Hidemasa Bono

Hidemasa Bono

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Hidemasa Bono

Publications by authors named "Hidemasa Bono"

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Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum.

BMC Genomics 2020 Feb 11;21(1):152. Epub 2020 Feb 11.

Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.

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http://dx.doi.org/10.1186/s12864-020-6559-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014612PMC
February 2020

GLIS1, a novel hypoxia-inducible transcription factor, promotes breast cancer cell motility via activation of WNT5A.

Carcinogenesis 2020 Feb 12. Epub 2020 Feb 12.

Department of Radiation Disaster Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.

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http://dx.doi.org/10.1093/carcin/bgaa010DOI Listing
February 2020

Meta-Analysis of Hypoxic Transcriptomes from Public Databases.

Biomedicines 2020 Jan 9;8(1). Epub 2020 Jan 9.

Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan.

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http://dx.doi.org/10.3390/biomedicines8010010DOI Listing
January 2020

All of gene expression (AOE): An integrated index for public gene expression databases.

Authors:
Hidemasa Bono

PLoS One 2020 24;15(1):e0227076. Epub 2020 Jan 24.

Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima,Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227076PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980531PMC
January 2020

Apoptosis-mediated vasa down-regulation controls developmental transformation in Japanese Copidosoma floridanum female soldiers.

Dev Biol 2019 Dec 19;456(2):226-233. Epub 2019 Sep 19.

Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2019.09.005DOI Listing
December 2019

Superoxide dismutase down-regulation and the oxidative stress is required to initiate pupation in Bombyx mori.

Sci Rep 2019 Oct 11;9(1):14693. Epub 2019 Oct 11.

Department of United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.

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http://dx.doi.org/10.1038/s41598-019-51163-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788986PMC
October 2019

Construction of a simple evaluation system for the intestinal absorption of an orally administered medicine using Bombyx mori larvae.

Drug Discov Ther 2018;12(1):7-15

Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology.

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http://dx.doi.org/10.5582/ddt.2018.01004DOI Listing
August 2019

Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori.

Sci Rep 2019 Feb 18;9(1):2170. Epub 2019 Feb 18.

Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.

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http://www.nature.com/articles/s41598-018-38384-8
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http://dx.doi.org/10.1038/s41598-018-38384-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379424PMC
February 2019

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes.

Sci Data 2017 08 29;4:170105. Epub 2017 Aug 29.

Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan.

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http://dx.doi.org/10.1038/sdata.2017.105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574374PMC
August 2017

Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes.

BMC Genomics 2017 01 13;18(1):83. Epub 2017 Jan 13.

Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.

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http://dx.doi.org/10.1186/s12864-016-3455-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237310PMC
January 2017

Can the silkworm (Bombyx mori) be used as a human disease model?

Drug Discov Ther 2016 Feb 7;10(1):3-8. Epub 2016 Feb 7.

Department of Biological Production, Faculty of Agriculture, Tokyo university of Agriculture and Technology.

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http://dx.doi.org/10.5582/ddt.2016.01011DOI Listing
February 2016

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

Bioinformatics 2015 Apr 20;31(7):1120-3. Epub 2014 Nov 20.

Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan and Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382898PMC
April 2015

Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

PLoS One 2013 22;8(10):e77910. Epub 2013 Oct 22.

Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077910PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3805581PMC
May 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

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

Nucleic Acids Res 2012 Jul 28;40(Web Server issue):W592-6. Epub 2012 May 28.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/nar/gks448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394333PMC
July 2012

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

Brief Bioinform 2012 Mar 29;13(2):258-68. Epub 2011 Jul 29.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/bib/bbr039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294242PMC
March 2012

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

Database (Oxford) 2011 15;2011:bar013. Epub 2011 Apr 15.

Database Center for Life Science, Bunkyo-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/database/bar013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077826PMC
September 2011

Gene expression profiling in multipotent DFAT cells derived from mature adipocytes.

Biochem Biophys Res Commun 2011 Apr 16;407(3):562-7. Epub 2011 Mar 16.

Laboratory of Cell and Tissue Biology, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2011.03.063DOI Listing
April 2011

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

Nucleic Acids Res 2009 Jul 4;37(Web Server issue):W166-9. Epub 2009 Jun 4.

Database Center for Life Science, Research Organization of Information and Systems, Faculty of Engineering Building 12, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/nar/gkp483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703956PMC
July 2009

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes.

In Silico Biol 2008 ;8(1):53-61

Bio-IT Business Promotion Center, NEC Corporation, 34 Miyukigaoka, Tsukuba, Ibaraki 305-8501, Japan.

