Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. - Yoshinori Tamada; Hideo Bannai; Seiya Imoto; Toshiaki Katayama; Minoru Kanehisa; Satoru Miyano (J. Bioinform. Comput. Biol., 2005)

From genomics to chemical genomics: new developments in KEGG. - Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F. Aoki-Kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa (Nucleic Acids Res., 2006)

ODB: a database of operons accumulating known operons across multiple genomes. - Shujiro Okuda; Toshiaki Katayama; Shuichi Kawashima; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2006)

KEGG for linking genomes to life and the environment. - Minoru Kanehisa; Michihiro Araki; Susumu Goto; Masahiro Hattori; Mika Hirakawa; Masumi Itoh; Toshiaki Katayama; Shuichi Kawashima; Shujiro Okuda; Toshiaki Tokimatsu; Yoshihiro Yamanishi (Nucleic Acids Res., 2008)

AAindex: amino acid index database, progress report 2008. - Shuichi Kawashima; Piotr Pokarowski; Maria Pokarowska; Andrzej Kolinski; Toshiaki Katayama; Minoru Kanehisa (Nucleic Acids Res., 2008)

KEGG Atlas mapping for global analysis of metabolic pathways. - Shujiro Okuda; Takuji Yamada; Masami Hamajima; Masumi Itoh; Toshiaki Katayama; Peer Bork; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2008)

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. - Hiroyuki Wakaguri; Yutaka Suzuki; Toshiaki Katayama; Shuichi Kawashima; Eri Kibukawa; Kazushi Hiranuka; Masahide Sasaki; Sumio Sugano; Junichi Watanabe (Nucleic Acids Res., 2009)

BioRuby: bioinformatics software for the Ruby programming language. - Naohisa Goto; Pjotr Prins; Mitsuteru Nakao; Raoul Jean Pierre Bonnal; Jan Aerts; Toshiaki Katayama (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)

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. - Toshiaki Katayama; Mitsuteru Nakao; Toshihisa Takagi (Nucleic Acids Res., 2010)

BioMart Central Portal: an open database network for the biological community. - Jonathan M. Guberman; Jiye Ai; Olivier Arnaiz; Joachim Baran; Andrew Blake 003; Richard A. Baldock; Claude Chelala; David Croft 001; Anthony Cros; Rosalind J. Cutts; Alex Di Génova; Simon A. Forbes; et al. (Database J. Biol. Databases Curation, 2011)

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)

Semantic Integration of the Genome Annotations. - Toshiaki Katayama; Shinobu Okamoto; Shuichi Kawashima; Hiroshi Mori; Takatomo Fujisawa (SWAT4LS, 2012)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. - Raoul Jean Pierre Bonnal; Jan Aerts; George Githinji; Naohisa Goto; Daniel MacLean; Chase A. Miller; Hiroyuki Mishima; Massimiliano Pagani; Ricardo Ramirez-Gonzalez; Geert Smant; Francesco Strozzi; Rob Syme; et al. (Bioinform., 2012)

The Ruby UCSC API: accessing the UCSC genome database using Ruby. - Hiroyuki Mishima; Jan Aerts; Toshiaki Katayama; Raoul Jean Pierre Bonnal; Koh-ichiro Yoshiura (BMC Bioinform., 2012)

Interactive Platform for Semantic Gene Expression Analysis of Alzheimer's Disease. - Toshiaki Katayama; Masataka Kikuchi; Soichi Ogishima (SWAT4LS, 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)

D3SPARQL: JavaScript Library for Visualization of SPARQL Results. - Toshiaki Katayama (SWAT4LS, 2014)

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)

Community-driven development for computational biology at Sprints, Hackathons and Codefests. - Steffen Möller; Enis Afgan; Michael Banck; Raoul Jean Pierre Bonnal; Timothy Booth; John Chilton; Peter J. A. Cock; Markus Gumbel; Nomi L. Harris; Richard C. G. Holland; Matús Kalas; László Kaján; et al. (BMC 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)

CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. - Takatomo Fujisawa; Shinobu Okamoto; Toshiaki Katayama; Mitsuteru Nakao; Hidehisa Yoshimura; Hiromi Kajiya-Kanegae; Sumiko Yamamoto; Chiyoko Yano; Yuka Yanaka; Hiroko Maita; Takakazu Kaneko; Satoshi Tabata; et al. (Nucleic Acids Res., 2014)

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. - Shin Kawano; Tsutomu Watanabe; Sohei Mizuguchi; Norie Araki; Toshiaki Katayama; Atsuko Yamaguchi (Nucleic Acids Res., 2014)

D2RQ Mapper. - Yasunori Yamamoto; Toshiaki Katayama (SWAT4LS, 2015)

SPARQL-enabled identifier conversion with Identifiers.org. - Sarala M. Wimalaratne; Jerven T. Bolleman; Nick S. Juty; Toshiaki Katayama; Michel Dumontier; Nicole Redaschi; Nicolas Le Novère; Henning Hermjakob; Camille Laibe (Bioinform., 2015)

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)

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. - Yuichi Kodama; Jun Mashima; Takehide Kosuge; Toshiaki Katayama; Takatomo Fujisawa; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura (Nucleic Acids Res., 2015)

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. - Jerven T. Bolleman; Christopher J. Mungall; Francesco Strozzi; Joachim Baran; Michel Dumontier; Raoul Jean Pierre Bonnal; Robert M. Buels; Robert Hoehndorf; Takatomo Fujisawa; Toshiaki Katayama; Peter J. A. Cock (J. Biomed. Semant., 2016)

DNA data bank of Japan (DDBJ) progress report. - Jun Mashima; Yuichi Kodama; Takehide Kosuge; Takatomo Fujisawa; Toshiaki Katayama; Hideki Nagasaki; Yoshihiro Okuda; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Yasukazu Nakamura; Toshihisa Takagi (Nucleic Acids Res., 2016)

Construction of Knowledge-Base for Clinical Interpretation of Genomic Variants. - Mayumi Kamada; Toshiaki Katayama; Shuichi Kawashima; Ryosuke Kojima; Masahiko Nakatsui; Yasushi Okuno (SWAT4LS, 2017)

SPARQList: Markdown-Based Highly Configurable REST API Hosting Server for SPARQL. - Toshiaki Katayama; Shuichi Kawashima (SWAT4LS, 2017)

SPARQL-Proxy: A Generic Proxy Server for SPARQL Endpoint. - Shuichi Kawashima; Toshiaki Katayama (SWAT4LS, 2017)

DNA Data Bank of Japan. - Jun Mashima; Yuichi Kodama; Takatomo Fujisawa; Toshiaki Katayama; Yoshihiro Okuda; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Yasukazu Nakamura; Toshihisa Takagi (Nucleic Acids Res., 2017)

NBDC RDF portal: a comprehensive repository for semantic data in life sciences. - Shuichi Kawashima; Toshiaki Katayama; Hideki Hatanaka; Tatsuya Kushida; Toshihisa Takagi (Database J. Biol. Databases Curation, 2018)

Med2RDF: Semantic Biomedical Knowledge-base and APIs for the Clinical Genome Medicine. - Mayumi Kamada; Toshiaki Katayama; Shuichi Kawashima; Ryosuke Kojima; Masahiko Nakatsui; Yasushi Okuno (SWAT4HCLS, 2019)

MetaStanza: Generic WebComponents Widgets for Visualizing SPARQL Results on the Web. - Toshiaki Katayama (SWAT4HCLS, 2019)

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)

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)

Ten simple rules to run a successful BioHackathon. - Leyla J. García; Erick Antezana; Alexander García Castro; Evan Bolton; Rafael C. Jiménez; Pjotr Prins; Juan M. Banda; Toshiaki Katayama (PLoS Comput. Biol., 2020)

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)

Genome Variation Ontology for annotation of complex structural variations. - Shuichi Kawashima; Takatomo Fujisawa; Toshiaki Katayama (SWAT4HCLS, 2023)

Predicting the effects of drugs and unveiling their mechanisms of action using an interpretable pharmacodynamic mechanism knowledge graph (IPM-KG). - Tatsuya Tanaka; Toshiaki Katayama; Takeshi Imai (Comput. Biol. Medicine, 2025)

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)