Updated on 2024/06/07

写真a

 
OGATA Yoshiyuki
 
Organization
Graduate School of Agriculture Department of Agricultural Biology Associate Professor
School of Agriculture Department of Agricultural Biology
Title
Associate Professor
Affiliation
Institute of Agriculture
Affiliation campus
Nakamozu Campus

Position

  • Graduate School of Agriculture Department of Agricultural Biology 

    Associate Professor  2022.04 - Now

  • School of Agriculture Department of Agricultural Biology 

    Associate Professor  2022.04 - Now

Degree

  • Doctor (Agriculture) ( Kyoto University ) (   Kyoto University )

  • Master (Agriculture) ( Kyoto University ) (   Kyoto University )

Research Areas

  • Life Science / System genome science

  • Life Science / Genome biology  / Genomics

  • Life Science / Biodiversity and systematics

  • Informatics / Life, health and medical informatics

  • Life Science / Applied molecular and cellular biology

  • Informatics / Life, health and medical informatics  / Microbiomics

  • Life Science / System genome science  / Bioinformatics

  • Life Science / Genome biology  / Comparative genomics

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Research Interests

  • gene function

  • microbiome

  • big data analysis

  • bioinformatics

  • database

  • genome evolution

Research subject summary

  • 配列相同性解析に基づく遺伝子の機能と進化の追跡

  • 遺伝子ホモロジー解析データベース Gcorn

  • SARS-CoV-2変異解析データベース Vcorn

  • マイクロバイオーム解析データベース Micorn

  • 相関ネットワーク解析ツール ConfeitoGUI

  • 遺伝子発現解析データベース Xcorn

  • 次世代シーケンシング解析ツール MagicSuite

Research Career

  • Gcorn: databases to retrieve homologous genes in all organisms

    gene evolution, gene function, homologgy, database, phylogenetic estimation  Individual

    2018.04 - Now 

  • Gcorn bacteria: a database to retrieve gene homology in prokaryotes

    gene evolution, gene function, homology, database, prokaryotes  Individual

    2020.04 - Now 

  • Vcorn SARS-CoV-2: a database to analyze mutation in SARS-CoV-2

    gene evolution, gene mutation, homology, database, SARS-CoV-2  Individual

    2020.04 - Now 

  • Gcorn fungi: a database to retrieve gene homology in fungi

    gene evolution, gene function, homology, database, fungi  Individual

    2019.04 - Now 

  • Gcorn plant: a database to retrieve gene homology in plants

    gene evolution, gene function, homology, database, plant  Individual

    2018.04 - Now 

  • Gcorn mammalian: a database to retrieve gene homology in mammalians

    gene evolution, gene function, homology, database, mammalian  Individual

    2020.10 - Now 

  • Gcorn vertebrate: a database to retrieve gene homology in vertebrates

    gene evolution, gene function, homology, database, vertebrate  Individual

    2020.10 - Now 

  • Gcorn invertebrate: a database to retrieve gene homology in invertebrates

    gene evolution, gene function, homology, database, invertebrate  Individual

    2020.10 - Now 

Professional Memberships

  • The Molecular Biology Society of Japan

    2005.11 - Now   Domestic

  • The Japanese Society of Plant Physiologists

    2005.12 - Now   Domestic

  • ASPB

    2019.04 - Now   Overseas

  • The Japan Wood Research Society

    1994.01 - Now   Domestic

  • International Association of Wood Anatomists

    1994.01 - Now   Overseas

  • Japanese Society for Plant Cell and Molecular Biology

    2007.01 - Now   Domestic

  • The Society for Molecular Biology and Evolution

    2009.01 - Now   Overseas

  • The Society for Biotechnology, Japan

    2010.09 - Now   Domestic

  • Japan Society for Bioscience, Biotechnology, and Agrochemistry

    2010.09 - 2012.03   Domestic

  • Japanese Society for Bioinformatics

    2006.01 - 2008.12   Domestic

  • THE JAPANESE SOCIETY OF PLANT PHYSIOLOGISTS

  • THE JAPAN WOOD RESEARCH SOCIETY

  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

  • The American Society of Plant Biologists

  • Society for Molecular Biology & Evolution

  • International Association of Wood Anatomists

  • American Association for the Advancement of Science

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Awards

  • The JSPCMB Award for Young Scientists

    2010.09   Japanese Society for Plant Cell and Molecular Biology  

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    Country:Japan

Job Career (off-campus)

  • Osaka Metropolitan University   Graduate School of Agriculture

    2022.04 - Now

Papers

  • Analyses of S Protein Homology Using the Genomes of SARS-CoV-2 Specimens Unveil Missing Links in the Temporal Order of Mutations in Its Variants Reviewed

    Kitayama R.

