Hidemasa Bono

According to our database, Hidemasa Bono authored at least 17 papers between 1999 and 2025.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2025

PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing.

Kazuki Nakamae, Saya Ide, Nagaki Ohnuki, Yoshiko Nakagawa, Keisuke Okuhara, Hidemasa Bono

BMC Bioinform., December, 2025

Pipeline to explore information on genome editing using large language models and genome editing meta-database.

Takayuki Suzuki, Hidemasa Bono

Database J. Biol. Databases Curation, 2025

2021

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

Imad Abugessaisa, Jordan A. Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi, Michihira Tagami, Fumi Hori, Saumya Agrawal, Chung-Chau Hon, Mélissa Cardon, Shuya Ikeda, Hiromasa Ono, Hidemasa Bono, Masaki Kato, Kosuke Hashimoto, Alessandro Bonetti, Norio Kobayashi, Jay W. Shin, Michiel J. L. de Hoon, Yoshihide Hayashizaki, Piero Carninci, Hideya Kawaji, Takeya Kasukawa

Nucleic Acids Res., 2021

2020

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, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

F1000Research, 2020

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, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi

F1000Research, 2019

2017

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David J. Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A. Ramilowski, Owen J. L. Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Takeya Kasukawa, Hideya Kawaji

Nucleic Acids Res., 2017

2015

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.

Yuki Naito, Kimihiro Hino, Hidemasa Bono, Kumiko Ui-Tei

Bioinform., 2015

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, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-an Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin

J. Biomed. Semant., 2014

2012

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

Yuki Naito, Hidemasa Bono

Nucleic Acids Res., 2012

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.

Shin Kawano, Hiromasa Ono, Toshihisa Takagi, Hidemasa Bono

Briefings Bioinform., 2012

2011

Allie: a database and a search service of abbreviations and long forms.

Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono, Toshihisa Takagi

Database J. Biol. Databases Curation, 2011

2009

Gendoo: Functional profiling of gene and disease features using MeSH vocabulary.

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi

Nucleic Acids Res., 2009

2008

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, Minoru Asogawa

Silico Biol., 2008

2003

MaXML: mouse annotation XML.

Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda

Silico Biol., 2003

2002

READ: RIKEN Expression Array Database.

Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki

Nucleic Acids Res., 2002

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki

Nucleic Acids Res., 2002

1999

KEGG: Kyoto Encyclopedia of Genes and Genomes.

Hiroyuki Ogata, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono, Minoru Kanehisa

Nucleic Acids Res., 1999