Hidemasa Bono

J-GLOBAL         Last updated: Aug 25, 2018 at 12:16
Hidemasa Bono
Research Organization of Information and Systems
Database Center for Life Science
Job title
Project Associate Professor
Other affiliation
Graduate School of Frontier Sciences The University of Tokyo
Research funding number
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

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...
Ohta T, Nakazato T, Bono H
Gigascience   6 gix029   Apr 2017   [Refereed]
It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents use...
Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H
Nucleic Acids Research   45(D1) D737-D743   Jan 2017   [Refereed]
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp)...
Kikuchi A, Nakazato T, Ito K, Nojima Y, Yokoyama T, Iwabuchi K, Bono H, Toyoda A, Fujiyama A, Sato R, Tabunoki H
BMC Genomics   18 83   Jan 2017   [Refereed]
Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these da...
Miyawaki S, Kawamura Y, Oiwa Y, Shimizu A, Hachiya T, Bono H, Koya I, Okada Y, Kimura T, Tsuchiya Y, Suzuki S, Onishi N, Kuzumaki N, Matsuzaki Y, Narita M, Ikeda E, Okanoya K, Seino K, Saya H, Okano H, Miura K
Nature communications   7 11471   May 2016   [Refereed]
The naked mole-rat (NMR, Heterocephalus glaber), which is the longest-lived rodent species, exhibits extraordinary resistance to cancer. Here we report that NMR somatic cells exhibit a unique tumour-suppressor response to reprogramming induction. ...
Tabunoki H, Bono H, Ito K, Yokoyama T
Drug Discoveries & Therapeutics   10(1) 3-8   Feb 2016   [Invited]
Bombyx mori (silkworm) is the most famous lepidopteran in Japan. B. mori has long been used in the silk industry and also as a model insect for agricultural research. In recent years, B. mori has attracted interest in its potential for use in path...
Nojima Y, Ito K, Ono H, Nakazato T, Bono H, Yokoyama T, Sato R, Suetsugu Y, Nakamura Y, Yamamoto K, Satoh J, Tabunoki H, Fugo H
PloS one   10 e0116007   Feb 2015   [Refereed]
Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H
Genome Biology   16 22   Jan 2015   [Refereed]
Yuki Naito, Kimihiro Hino, Hidemasa Bono, Kumiko Ui-Tei
Bioinformatics   31(7) 1120-1123   Nov 2014   [Refereed]
CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided ...
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T
J Biomed Semantics   5(1) 5   Feb 2014   [Refereed]
Takeru Nakazato,Tazro Ohta, Hidemasa Bono
PLOS ONE   8(10) e77910   Oct 2013   [Refereed]
Hiroko Tabunoki, Hiromasa Ono, Hiroaki Ode, Kazuhiro Ishikawa, Natsuki Kawana, Yutaka Banno, Toru Shimada, Yuki Nakamura,Kimiko Yamamoto, Jun-ichi Satoh, Hidemasa Bono
PLOS ONE   8(7) e69130   Jul 2013   [Refereed]
Plasma uric acid (UA) levels decrease following clinical progression and stage development of Parkinson's disease (PD). However, the molecular mechanisms underlying decreases in plasma UA levels remain unclear, and the potential to apply mutagenes...
Yuki Naito, Hidemasa Bono
Nucleic Acids Research   40 W592-W596   Jul 2012   [Refereed]
Kawano S, Ono H, Takagi T, Bono H
Briefings in bioinformatics      Jul 2011   [Refereed]


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

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