| 2006 | CHI | Active CyberCode: a directly controllable 2D code. | Yuji Ayatsuka, Jun Rekimoto |
| 2005 | CHI | tranSticks: physically manipulatable virtual connections. | Yuji Ayatsuka, Jun Rekimoto |
| 2003 | CHI | ShownPass: an easy access control with a displayed password. | Yuji Ayatsuka, Michimune Kohno, Jun Rekimoto |
| 2003 | Interact | Proximal Interactions: A Direct Manipulation Technique for Wireless Networking. | Jun Rekimoto, Yuji Ayatsuka, Michimune Kohno, Haruo Oba |
| 2001 | CHI | ChatScape: a visual informal communication tool in communities. | Yuji Ayatsuka, Nobuyuki Matsushita, Jun Rekimoto |
| 2000 | CHI | HyperPalette: a hybrid computing environment for small computing devices. | Yuji Ayatsuka, Nobuyuki Matsushita, Jun Rekimoto |
| 2000 | ISWC | Wearable Key: Device for Personalizing Nearby Environment. | Nobuyuki Matsushita, Shigeru Tajima, Yuji Ayatsuka, Jun Rekimoto |
| 2000 | UIST | Dual touch: a two-handed interface for pen-based PDAs. | Nobuyuki Matsushita, Yuji Ayatsuka, Jun Rekimoto |
| 1998 | CHI | Adding another communication channel to reality: an experience with a chat-augmented conference. | Jun Rekimoto, Yuji Ayatsuka, Hitoraka Uoi, Toshifumi Arai |
| 1998 | ISWC | Augment-able Reality: Situated Communication through Physical and Digital Spaces. | Jun Rekimoto, Yuji Ayatsuka, Kazuteru Hayashi |
| 1998 | UIST | Popup Vernier: A Tool for Sub-Pixel-Pitch Dragging with Smooth Mode Transition. | Yuji Ayatsuka, Jun Rekimoto, Satoshi Matsuoka |
| 1996 | UIST | Penumbrae for 3D Interactions. | Yuji Ayatsuka, Satoshi Matsuoka, Jun Rekimoto |