Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. - Akira R. Kinjo; Ken Nishikawa (Bioinform., 2004)

Recoverable one-dimensional encoding of three-dimensional protein structures. - Akira R. Kinjo; Ken Nishikawa (Bioinform., 2005)

CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. - Akira R. Kinjo; Ken Nishikawa (BMC Bioinform., 2006)

Protein structure databases with new web services for structural biology and biomedical research. - Daron M. Standley; Akira R. Kinjo; Kengo Kinoshita; Haruki Nakamura (Briefings Bioinform., 2008)

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. - Akira R. Kinjo; Reiko Yamashita; Haruki Nakamura (Database J. Biol. Databases Curation, 2010)

SeSAW: balancing sequence and structural information in protein functional mapping. - Daron M. Standley; Reiko Yamashita; Akira R. Kinjo; Hiroyuki Toh; Haruki Nakamura (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

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)

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. - Akira R. Kinjo; Hirofumi Suzuki; Reiko Yamashita; Yasuyo Ikegawa; Takahiro Kudou; Reiko Igarashi; Yumiko Kengaku; Hasumi Cho; Daron M. Standley; Atsushi Nakagawa; Haruki Nakamura (Nucleic Acids Res., 2012)

Implementation of linked data in the life sciences at BioHackathon 2011. - Kiyoko F. Aoki-Kinoshita; Akira R. Kinjo; Mizuki Morita; Yoshinobu Igarashi; Yi-an Chen; Yasumasa Shigemoto; Takatomo Fujisawa; Yukie Akune; Takeo Katoda; Anna Kokubu; Takaaki Mori; Mitsuteru Nakao; et al. (J. Biomed. Semant., 2015)

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. - Masashi Yokochi; Naohiro Kobayashi; Eldon L. Ulrich; Akira R. Kinjo; Takeshi Iwata; Yannis E. Ioannidis; Miron Livny; John L. Markley; Haruki Nakamura; Chojiro Kojima; Toshimichi Fujiwara (J. Biomed. Semant., 2016)

Molmil: a molecular viewer for the PDB and beyond. - Gert-Jan Bekker; Haruki Nakamura; Akira R. Kinjo (J. Cheminformatics, 2016)

Neuro-symbolic representation learning on biological knowledge graphs. - Mona Alshahrani; Mohammad Asif Khan 001; Omar Maddouri; Akira R. Kinjo; Núria Queralt-Rosinach; Robert Hoehndorf (Bioinform., 2017)

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. - Akira R. Kinjo; Gert-Jan Bekker; Hirofumi Suzuki; Yuko Tsuchiya; Takeshi Kawabata; Yasuyo Ikegawa; Haruki Nakamura (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)

Hybrid Fuzzy-Crisp Clustering Algorithm: Theory and Experiments. - Akira R. Kinjo; Daphne Teck Ching Lai (CoRR, 2023)