Towards parallel evaluation and learning of Boolean μ-formulas with molecules. - Masami Hagiya; Masanori Arita; Daisuke Kiga; Kensaku Sakamoto; Shigeyuki Yokoyama (DNA Based Computers, 1997)

Successive State Transitions with I/O Interface by Molecules. - Ken Komiya; Kensaku Sakamoto; Hidetaka Gouzu; Shigeyuki Yokoyama; Masanori Arita; Akio Nishikawa; Masami Hagiya (DNA Computing, 2000)

Genome-Wide Functional Annotation Environment forin OBIGrid. - Akinobu Fukuzaki; Takeshi Nagashima; Kaori Ide; Fumikazu Konishi; Mariko Hatakeyama; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (LSGRID, 2004)

ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences. - Eisuke Chikayama; Atsushi Kurotani; Yutaka Kuroda; Shigeyuki Yokoyama (Bioinform., 2004)

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. - Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (Bioinform., 2005)

Identification of putative domain linkers by a neural network - application to a large sequence database. - Satoshi Miyazaki; Yutaka Kuroda; Shigeyuki Yokoyama (BMC Bioinform., 2006)

Mathematical model for empirically optimizing large scale production of soluble protein domains. - Eisuke Chikayama; Atsushi Kurotani; Takanori Tanaka; Takashi Yabuki; Satoshi Miyazaki; Shigeyuki Yokoyama; Yutaka Kuroda (BMC Bioinform., 2010)

Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening. - Tomohiro Sato; Teruki Honma; Shigeyuki Yokoyama (J. Chem. Inf. Model., 2010)

Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning. - Daisuke Takaya; Tomohiro Sato; Hitomi Yuki; Shunta Sasaki; Akiko Tanaka; Shigeyuki Yokoyama; Teruki Honma (J. Chem. Inf. Model., 2013)

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach. - Chiduru Watanabe; Hirofumi Watanabe; Kaori Fukuzawa; Lorien J. Parker; Yoshio Okiyama; Hitomi Yuki; Shigeyuki Yokoyama; Hirofumi Nakano; Shigenori Tanaka; Teruki Honma (J. Chem. Inf. Model., 2017)