Hidemasa Bono

J-GLOBAL         Last updated: Oct 18, 2019 at 14:49
 
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Name
Hidemasa Bono
Nickname
bonohu
URL
http://dbcls.rois.ac.jp/~bono/
Affiliation
Research Organization of Information and Systems
Section
Database Center for Life Science
Job title
Project Associate Professor
Degree
Ph.D
Twitter ID
drbonohu
ORCID ID
0000-0003-4413-0651

Research Areas

 

Academic & Professional Experience

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

Published Papers

 
Yokoi K, Tsubota T, Sun J, Joraku A, Sezutsu H, Bono H
bioRxiv   805978   Oct 2019
The silkworm Bombyx mori has long been used in the silk industry and utilized in studies of physiology, genetics, molecular biology, and pathology. We recently reported high quality reference genome data for B. mori. In the present study, we const...
Katayama T , Kawashima S , Micklem G , Kawano S , Kim J , Kocbek S , Okamoto S , Wang Y , Wu H , Yamaguchi A , Yamamoto Y , Antezana E , Aoki-Kinoshita KF , Arakawa K , Banno M , Baran J , Bolleman JT , Bonnal RJ , Bono H , Fernández-Breis JT , Buels R , Campbell MP , Chiba H , Cock PJA , Cohen KB , Dumontier M , Fujisawa T , Fujiwara T , Garcia L , Gaudet P , Hattori E , Hoehndorf R , Itaya K , Ito M , Jamieson D , Jupp S , Juty N , Kalderimis A , Kato F , Kawaji H , Kawashima T , Kinjo AR , Komiyama Y , Kotera M , Kushida T , Malone J , Matsubara M , Mizuno S , Mizutani S , Mori H , Moriya Y , Murakami K , Nakazato T , Nishide H , Nishimura Y , Ogishima S , Ohta T , Okuda S , Ono H , Perez-Riverol Y , Shinmachi D , Splendiani A , Strozzi F , Suzuki S , Takehara J , Thompson M , Tokimatsu T , Uchiyama I , Verspoor K , Wilkinson MD , Wimalaratne S , Yamada I , Yamamoto N , Yarimizu M , Kawamoto S , Takagi T
F1000Research      Sep 2019   [Refereed]
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual Bi...
Ohno H, Sakamoto T, Okochi R, Nishiko M, Sasaki S, Bono H, Tabunoki H, Iwabuchi K
Developmental Biology      Sep 2019   [Refereed]
Copidosoma floridanum is a polyembryonic, caste-forming, wasp species. The ratio of investment in different castes changes with environmental stressors (e.g. multi-parasitism with competitors). The vasa gene was first identified in Drosophila mela...
Nojima Y, Bono H, Yokoyama T, Iwabuchi K, Sato R, Arai K, Tabunoki H
Scientific Reports   9 14693   Oct 2019   [Refereed]
Perhaps, oxidative stress progresses pupation in some Lepidopteran insects; however, the reasons for this remain obscure. In our previous study, we clarified Bombyx mori SOD1 (BmSOD1) and B. mori SOD2 (BmSOD2) proteins respond in common to ultravi...
Ramilowski J , Yip CW , Agrawal S , Chang J , Ciani Y , Kulakovskiy IV , Mendez M , Ooi JLC , Ouyang JF , Parkinson N , Petri A , Roos L , Severin J , Yasuzawa K , Abugessaisa I , Akalin A , Antonov I , Arner E , Bonetti A , Bono H , Borsari B , Brombacher F , Cannistraci CV , Cardenas R , Cardon M , Chang H , Dostie J , Ducoli L , Favorov A , Fort A , Garrido D , Gil N , Gimenez J , Guler R , Handoko L , Harshbarger J , Hasegawa A , Hasegawa Y , Hashimoto K , Hayatsu N , Heutink P , Hirose T , Imada EL , Itoh M , Kaczkowski B , Kanhere A , Kawabata E , Kawaji H , Kawashima T , Kelly T , Kojima M , Kondo N , Koseki H , Kouno T , Kratz A , Kurowska-Stolarska M , Kwon ATJ , Leek J , Lennartsson A , Lizio M , Lopez F , Luginbühl J , Maeda S , Makeev V , Marchionni L , Medvedeva YA , Minoda A , Müller F , Aguirre MM , Murata M , Nishiyori H , Nitta K , Noguchi S , Noro Y , Nurtdinov R , Okazaki Y , Orlando V , Paquette D , Parr C , Rackham OJ , Rizzu P , Sanchez DF , Sandelin A , Sanjana P , Semple CA , Sharma H , Shibayama Y , Sivaraman D , Suzuki T , Szumowski S , Tagami M , Taylor MS , Terao C , Thodberg M , Thongjuea S , Tripathi V , Ulitsky I , Verardo R , Vorontsov I , Yamamoto C , Young RS , Baillie JK , Forrest AR , Guigó R , Hoffman MM , Hon CC , Kasukawa T , Kauppinen S , Kere J , Lenhard B , Schneider C , Suzuki H , Yagi K , de Hoon M , Shin JW , Carninci P , FANTOM consortium
bioRxiv   700864   Jul 2019
Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes and yet, their functions remain largely unknown. We systematically suppressed 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morpho...
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...
Scientific Reports   8 8987   Jun 2018   [Refereed]
A line of studies strongly suggest that the intravenous anesthetic, propofol, suppresses mitochondrial oxygen metabolism. It is also indicated that propofol induces the cell death in a reactive oxygen species (ROS)-dependent manner. Because hypoxi...

Misc

 
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)
Springer   

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   

Works

 
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