PROGRAPE-1: A Programmable Special-Purpose Computer for Many-Body Simulations. - Tsuyoshi Hamada; Toshiyuki Fukushige; Atsushi Kawai; Junichiro Makino (FCCM, 1998)

Massively Parallel Processors Generator for Reconfigurable System. - Tsuyoshi Hamada; Naohito Nakasato (FCCM, 2005)

Astrophysical Hydrodynamics Simulations on a Reconfigurable System. - Naohito Nakasato; Tsuyoshi Hamada (FCCM, 2005)

PGR: A Software Package for Reconfigurable Super-Computing. - Tsuyoshi Hamada; Naohito Nakasato (FPL, 2005)

Bayesian Multi-topic Microarray Analysis with Hyperparameter Reestimation. - Tomonari Masada; Tsuyoshi Hamada; Yuichiro Shibata; Kiyoshi Oguri (ADMA, 2009)

A Comparative Study on ASIC, FPGAs, GPUs and General Purpose Processors in the O(N^2) Gravitational N-body Simulation. - Tsuyoshi Hamada; Khaled Benkrid; Keigo Nitadori; Makoto Taiji (AHS, 2009)

Accelerating Phase Correlation Functions Using GPU and FPGA. - Kentaro Matsuo; Tsuyoshi Hamada; Masayuki Miyoshi; Yuichiro Shibata; Kiyoshi Oguri (AHS, 2009)

Dynamic hyperparameter optimization for bayesian topical trend analysis. - Tomonari Masada; Daiji Fukagawa; Atsuhiro Takasu; Tsuyoshi Hamada; Yuichiro Shibata; Kiyoshi Oguri (CIKM, 2009)

Accelerating Collapsed Variational Bayesian Inference for Latent Dirichlet Allocation with Nvidia CUDA Compatible Devices. - Tomonari Masada; Tsuyoshi Hamada; Yuichiro Shibata; Kiyoshi Oguri (IEA/AIE, 2009)

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs. - Cheng Ling; Khaled Benkrid; Tsuyoshi Hamada (SASP, 2009)

42 TFlops hierarchical N-body simulations on GPUs with applications in both astrophysics and turbulence. - Tsuyoshi Hamada; Tetsu Narumi; Rio Yokota; Kenji Yasuoka; Keigo Nitadori; Makoto Taiji (SC, 2009)

Bag of Timestamps: A Simple and Efficient Bayesian Chronological Mining. - Tomonari Masada; Atsuhiro Takasu; Tsuyoshi Hamada; Yuichiro Shibata; Kiyoshi Oguri (APWeb/WAIM, 2009)

A novel multiple-walk parallel algorithm for the Barnes-Hut treecode on GPUs - towards cost effective, high performance N-body simulation. - Tsuyoshi Hamada; Keigo Nitadori; Khaled Benkrid; Yousuke Ohno; Gentaro Morimoto; Tomonari Masada; Yuichiro Shibata; Kiyoshi Oguri; Makoto Taiji (Comput. Sci. Res. Dev., 2009)

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs. - Keisuke Dohi; Khaled Benkrid; Cheng Ling; Tsuyoshi Hamada; Yuichiro Shibata (ASAP, 2010)

190 TFlops Astrophysical N-body Simulation on a Cluster of GPUs. - Tsuyoshi Hamada; Keigo Nitadori (SC, 2010)

Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs - Rio Yokota; Tsuyoshi Hamada; Jaydeep P. Bardhan; Matthew G. Knepley; Lorena A. Barba (CoRR, 2010)

Implementation of a programming environment with a multithread model for reconfigurable systems. - Keisuke Dohi; Yuichiro Shibata; Tsuyoshi Hamada; Tomonari Masada; Kiyoshi Oguri; Duncan A. Buell (SIGARCH Comput. Archit. News, 2010)

Astrophysical SPH Simulations with raceSPH Library. - Lei Liu; Guillermo Marcus Martinez; Peter Berczik; Tsuyoshi Hamada; Ingo Berentzen; Andreas Kugel; Reinhard Männer; Robi Banerjee; Ralf Klessen; Rainer Spurzem (CSE, 2011)

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns. - Rio Yokota; Jaydeep P. Bardhan; Matthew G. Knepley; Lorena A. Barba; Tsuyoshi Hamada (Comput. Phys. Commun., 2011)

Astrophysical particle simulations with large custom GPU clusters on three continents. - Rainer Spurzem; Peter Berczik; Ingo Berentzen; Keigo Nitadori; Tsuyoshi Hamada; Guillermo Marcus Martinez; Andreas Kugel; Reinhard Männer; J. Fiestas; Robi Banerjee; Ralf Klessen (Comput. Sci. Res. Dev., 2011)

High performance phylogenetic analysis on CUDA-compatible GPUs. - Cheng Ling; Khaled Benkrid; Tsuyoshi Hamada (SIGARCH Comput. Archit. News, 2012)

Up to 700k GPU Cores, Kepler, and the Exascale Future for Simulations of Star Clusters Around Black Holes. - Peter Berczik; Rainer Spurzem; Shiyan Zhong; Long Wang 014; Keigo Nitadori; Tsuyoshi Hamada; Alexander Veles (ISC, 2013)

A GRASS GIS parallel module for radio-propagation predictions. - Lucas Benedicic; Felipe A. Cruz; Tsuyoshi Hamada; Peter Korosec (Int. J. Geogr. Inf. Sci., 2014)

Optimizing the Bayesian Inference of Phylogeny on Graphic Processors. - Cheng Ling; Chunbao Zhou; Arong Luo; Guoguang Zhao; Tsuyoshi Hamada; Xiaoyan Zhu 001 (CCGRID, 2015)

An Open Approach to Autonomous Vehicles. - Shinpei Kato; Eijiro Takeuchi; Yoshio Ishiguro; Yoshiki Ninomiya; Kazuya Takeda; Tsuyoshi Hamada (IEEE Micro, 2015)

MrBayes tgMC3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method. - Cheng Ling; Tsuyoshi Hamada; Jing-Yang Gao; Guoguang Zhao; Donghong Sun; Weifeng Shi (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Biomarker correlation network in colorectal carcinoma by tumor anatomic location. - Reiko Nishihara; Kimberly Glass; Kosuke Mima; Tsuyoshi Hamada; Jonathan A. Nowak; Zhi Rong Qian; Peter Kraft; Edward L. Giovannucci; Charles S. Fuchs; Andrew T. Chan; John Quackenbush; Shuji Ogino; et al. (BMC Bioinform., 2017)

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment. - Mai Chan Lau; Jennifer Borowsky; Juha P. Väyrynen; Koichiro Haruki; Melissa Zhao; Andressa Dias Costa; Simeng Gu; Annacarolina Da Silva; Tomotaka Ugai; Kota Arima; Minh N. Nguyen; Yasutoshi Takashima; et al. (PLoS Comput. Biol., 2025)