell J. Deaton |
| 1997 | ICEC | A DNA based implementation of an evolutionary search for good encodings for DNA computation. | Russell J. Deaton, R. C. Murphy, John A. Rose, Max H. Garzon, Donald R. Franceschetti, S. E. Stevens |