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July 2008

Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation.

Biochem Biophys Res Commun 2008 Jul 19;372(2):362-6. Epub 2008 May 19.

Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2008.05.037DOI Listing
July 2008

[Portal services of life science database project in Japan].

Tanpakushitsu Kakusan Koso 2008 Mar;53(3):281-7

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March 2008

Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements.

Biochem Biophys Res Commun 2006 Jan 8;339(1):99-106. Epub 2005 Nov 8.

Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical School, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2005.10.188DOI Listing
January 2006

SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements.

Authors:
Hidemasa U Bono

Gene 2005 Dec 24;364:74-8. Epub 2005 Aug 24.

Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical School, 1397-1 Yamane, Hidaka, Saitama 350-1241, Japan.

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http://dx.doi.org/10.1016/j.gene.2005.05.039DOI Listing
December 2005

The study of metabolic pathways in tumors based on the transcriptome.

Semin Cancer Biol 2005 Aug;15(4):290-9

Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical School, 1397-1 Yamane, Hidaka, Saitama 350-1241, Japan.

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http://dx.doi.org/10.1016/j.semcancer.2005.04.008DOI Listing
August 2005

MaXML: mouse annotation XML.

In Silico Biol 2004 26;4(1):7-15. Epub 2003 Dec 26.

Network Service Solution Business Group, Content Sharing Service Business Unit, NTT Software Corporation, Yokohama, Kanagawa, Japan.

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December 2004

Identification and functional analysis of consensus androgen response elements in human prostate cancer cells.

Biochem Biophys Res Commun 2004 Dec;325(4):1312-7

Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical School, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2004.10.174DOI Listing
December 2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Authors:
Tadashi Imanishi Takeshi Itoh Yutaka Suzuki Claire O'Donovan Satoshi Fukuchi Kanako O Koyanagi Roberto A Barrero Takuro Tamura Yumi Yamaguchi-Kabata Motohiko Tanino Kei Yura Satoru Miyazaki Kazuho Ikeo Keiichi Homma Arek Kasprzyk Tetsuo Nishikawa Mika Hirakawa Jean Thierry-Mieg Danielle Thierry-Mieg Jennifer Ashurst Libin Jia Mitsuteru Nakao Michael A Thomas Nicola Mulder Youla Karavidopoulou Lihua Jin Sangsoo Kim Tomohiro Yasuda Boris Lenhard Eric Eveno Yoshiyuki Suzuki Chisato Yamasaki Jun-ichi Takeda Craig Gough Phillip Hilton Yasuyuki Fujii Hiroaki Sakai Susumu Tanaka Clara Amid Matthew Bellgard Maria de Fatima Bonaldo Hidemasa Bono Susan K Bromberg Anthony J Brookes Elspeth Bruford Piero Carninci Claude Chelala Christine Couillault Sandro J de Souza Marie-Anne Debily Marie-Dominique Devignes Inna Dubchak Toshinori Endo Anne Estreicher Eduardo Eyras Kaoru Fukami-Kobayashi Gopal R Gopinath Esther Graudens Yoonsoo Hahn Michael Han Ze-Guang Han Kousuke Hanada Hideki Hanaoka Erimi Harada Katsuyuki Hashimoto Ursula Hinz Momoki Hirai Teruyoshi Hishiki Ian Hopkinson Sandrine Imbeaud Hidetoshi Inoko Alexander Kanapin Yayoi Kaneko Takeya Kasukawa Janet Kelso Paul Kersey Reiko Kikuno Kouichi Kimura Bernhard Korn Vladimir Kuryshev Izabela Makalowska Takashi Makino Shuhei Mano Regine Mariage-Samson Jun Mashima Hideo Matsuda Hans-Werner Mewes Shinsei Minoshima Keiichi Nagai Hideki Nagasaki Naoki Nagata Rajni Nigam Osamu Ogasawara Osamu Ohara Masafumi Ohtsubo Norihiro Okada Toshihisa Okido Satoshi Oota Motonori Ota Toshio Ota Tetsuji Otsuki Dominique Piatier-Tonneau Annemarie Poustka Shuang-Xi Ren Naruya Saitou Katsunaga Sakai Shigetaka Sakamoto Ryuichi Sakate Ingo Schupp Florence Servant Stephen Sherry Rie Shiba Nobuyoshi Shimizu Mary Shimoyama Andrew J Simpson Bento Soares Charles Steward Makiko Suwa Mami Suzuki Aiko Takahashi Gen Tamiya Hiroshi Tanaka Todd Taylor Joseph D Terwilliger Per Unneberg Vamsi Veeramachaneni Shinya Watanabe Laurens Wilming Norikazu Yasuda Hyang-Sook Yoo Marvin Stodolsky Wojciech Makalowski Mitiko Go Kenta Nakai Toshihisa Takagi Minoru Kanehisa Yoshiyuki Sakaki John Quackenbush Yasushi Okazaki Yoshihide Hayashizaki Winston Hide Ranajit Chakraborty Ken Nishikawa Hideaki Sugawara Yoshio Tateno Zhu Chen Michio Oishi Peter Tonellato Rolf Apweiler Kousaku Okubo Lukas Wagner Stefan Wiemann Robert L Strausberg Takao Isogai Charles Auffray Nobuo Nomura Takashi Gojobori Sumio Sugano

