BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. - Hongyan Wu; Toyofumi Fujiwara; Yasunori Yamamoto; Jerven T. Bolleman; Atsuko Yamaguchi (J. Biomed. Semant., 2014)

Colil: a database and search service for citation contexts in the life sciences domain. - Toyofumi Fujiwara; Yasunori Yamamoto (J. Biomed. Semant., 2015)

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)

Gene Ranking based on Paths from Phenotypes to Genes on Knowledge Graph. - Atsuko Yamaguchi; Jae-Moon Shin; Toyofumi Fujiwara (IJCKG, 2021)

Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases. - Jae-Moon Shin; Toyofumi Fujiwara; Atsuko Yamaguchi (SWAT4HCLS, 2023)

Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases. - Jae-Moon Shin; Toyofumi Fujiwara; Hirotomo Saitsu; Atsuko Yamaguchi (BMC Medical Informatics Decis. Mak., 2025)