KAAS: an automatic genome annotation and pathway reconstruction server. - Yuki Moriya; Masumi Itoh; Shujiro Okuda; Akiyasu C. Yoshizawa; Minoru Kanehisa (Nucleic Acids Res., 2007)

CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. - Toshinori Endo; Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Kohji Hotta; Yutaka Satou; Lixy Yamada; Michio Ogasawara; Hiroki Takahashi; Ayako Nakajima; Mia Nakachi; Mamoru Nomura; et al. (Nucleic Acids Res., 2011)

ODB: a database for operon organizations, 2011 update. - Shujiro Okuda; Akiyasu C. Yoshizawa (Nucleic Acids Res., 2011)

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. - Akihiro Nakaya; Toshiaki Katayama; Masumi Itoh; Kazushi Hiranuka; Shuichi Kawashima; Yuki Moriya; Shujiro Okuda; Michihiro Tanaka; Toshiaki Tokimatsu; Yoshihiro Yamanishi; Akiyasu C. Yoshizawa; Minoru Kanehisa; et al. (Nucleic Acids Res., 2013)

A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry. - Ken Aoshima; Kentaro Takahashi; Masayuki Ikawa; Takayuki Kimura; Mitsuru Fukuda; Satoshi Tanaka; Howell E. Parry; Yuichiro Fujita; Akiyasu C. Yoshizawa; Shin-ichi Utsunomiya; Shigeki Kajihara; Koichi Tanaka; et al. (BMC Bioinform., 2014)

GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry. - Kentaro Morimoto; Takashi Nishikaze; Akiyasu C. Yoshizawa; Shigeki Kajihara; Ken Aoshima; Yoshiya Oda; Koichi Tanaka (Bioinform., 2015)

jPOSTrepo: an international standard data repository for proteomes. - Shujiro Okuda; Yu Watanabe; Yuki Moriya; Shin Kawano; Tadashi Yamamoto; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Norie Araki; Akiyasu C. Yoshizawa; Tsuyoshi Tabata; Naoyuki Sugiyama; et al. (Nucleic Acids Res., 2017)

The jPOST environment: an integrated proteomics data repository and database. - Yuki Moriya; Shin Kawano; Shujiro Okuda; Yu Watanabe; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Yoshinori Yamanouchi; Norie Araki; Akiyasu C. Yoshizawa; Tsuyoshi Tabata; Mio Iwasaki; et al. (Nucleic Acids Res., 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)

Insights into predicting small molecule retention times in liquid chromatography using deep learning. - Yuting Liu; Akiyasu C. Yoshizawa; Yiwei Ling; Shujiro Okuda (J. Cheminformatics, 2024)