| 2015 | CCGRID | Optimizing the Bayesian Inference of Phylogeny on Graphic Processors. | Cheng Ling, Chunbao Zhou, Arong Luo, Guoguang Zhao, Tsuyoshi Hamada, Xiaoyan Zhu |
| 2010 | SC | 190 TFlops Astrophysical N-body Simulation on a Cluster of GPUs. | Tsuyoshi Hamada, Keigo Nitadori |
| 2009 | ADMA | Bayesian Multi-topic Microarray Analysis with Hyperparameter Reestimation. | Tomonari Masada, Tsuyoshi Hamada, Yuichiro Shibata, Kiyoshi Oguri |
| 2009 | CIKM | Dynamic hyperparameter optimization for bayesian topical trend analysis. | Tomonari Masada, Daiji Fukagawa, Atsuhiro Takasu, Tsuyoshi Hamada, Yuichiro Shibata, Kiyoshi Oguri |
| 2009 | SC | 42 TFlops hierarchical | Tsuyoshi Hamada, Tetsu Narumi, Rio Yokota, Kenji Yasuoka, Keigo Nitadori, Makoto Taiji |
| 2005 | FCCM | Massively Parallel Processors Generator for Reconfigurable System. | Tsuyoshi Hamada, Naohito Nakasato |
| 2005 | FCCM | Astrophysical Hydrodynamics Simulations on a Reconfigurable System. | Naohito Nakasato, Tsuyoshi Hamada |
| 2005 | FPL | PGR: A Software Package for Reconfigurable Super-Computing. | Tsuyoshi Hamada, Naohito Nakasato |
| 1998 | FCCM | PROGRAPE-1: A Programmable Special-Purpose Computer for Many-Body Simulations. | Tsuyoshi Hamada, Toshiyuki Fukushige, Atsushi Kawai, Junichiro Makino |