KEGG: Kyoto Encyclopedia of Genes and Genomes. - Hiroyuki Ogata; Susumu Goto; Kazushige Sato; Wataru Fujibuchi; Hidemasa Bono; Minoru Kanehisa (Nucleic Acids Res., 1999)

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. - Hidemasa Bono; Takeya Kasukawa; Masaaki Furuno; Yoshihide Hayashizaki; Yasushi Okazaki (Nucleic Acids Res., 2002)

READ: RIKEN Expression Array Database. - Hidemasa Bono; Takeya Kasukawa; Yoshihide Hayashizaki; Yasushi Okazaki (Nucleic Acids Res., 2002)

MaXML: mouse annotation XML. - Takeya Kasukawa; Hidemasa Bono; Yoshihide Hayashizaki; Yasushi Okazaki; Hideo Matsuda (Silico Biol., 2003)

BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes. - Takeru Nakazato; Toru Takinaka; Hironori Mizuguchi; Hideo Matsuda; Hidemasa Bono; Minoru Asogawa (Silico Biol., 2008)

Gendoo: Functional profiling of gene and disease features using MeSH vocabulary. - Takeru Nakazato; Hidemasa Bono; Hideo Matsuda; Toshihisa Takagi (Nucleic Acids Res., 2009)

Allie: a database and a search service of abbreviations and long forms. - Yasunori Yamamoto; Atsuko Yamaguchi; Hidemasa Bono; Toshihisa Takagi (Database J. Biol. Databases Curation, 2011)

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. - Shin Kawano; Hiromasa Ono; Toshihisa Takagi; Hidemasa Bono (Briefings Bioinform., 2012)

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

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. - Toshiaki Katayama; Mark D. Wilkinson; Kiyoko F. Aoki-Kinoshita; Shuichi Kawashima; Yasunori Yamamoto; Atsuko Yamaguchi; Shinobu Okamoto; Shin Kawano; Jin-Dong Kim; Yue Wang 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

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

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. - Marina Lizio; Jayson Harshbarger; Imad Abugessaisa; Shuei Noguchi; Atsushi Kondo; Jessica Severin; Chris Mungall; David J. Arenillas; Anthony Mathelier; Yulia A. Medvedeva; Andreas Lennartsson; Finn Drabløs; et al. (Nucleic Acids Res., 2017)

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)

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)

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. - Imad Abugessaisa; Jordan A. Ramilowski; Marina Lizio; Jesicca Severin; Akira Hasegawa; Jayson Harshbarger; Atsushi Kondo; Shuhei Noguchi; Chi Wai Yip; Jasmine Li Ching Ooi; Michihira Tagami; Fumi Hori; et al. (Nucleic Acids Res., 2021)

Pipeline to explore information on genome editing using large language models and genome editing meta-database. - Takayuki Suzuki; Hidemasa Bono (Database J. Biol. Databases Curation, 2025)

PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing. - Kazuki Nakamae; Saya Ide; Nagaki Ohnuki; Yoshiko Nakagawa; Keisuke Okuhara; Hidemasa Bono (BMC Bioinform., 2025)