    Viruses   15 ( 11 )   2023.11

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    Authorship:Last author, Corresponding author   Publishing type:Research paper (scientific journal)   Kind of work:Joint Work   International / domestic magazine:International journal  

    DOI: 10.3390/v15112182

    PubMed

  • A database for retrieving information on SARS-CoV-2 S protein mutations based on correlation network analysis

    Ogata Y.

    BMC Genomic Data   23 ( 1 )   34   2022.12( ISSN:27306844

  • 馬糞便マイクロバイオーム解析法の胃腸の健康状態把握における有用性

    尾形 善之, 井貫 雄太

    Hippophile   ( 88 )   1 - 8   2022.03( ISSN:1883-6062

  • Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi Reviewed

    Kawachi T, Inuki Y, Ogata Y

    Journal of Fungi 雑誌   7 ( 11 )   2021.11

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    Kind of work:Joint Work  

  • Gcorn Plant: A Database for Retrieving Functional and Evolutionary Traits of Plant Genes Reviewed

    Ogata Y, Kimura N, Sano R

    Plant Physiology 雑誌   180 ( 2 )   2019.06

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    Kind of work:Joint Work  

  • ConfeitoGUI: A toolkit for size-sensitive community detection from a correlation network Reviewed

    Ogata Y, Mannen K, Kotani Y, Kimura N, Sakurai N, Shibata D, Suzuki H

    PLoS One 雑誌   13 ( 10 )   2018.10

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    Kind of work:Joint Work  

  • CoP: a database for characterizing a group of co-expressed genes in plants Reviewed

    Y. Ogata, H. Suzuki, N. Sakurai, D. Shibata

    Bioinformatics 雑誌 Oxford Journals   26   1267 - 1268   2010.04

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    Kind of work:Joint Work  

  • The prediction of local modular structures in a co-expression network based on gene expression datasets Reviewed

    Y. Ogata, N. Sakurai, H. Suzuki, K. Aoki, K. Saito, D. Shibata

    Genome Inform. 雑誌 Japanese Society for Bioinformatics   23   117 - 127   2009.12

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    Kind of work:Joint Work  

  • KAGIANA: An Excel-based tool for retrieving summary information on Arabidopsis genes Reviewed

    Y. Ogata, N. Sakurai, K. Aoki, H. Suzuki, K. Okazaki, K. Saito, D. Shibata

    Plant Cell Physiol. 雑誌 The Japanese Society of Plant Physiologists   50   173 - 177   2009.01

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    Kind of work:Joint Work  

  • Z-axis calibration in optical sectioning from xylem cross sections for grain angle measurement Reviewed

    Y. Ogata, M. Fujita

    IAWA J. 雑誌 International Association of Wood Anatomists   26   427 - 441   2005.12

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    Kind of work:Joint Work  

  • New anatomical method of grain measurement using confocal microscopy and image cross-correlation Reviewed

    Y. Ogata, M. Fujita

    Trees 雑誌 Springer Verlag   19   73 - 80   2005.01

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    Kind of work:Joint Work  

  • Macroscopic and anatomical investigation of interlocked grain in Acacia mangium Reviewed

    Y. Ogata, T. Nobuchi, M. Fujita, M.H. Sahri

    IAWA J. 雑誌 International Association of Wood Anatomists   24   13 - 26   2003.03

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    Kind of work:Joint Work  

  • Arabidopsis thaliana Subclass I ACTIN DEPOLYMERIZING FACTORs Regulate Nuclear Organization and Gene Expression Reviewed

    Matsumoto T.

    Plant and Cell Physiology   64 ( 10 )   1231 - 1242   2023.10( ISSN:00320781

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    Publishing type:Research paper (scientific journal)   Kind of work:Joint Work   International / domestic magazine:Domestic journal  

    DOI: 10.1093/pcp/pcad092

    PubMed

  • Zinc deficiency-induced defensin-like proteins are involved in the regulation of root growth in Arabidopsis.

