EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. - Ali Masoudi-Nejad; Koichiro Tonomura; Shuichi Kawashima; Yuki Moriya; Masanori Suzuki; Masumi Itoh; Minoru Kanehisa; Takashi Endo; Susumu Goto (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)

PathPred: an enzyme-catalyzed metabolic pathway prediction server. - Yuki Moriya; Daichi Shigemizu; Masahiro Hattori; Toshiaki Tokimatsu; Masaaki Kotera; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2010)

GENIES: gene network inference engine based on supervised analysis. - Masaaki Kotera; Yoshihiro Yamanishi; Yuki Moriya; Minoru Kanehisa; Susumu Goto (Nucleic Acids Res., 2012)

KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Yuki Moriya; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (BMC Syst. Biol., 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)

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. - Masaaki Kotera; Yasuo Tabei; Yoshihiro Yamanishi; Ai Muto; Yuki Moriya; Toshiaki Tokimatsu; Susumu Goto (Bioinform., 2014)

PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list. - Masaaki Kotera; Yosuke Nishimura; Zenichi Nakagawa; Ai Muto; Yuki Moriya; Shinobu Okamoto; Shuichi Kawashima; Toshiaki Katayama; Toshiaki Tokimatsu; Minoru Kanehisa; Susumu Goto (J. Bioinform. Comput. Biol., 2014)

DINIES: drug-target interaction network inference engine based on supervised analysis. - Yoshihiro Yamanishi; Masaaki Kotera; Yuki Moriya; Ryusuke Sawada; Minoru Kanehisa; Susumu Goto (Nucleic Acids Res., 2014)

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)

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)

Integrated Growth Media Database by Standardizing Ingredient Information. - Shuichi Kawashima; Toshiaki Katayama; Yuki Moriya; Shinobu Okamoto; Yasunori Yamamoto; Susumu Goto (SWAT4HCLS, 2019)

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 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)

Happy Text Entering: Promoting Subjective Well-Being Using an Input Method for Presenting Positive Words and Phrases. - Kentaro Go; Yuki Moriya; Yuichiro Kinoshita; Jiyi Li; Fumiyo Fukumoto (OZCHI, 2021)

Design of a Hybrid Wavelength Selective Crossconnect Utilizing a Silicon Optical Switch Array. - Yuki Moriya; Fumi Nakamura; Kunio Kobayashi; Hitoshi Kawashima; Haoshuo Chen; Hiroyuki Tsuda (OECC/PSC, 2022)

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)

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)

Silicon monolithic wavelength selective switch utilizing arrayed waveguide gratings and Bragg grating filters. - Yuki Moriya; Yuta Yagi; Yuta Mizoguchi; Hiroyuki Tsuda (IEICE Electron. Express, 2024)

Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features. - Shuya Ikeda; Kiyoko F. Aoki-Kinoshita; Hirokazu Chiba; Susumu Goto; Masae Hosoda; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Tazro Ohta; Hiromasa Ono; Terue Takatsuki; Yasunori Yamamoto; et al. (J. Biomed. Semant., 2025)