The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated application
Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul JP Bonnal, José M Fernández, Takatomo Fujisawa, Paul MK Gordon, Naohisa Goto, Syed Haider, Todd Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Greg von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh and Toshihisa Takagi
Journal of Biomedical Semantics 2011, 2:4 doi:10.1186/2041-1480-2-4

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV
Shin Kawano, Hiromasa Ono, Toshihisa Takagi and Hidemasa Bono
Brief Bioinform (2011) doi: 10.1093/bib/bbr039

Allie: a database and a search service of abbreviations and long forms
Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono and Toshihisa Takagi
Database (2011) 2011 doi: 10.1093/database/bar013

TogoDoc Server/Client System: Smart Recommendation and Efficient Management of Life Science Literature
Wataru Iwasaki, Yasunori Yamamoto, Toshihisa Takagi
PLoS ONE 5, e15305. (2010)

BioRuby: Bioinformatics software for the Ruby programming language
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama
Bioinformatics, doi:10.1093/bioinformatics/btq475

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, Load Hendrix Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, Jose M Fernendez, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, Rene Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai and Toshihisa Takagi
Journal of Biomedical Semantics 2010, 1:8doi:10.1186/2041-1480-1-8

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services
Toshiaki Katayama, Mitsuteru Nakao and Toshihisa Takagi
Nucleic Acids Research Web Server Issue

Gendoo: Functional profiling of gene and disease features using MeSH vocabulary
Takeru Nakazato, Hidemasa Bono, Hideo Matsuda and Toshihisa Takagi
Nucleic Acids Research Web Server Issue, 2009, Vol. 37, No. suppl_2 W166-W169

BodyParts3D: 3D structure database for anatomical concepts
Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi and Kousaku Okubo
Nucleic Acids Research Database Issue,

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 and Minoru Asogawa
In Silico Biology 8, 0006 (2007)

OReFiL: an online resource finder for life sciences
Yasunori Yamamoto and Toshihisa Takagi
BMC Bioinformatics 2007, 8:287