ODB: a database of operons accumulating known operons across multiple genomes. - Shujiro Okuda; Toshiaki Katayama; Shuichi Kawashima; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2006)

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

KEGG for linking genomes to life and the environment. - Minoru Kanehisa; Michihiro Araki; Susumu Goto; Masahiro Hattori; Mika Hirakawa; Masumi Itoh; Toshiaki Katayama; Shuichi Kawashima; Shujiro Okuda; Toshiaki Tokimatsu; Yoshihiro Yamanishi (Nucleic Acids Res., 2008)

KEGG Atlas mapping for global analysis of metabolic pathways. - Shujiro Okuda; Takuji Yamada; Masami Hamajima; Masumi Itoh; Toshiaki Katayama; Peer Bork; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2008)

Extraction and Analysis of Chemical Modification Patterns in Drug Development. - Daichi Shigemizu; Michihiro Araki; Shujiro Okuda; Susumu Goto; Minoru Kanehisa (J. Chem. Inf. Model., 2009)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. - Toshiaki Katayama; Mark D. Wilkinson; Rutger A. Vos; Takeshi Kawashima; Shuichi Kawashima; Mitsuteru Nakao; Yasunori Yamamoto; Hong-Woo Chun; Atsuko Yamaguchi; Shin Kawano; Jan Aerts; Kiyoko F. Aoki-Kinoshita; et al. (J. Biomed. Semant., 2011)

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

iPath2.0: interactive pathway explorer. - Takuji Yamada; Ivica Letunic; Shujiro Okuda; Minoru Kanehisa; Peer Bork (Nucleic Acids Res., 2011)

Introducing glycomics data into the Semantic Web. - Kiyoko F. Aoki-Kinoshita; Jerven T. Bolleman; Matthew P. Campbell; Shin Kawano; Jin-Dong Kim; Thomas Lütteke; Masaaki Matsubara; Shujiro Okuda; René Ranzinger; Hiromichi Sawaki; Toshihide Shikanai; Daisuke Shinmachi; et al. (J. Biomed. Semant., 2013)

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)

GlycoRDF: an ontology to standardize glycomics data in RDF. - René Ranzinger; Kiyoko F. Aoki-Kinoshita; Matthew P. Campbell; Shin Kawano; Thomas Lütteke; Shujiro Okuda; Daisuke Shinmachi; Toshihide Shikanai; Hiromichi Sawaki; Philip V. Toukach; Masaaki Matsubara; Issaku Yamada; et al. (Bioinform., 2015)

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. - Yuki Moriya; Takuji Yamada; Shujiro Okuda; Zenichi Nakagawa; Masaaki Kotera; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (J. Chem. Inf. Model., 2016)

GlyTouCan 1.0 - The international glycan structure repository. - Kiyoko F. Aoki-Kinoshita; Sanjay Agravat; Nobuyuki P. Aoki; Sena Arpinar; Richard D. Cummings; Akihiro Fujita; Noriaki Fujita; Gerald M. Hart; Stuart M. Haslam; Toshisuke Kawasaki; Masaaki Matsubara; Kelley W. Moreman; et al. (Nucleic Acids Res., 2016)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

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)

Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. - Jin-Dong Kim; Yue Wang 040; Toyofumi Fujiwara; Shujiro Okuda; Tiffany J. Callahan; K. Bretonnel Cohen (Bioinform., 2019)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

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)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. - Hayato Takihara; Nobuaki Miura; Kiyoko F. Aoki-Kinoshita; Shujiro Okuda (BMC Bioinform., 2021)

GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. - Yu Watanabe; Kiyoko F. Aoki-Kinoshita; Yasushi Ishihama; Shujiro Okuda (Nucleic Acids Res., 2021)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)

Enteropathway: the metabolic pathway database for the human gut microbiota. - Hirotsugu Shiroma; Youssef Darzi; Etsuko Terajima; Zenichi Nakagawa; Hirotaka Tsuchikura; Naoki Tsukuda; Yuki Moriya; Shujiro Okuda; Susumu Goto; Takuji Yamada (Briefings Bioinform., 2024)

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)