Hidemasa Bono

J-GLOBAL         Last updated: May 19, 2019 at 09:31
Hidemasa Bono
Research Organization of Information and Systems
Database Center for Life Science
Job title
Project Associate Professor
Twitter ID

Research Areas


Academic & Professional Experience

Jul 2007
Project Associate Professor, Database Center for Life Science, Research Organization of Information and Systems

Published Papers

Hidemasa Bono
BioRxiv   https://doi.org/10.1101/626754   May 2019
Gene expression data have been archived as microarray and RNA-seq data in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, DNA DataBank of Japan started similar repository called Genomic Expression Archive (GEA)....
Sumi C, Matsuo Y, Kusunoki M, Shoji T, Uba T, Iwai T, Bono H, Hirota K
PLOS ONE   14(4) e0215072   Apr 2019   [Refereed]
Kobayashi Y, Nojima Y, Sakamoto T, Iwabuchi K, Nakazato T, Bono H, Toyoda A, Fujiyama A, Kanost MR, Tabunoki H
Scientific Reports   9(1) 2170   Feb 2019   [Refereed]
Insects are well adapted to changing environmental conditions. They have unique systems for eliminating reactive oxygen species (ROS). Superoxide dismutase (SOD) is a key enzyme that plays a primary role in removing ROS. Bombyx mori is a lepidopte...
Sumi C, Matsuo Y, Iwai T, Bono H, Hirota K
BioRxiv   https://doi.org/10.1101/375311   Jul 2018
The possibility that anesthesia during cancer surgery may affect cancer recurrence, metastasis, and patient prognosis has become one of the most important topic of interest in cancer treatment. For example, the volatile anesthetic isoflurane was r...
Ichino F, Bono H, Nakazato T, Toyoda A, Fujiyama A, Iwabuchi K, Sato R, Tabunoki H
Drug Discoveries & Therapeutics   12(1) 7-15   Mar 2018   [Refereed]
Human intestinal absorption is estimated using a human colon carcinoma cell line (Caco-2) cells from human colorectal adenocarcinoma, intestinal perfusion, or a mammalian model. These current evaluation systems are limited in their ability to esti...
Piulats JM, Kondo J, Endo H, Ono H, Hagihara T, Okuyama H, Nishizawa Y, Tomita Y, Ohue M, Okita K, Oyama H, Bono H, Masuko T, Inoue M
Oncotarget   9 15968-15983   Mar 2018   [Refereed]
Individual and small clusters of cancer cells may detach from the edges of a main tumor and invade vessels, which can act as the origin of metastasis; however, the mechanism for this phenomenon is not well understood. Using cancer tissue-originate...
Hidemasa Bono
BioRxiv   https://doi.org/10.1101/267310   Feb 2018
Hypoxia is an insufficient level of oxygen supply in the cell, and hypoxia-inducible factor is a central regulator of oxygen homeostasis. In order to elucidate functional insights in hypoxic response in data-driven way, we attempted meta-analysis ...
Nakamura H, Bono H, Hiyama K, Kawamoto T, Kato Y, Nakanishi T, Nishiyama M, Hiyama E, Hirohashi N, Sueoka E, Poellinger L, Tanimoto K
PLOS ONE   13(2) e0192136   Feb 2018   [Refereed]
Tumor hypoxia contributes to a biologically aggressive phenotype and therapeutic resistance. Recent studies have revealed that hypoxia reduces expression of several DNA damage recognition and repair (DRR) genes via both hypoxia-inducible factor (H...
Ono H, Ogasawara O, Okubo K, Bono H
Scientific Data   4 170105   Aug 2017   [Refereed]
Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and com...
Okamoto A, Sumi C, Tanaka H, Kusunoki M, Iwai T, Nishi K, Matsuo Y, Harada H, Takenaga K, Bono H, Hirota K
Scientific Reports   7 3816   Jun 2017   [Refereed]
The local anesthetic lidocaine induces cell death by altering reactive oxygen species (ROS) generation and mitochondrial electron transport chain function. Because hypoxia-inducible factor 1 (HIF-1) is involved in determining oxygen metabolism and...


