Computational Challenges in Cell Simulation: A Software Engineering Approach. - Kouichi Takahashi; Katsuyuki Yugi; Kenta Hashimoto; Yohei Yamada; Christopher J. F. Pickett; Masaru Tomita (IEEE Intell. Syst., 2002)

KEGG-Based Pathway Visualization Tool for Complex Omics Data. - Kazuharu Arakawa; Nobuaki Kono; Yohei Yamada; Hirotada Mori; Masaru Tomita (Silico Biol., 2005)

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. - Kazuharu Arakawa; Yohei Yamada; Kosaku Shinoda; Yoichi Nakayama; Masaru Tomita (BMC Bioinform., 2006)

Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli. - Yousuke Nishio; Soichi Ogishima; Masao Ichikawa; Yohei Yamada; Yoshihiro Usuda; Tadashi Masuda; Hiroshi Tanaka (BMC Syst. Biol., 2013)

Scalable rank-mapping algorithm for an icosahedral grid system on the massive parallel computer with a 3-D torus network. - Chihiro Kodama; Masaaki Terai; Akira T. Noda; Yohei Yamada; Masaki Satoh; Tatsuya Seiki; Shin-ichi Iga; Hisashi Yashiro; Hirofumi Tomita; Kazuo Minami (Parallel Comput., 2014)