PLoS Biol 2004 Jun 20;2(6):e162. Epub 2004 Apr 20.

Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pbio.0020162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393292PMC
June 2004

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.

Genomics 2004 Jun;83(6):1012-23

Department of Biomedical Sciences, Creighton University, 2500 California, Omaha, NE 68178, USA.

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http://dx.doi.org/10.1016/j.ygeno.2004.01.006DOI Listing
June 2004

Gene discovery in genetically labeled single dopaminergic neurons of the retina.

Proc Natl Acad Sci U S A 2004 Apr 26;101(14):5069-74. Epub 2004 Mar 26.

Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.0400913101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387375PMC
April 2004

Molecular basis of constitutive production of basement membrane components. Gene expression profiles of Engelbreth-Holm-Swarm tumor and F9 embryonal carcinoma cells.

J Biol Chem 2003 Dec 10;278(50):50691-701. Epub 2003 Sep 10.

Sekiguchi Biomatrix Signaling Project, ERATO, Japanese Science and Technology Agency (JST), Aichi Medical University, 21 Karimata, Yazako Nagakute-cho, Aichi-gun, Aichi, 480-1195, Japan.

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http://dx.doi.org/10.1074/jbc.M304985200DOI Listing
December 2003

Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice.

Carcinogenesis 2003 Nov 14;24(11):1819-26. Epub 2003 Aug 14.

Department of Experimental Oncology, Istituto Nazionale Tumori, Milan, Italy.

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http://dx.doi.org/10.1093/carcin/bgg133DOI Listing
November 2003

Comprehensive analysis of the mouse metabolome based on the transcriptome.

Genome Res 2003 Jun;13(6B):1345-9

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.974603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403659PMC
June 2003

The mouse secretome: functional classification of the proteins secreted into the extracellular environment.

Genome Res 2003 Jun;13(6B):1350-9

Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St. Lucia 4072, Australia.

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http://dx.doi.org/10.1101/gr.983703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403661PMC
June 2003

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.

Genome Res 2003 Jun;13(6B):1360-5

Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1101/gr.1056103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403663PMC
June 2003

Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.

Genome Res 2003 Jun;13(6B):1402-9

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.1055303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403673PMC
June 2003

G protein-coupled receptor genes in the FANTOM2 database.

Genome Res 2003 Jun;13(6B):1466-77

Howard Hughes Medical Institute, Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.1087603
Publisher Site
http://dx.doi.org/10.1101/gr.1087603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403690PMC
June 2003

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Genome Res 2003 Jun;13(6B):1542-51

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.992803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403710PMC
June 2003

Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure.

Physiol Genomics 2003 Feb 6;12(3):251-9. Epub 2003 Feb 6.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064 Japan.

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http://dx.doi.org/10.1152/physiolgenomics.00153.2002DOI Listing
February 2003

[Introduction to the practical analysis of DNA microarray data].

Tanpakushitsu Kakusan Koso 2003 Feb;48(2):167-72

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February 2003

[FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones].

Seikagaku 2003 Feb;75(2):149-52

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045.

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February 2003

Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts.

Curr Opin Struct Biol 2002 Jun;12(3):355-61

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Kanagawa Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1016/s0959-440x(02)00335-4DOI Listing
June 2002

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

Nucleic Acids Res 2002 Jan;30(1):116-8

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99137PMC
http://dx.doi.org/10.1093/nar/30.1.116DOI Listing
January 2002

READ: RIKEN Expression Array Database.

Nucleic Acids Res 2002 Jan;30(1):211-3

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99103PMC
http://dx.doi.org/10.1093/nar/30.1.211DOI Listing
January 2002