Gnome - an Internet-based sequence analysis tool. - Kenta Nakai; T. Tokimori; A. Ogiwara; Ikuo Uchiyama; T. Niiyama (Comput. Appl. Biosci., 1994)

Automatic Construction of Knowledge Base from Biological Papers. - Yoshihiro Ohta; Yasunori Yamamoto; Tomoko Okazaki; Ikuo Uchiyama; Toshihisa Takagi (ISMB, 1997)

MBGD: microbial genome database for comparative analysis. - Ikuo Uchiyama (Nucleic Acids Res., 2003)

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. - Ikuo Uchiyama; Toshio Higuchi; Ichizo Kobayashi (BMC Bioinform., 2006)

MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. - Ikuo Uchiyama (Nucleic Acids Res., 2007)

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. - Ikuo Uchiyama; Toshio Higuchi; Mikihiko Kawai (Nucleic Acids Res., 2010)

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. - Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba (Nucleic Acids Res., 2013)

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. - Hirokazu Chiba; Ikuo Uchiyama (BMC Bioinform., 2014)

SPANG: A Command-line Client Supporting Query Generation for Distributed SPARQL Endpoints. - Hirokazu Chiba; Ikuo Uchiyama (SWAT4LS, 2015)

Towards the Semantic Standardization of Orthology Content. - Jesualdo Tomás Fernández-Breis; María Del Carmen Legaz-García; Hirokazu Chiba; Ikuo Uchiyama (SWAT4LS, 2015)

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. - Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba (Nucleic Acids Res., 2015)

The Orthology Ontology: development and applications. - Jesualdo Tomás Fernández-Breis; Hirokazu Chiba; María Del Carmen Legaz-García; Ikuo Uchiyama (J. Biomed. Semant., 2016)

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. - Hirokazu Chiba; Ikuo Uchiyama (BMC Bioinform., 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)

MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons. - Ikuo Uchiyama; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba; Masaki Kato (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)