Hidemasa Bono, Yasukazu Nakamura
95(3) 152-155   Mar 2017   [Invited]
Reika Kawabata-Iwakawa, Hidemasa Bono, Masahiko Nishiyama
Molecular Targeted Therapy of Lung Cancer   97-115   Jan 2017   [Invited]
Improvement of next-generation sequencing (NGS) has revealed novel driver genes and new therapeutic targets for cancer patients. We summarize here the history of NGS development, current situation of typical analysis pipeline utilizing NGS – espec...
Takeru Nakazato, Hidemasa Bono
54(12) 873-877   Dec 2016   [Refereed][Invited]
Hidemasa Bono
4 e008   May 2015   [Refereed][Invited]
Yoshitaka Hayashi, Sugiko Futaki, Ken Yagi, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Kiyotoshi Sekiguchi
Animal Cell Technology: Basic & Applied Aspects   13 7-11   Jan 2003
Basement membranes support proliferation, survival, and differentiation of epithelial/parenchymal cells through interaction with cell membrane receptors. Laminins, which have a heterotrimeric structure, are the major class of basement membrane gly...
RefEx: Dataset for Reference Gene Expression
Hiromasa Ono, Hidemasa Bono
Practical Guide to Life Science Databases   in press   [Invited]

Books etc

岡崎 康司, 坊農 秀雅
メディカル・サイエンス・インターナショナル   Dec 2005   ISBN:4895924262
アーサー・M. レスク
メディカルサイエンスインターナショナル   Sep 2003   ISBN:4895923436
岡崎 康司, 坊農 秀雅, David W. Mount
メディカル・サイエンス・インターナショナル   May 2002   ISBN:489592307X
Next generation sequencing and bioinformatics
Reika Kawabata-Iwakawa, Hidemasa Bono, Masahiko Nishiyama (Part:Joint Work, Molecular Targeted Therapy of Lung Cancer)

Conference Activities & Talks

Facilitating the use of public high-throughput sequencing data for plant omics research [Invited]
Hidemasa Bono
Plant and Animal Genome Conference ASIA   30 May 2017   
Hidemasa Bono
The 1st SPARC Japan Seminar 2016 "Roads to Open Access for Japan"   9 Sep 2016   
Hidemasa Bono
bonohu   27 Apr 2015   
ウェブツール・データベースを活用した知のめぐりのよい生命科学研究 [Invited]
Hidemasa Bono
bonohu   21 Apr 2015   
Hidemasa Bono
bonohu   5 Mar 2015   
NA [Invited]
Hidemasa Bono
bonohu   12 Jun 2014   
Integrated database biology with well-curated and well-circulated knowledge [Invited]
Hidemasa Bono
Dec 2011   


Hidemasa Bono   Database   Oct 2014
Yuki Naito, Kimihiro Hino, Hidemasa Bono, Kumiko Ui-Tei   Web Service   2014
CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence.
Hiromasa Ono, Hidemasa Bono   Database   Oct 2011
Yuki Naito, Hidemasa Bono   Web Service   May 2011
Hidemasa Bono and other contributers   Web Service   Apr 2011
Takeru Nakazato, Tazro Ohta, Hidemasa Bono   Database   Apr 2011
Shin Kawano, Hiromasa Ono, Hidemasa Bono   Web Service   Jul 2007
distributing tutorial videos of bioinformatcs resources
Hidemasa Bono and other contributers   Educational Materials   Feb 2006

Research Grants & Projects

Development of fundamental technologies related to integration of databases
Japan Science and Technology Agency: National Bioscience Database Center: Projects of Core Technology Development Program
Project Year: Apr 2011 - Mar 2014    Investigator(s): Yuji Kohara