| 2017 | CiE | Counting Substrate Cycles in Topologically Restricted Metabolic Networks. | Robert D. Barish, Akira Suyama |
| 2012 | DNA | A DNA Based Molecular Logic Gate Capable of a Variety of Logical Operations. | Anton Kan, Ko-ichiroh Shohda, Akira Suyama |
| 2009 | DNA | Construction of AND Gate for RTRACS with the Capacity of Extension to NAND Gate. | Yoko Sakai, Yoriko Mawatari, Kiyonari Yamasaki, Ko-ichiroh Shohda, Akira Suyama |
| 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 |
| 2007 | DNA | Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics. | Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, Akira Suyama |
| 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 |
| 2005 | DNA | Control of DNA Molecules on a Microscopic Bead Using Optical Techniques for Photonic DNA Memory. | Yusuke Ogura, Taro Beppu, Masahiro Takinoue, Akira Suyama, Jun Tanida |
| 2004 | DNA | Methods for Manipulating DNA Molecules in a Micrometer Scale Using Optical Techniques. | Yusuke Ogura, Takashi Kawakami, Fumika Sumiyama, Satoru Irie, Akira Suyama, Jun Tanida |
| 2003 | CEC | The fidelity of the tag-antitag system II: reconciliation with the stringency picture. | John A. Rose, Masami Hagiya, Akira Suyama |
| 2003 | DNA | Autonomous Biomolecular Computer Modeled after Retroviral Replication. | Nao Nitta, Akira Suyama |
| 2003 | DNA | Parallel Translation of DNA Clusters by VCSEL Array Trapping and Temperature Control with Laser Illumination. | Yusuke Ogura, Takashi Kawakami, Fumika Sumiyama, Akira Suyama, Jun Tanida |
| 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 |
| 1997 | ICEC | Joining and rotating data with molecules. | Masanori Arita, Masami Hagiya, Akira Suyama |