| 2008 | DNA | Experimental Validation of Signal Dependent Operation in Whiplash PCR. | Ken Komiya, Masayuki Yamamura, John A. Rose |
| 2007 | CEC | An implementation of Aqueous memory molecules with light responsive DNAs. | Masayuki Yamamura, Noriko Hirayama, Ken Komiya |
| 2007 | DNA | An Interface for a Computing Model Using Methylation to Allow Precise Population Control by Quantitative Monitoring. | Ken Komiya, Noriko Hirayama, Masayuki Yamamura |
| 2007 | DNA | A Realization of DNA Molecular Machine That Walks Autonomously by Using a Restriction Enzyme. | Hiroyuki Sekiguchi, Ken Komiya, Daisuke Kiga, Masayuki Yamamura |
| 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 |
| 2003 | CEC | Branching DNA machines based on transitions of hairpin structures. | Mitsuhiro Kubota, Kazumasa Ohtake, Ken Komiya, Kensaku Sakamoto, Masami Hagiya |
| 2000 | DNA | Successive State Transitions with I/O Interface by Molecules. | Ken Komiya, Kensaku Sakamoto, Hidetaka Gouzu, Shigeyuki Yokoyama, Masanori Arita, Akio Nishikawa, Masami Hagiya |
| 2000 | GECCO | Improving Sequence Design for DNA Computing. | Masanori Arita, Akio Nishikawa, Masami Hagiya, Ken Komiya, Hidetaka Gouzu, Kensaku Sakamoto |