Ontology-Based Medical Information Service System. - Hirokazu Taki; Noriyuki Matsuda; Michiyasu Hiramatsu; Yuki Naito; Jiro Nakajima; Tadashi Nakamura; Akihisa Imagawa; Yuji Matsuzawa; Norihiro Abe; Satoshi Hori (KES, 2003)

siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. - Yuki Naito; Tomoyuki Yamada; Kumiko Ui-Tei; Shinichi Morishita; Kaoru Saigo (Nucleic Acids Res., 2004)

dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. - Yuki Naito; Tomoyuki Yamada; Takahiro Matsumiya; Kumiko Ui-Tei; Kaoru Saigo; Shinichi Morishita (Nucleic Acids Res., 2005)

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. - Yuki Naito; Kumiko Ui-Tei; Toru Nishikawa; Yutaka Takebe; Kaoru Saigo (Nucleic Acids Res., 2006)

Hardware-aware model of sigma-delta cellular neural network. - Hisashi Aomori; Yuki Naito; Tsuyoshi Otake; Nobuaki Takahashi; Ichiro Matsuda; Susumu Itoh; Mamoru Tanaka (ECCTD, 2009)

siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. - Yuki Naito; Jun Yoshimura; Shinichi Morishita; Kumiko Ui-Tei (BMC Bioinform., 2009)

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts. - Yuki Naito; Hidemasa Bono (Nucleic Acids Res., 2012)

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. - Yuki Naito; Kimihiro Hino; Hidemasa Bono; Kumiko Ui-Tei (Bioinform., 2015)

TogoGenome/TogoStanza: modularized Semantic Web genome database. - Toshiaki Katayama; Shuichi Kawashima; Shinobu Okamoto; Yuki Moriya; Hirokazu Chiba; Yuki Naito; Takatomo Fujisawa; Hiroshi Mori; Toshihisa Takagi (Database J. Biol. Databases Curation, 2019)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

Bowel sound-based features to investigate the effect of coffee and soda on gastrointestinal motility. - Kensuke Horiyama; Takahiro Emoto; Takeyuki Haraguchi; Takashi Uebanso; Yuki Naito; Takuma Gyobu; Kenta Kanemoto; Junichi Inobe; Ayumi Sano; Masatake Akutagawa; Akira Takahashi (Biomed. Signal Process. Control., 2021)

TogoID: an exploratory ID converter to bridge biological datasets. - Shuya Ikeda; Hiromasa Ono; Tazro Ohta; Hirokazu Chiba; Yuki Naito; Yuki Moriya; Shuichi Kawashima; Yasunori Yamamoto; Shinobu Okamoto; Susumu Goto; Toshiaki Katayama (Bioinform., 2022)

Quantum Query Lower Bounds for Key Recovery Attacks on the Even-Mansour Cipher. - Akinori Kawachi; Yuki Naito (COCOON (2), 2023)

Localizatome: a database for stress-dependent subcellular localization changes in proteins. - Takahide Matsushima; Yuki Naito; Tomoki Chiba; Ryota Kurimoto; Keiko Itano; Koji Ochiai; Koichi Takahashi; Naoki Goshima; Hiroshi Asahara (Database J. Biol. Databases Curation, 2025)