E-CELL: software environment for whole-cell simulation. - Masaru Tomita; Kenta Hashimoto; Koichi Takahashi; Thomas Simon Shimizu; Yuri Matsuzaki; Fumihiko Miyoshi; Kanako Saito; Sakura Tanida; Katsuyuki Yugi; J. Craig Venter; Clyde A. Hutchison III (Bioinform., 1999)

The E-CELL project: towards integrative simulation of cellular processes. - Masaru Tomita; Kenta Hashimoto; Koichi Takahashi; Yuri Matsuzaki; Ryo Matsushima; Katsuyuki Yugi; Fumihiko Miyoshi; Hisako Nakano; Yusuke Saito; Tom Shimizu; Yoichi Nakayama (RECOMB, 2000)

Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis. - Yuri Matsuzaki; Shinichi Kikuchi; Masaru Tomita (Artif. Intell. Medicine, 2007)

In silico Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis. - Yuri Matsuzaki; Yusuke Matsuzaki; Toshiyuki Sato; Yutaka Akiyama (J. Bioinform. Comput. Biol., 2009)

Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis. - Masahito Ohue; Yuri Matsuzaki; Takashi Ishida 002; Yutaka Akiyama (PRIB, 2012)

Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking. - Masahito Ohue; Yuri Matsuzaki; Takehiro Shimoda; Takashi Ishida 002; Yutaka Akiyama (BCB, 2013)

The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments. - Takehiro Shimoda; Masahito Ohue; Yuri Matsuzaki; Takayuki Fujiwara; Nobuyuki Uchikoga; Takashi Ishida 002; Yutaka Akiyama (BCB, 2013)

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments. - Yuri Matsuzaki; Nobuyuki Uchikoga; Masahito Ohue; Takehiro Shimoda; Toshiyuki Sato; Takashi Ishida 002; Yutaka Akiyama (Source Code Biol. Medicine, 2013)

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers. - Masahito Ohue; Takehiro Shimoda; Shuji Suzuki; Yuri Matsuzaki; Takashi Ishida 002; Yutaka Akiyama (Bioinform., 2014)

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. - Takanori Hayashi; Yuri Matsuzaki; Keisuke Yanagisawa; Masahito Ohue; Yutaka Akiyama (BMC Bioinform., 2018)

Development of Computational Pipeline Software for Genome/Exome Analysis on the K Computer. - Kento Aoyama; Masanori Kakuta; Yuri Matsuzaki; Takashi Ishida 002; Masahito Ohue; Yutaka Akiyama (Supercomput. Front. Innov., 2020)