    Kimura S, Vaattovaara A, Ohshita T, Yokoyama K, Yoshida K, Hui A, Kaya H, Ozawa A, Kobayashi M, Mori IC, Ogata Y, Ishino Y, Sugano SS, Nagano M, Fukao Y

    The Plant journal : for cell and molecular biology   115 ( 4 )   1071 - 1083   2023.05( ISSN:0960-7412

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  • Genetic Mapping of the HLA1 Locus Causing Hybrid Lethality in Nicotiana Interspecific Hybrids

    Tezuka T, Kitamura N, Imagawa S, Hasegawa A, Shiragaki K, He H, Yanase M, Ogata Y, Morikawa T, Yokoi S

    Plants (Basel) 雑誌   10 ( 10 )   2021.09

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    Kind of work:Joint Work  

  • Chemical genetic approach using β-rubromycin reveals that a RIO kinase-like protein is involved in morphological development in Phytophthora infestans.

    Shuji Tani, Naotaka Nishio, Kenji Kai, Daisuke Hagiwara, Yoshiyuki Ogata, Motoaki Tojo, Jun-Ichi Sumitani, Howard S Judelson, Takashi Kawaguchi

    Scientific reports   10 ( 1 )   22326 - 22326   2020.12

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    Publishing type:Research paper (scientific journal)   International / domestic magazine:International journal  

    To characterize the molecular mechanisms underlying life-stage transitions in Phytophthora infestans, we initiated a chemical genetics approach by screening for a stage-specific inhibitor of morphological development from microbial culture extracts prepared mostly from actinomycetes from soil in Japan. Of the more than 700 extracts, one consistently inhibited Ph. infestans cyst germination. Purification and identification of the active compound by ESI-MS, 1H-NMR, and 13C-NMR identified β-rubromycin as the inhibitor of cyst germination (IC50 = 19.8 μg/L); β-rubromycin did not inhibit growth on rye media, sporangium formation, zoospore release, cyst formation, or appressorium formation in Ph. infestans. Further analyses revealed that β-rubromycin inhibited the germination of cysts and oospores in Pythium aphanidermatum. A chemical genetic approach revealed that β-rubromycin stimulated the expression of RIO kinase-like gene (PITG_04584) by 60-fold in Ph. infestans. Genetic analyses revealed that PITG_04584, which lacks close non-oomycete relatives, was involved in zoosporogenesis, cyst germination, and appressorium formation in Ph. infestans. These data imply that further functional analyses of PITG_04584 may contribute to new methods to suppress diseases caused by oomycetes.

    DOI: 10.1038/s41598-020-79326-7

    PubMed

  • Chemical genetic approach using β-rubromycin reveals that a RIO kinase-like protein is involved in morphological development in Phytophthora infestans Reviewed

    Tani S, Nishio N, Kai K, Hagiwara D, Ogata Y, Tojo M, Sumitani JI, Judelson HS, Kawaguchi T

    Sci Rep 雑誌   10 ( 1 )   2020.12

  • An Artificial Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors Reviewed

    Hanano S, Tomatsu H, Ohnishi A, Kobayashi K, Kondo Y, Betsuyaku S, Takita E, Ogata Y, Ozawa K, Suda K, Hosouchi T, Nagase T, Suzuki H, Sakurai N, Masumoto H, Fukuda H, Shibata D

    iScience 雑誌   23 ( 7 )   2020.07

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    Kind of work:Joint Work  

  • Role of gut microbiota in sex- and diet-dependent metabolic disorders that lead to early mortality of androgen receptor-deficient male mice Reviewed

    Harada N, Hanada K, Minami Y, Kitakaze T, Ogata Y, Tokumoto H, Sato T, Kato S, Inui H, Yamaji R

    Am J Physiol Endocrinol Metab 雑誌   18 ( 4 )   2020.04

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    Kind of work:Joint Work  

  • Extracellular transglutaminase 2 induces myotube hypertrophy through G protein-coupled receptor 56 Reviewed

    Kitakaze T, Yoshikawa M, Kobayashi Y, Kimura N, Goshima N, Ishikawa T, Ogata Y, Yamashita Y, Ashida H, Harada N, Yamaji R

    Biochim Biophys Acta Mol Cell Res 雑誌   1867 ( 2 )   2020.02

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    Kind of work:Joint Work  

  • Correlation between toll-like receptor 4 and nucleotide-binding oligomerization domain 2 (NOD2) and pathological severity in dogs with chronic gastrointestinal diseases Reviewed

    Aono K, Azuma YT, Nabetani T, Hatoya S, Furuya M, Miki M, Hirota K, Fujimoto Y, Nishiyama K, Ogata Y, Mochizuki T, Tani H

    Veterinary Immunology and Immunopathology 雑誌   210   2019.04

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    Kind of work:Joint Work  

  • Gene cloning, expression, and X-ray crystallographic analysis of a β-mannanase from Eisenia fetida Reviewed

    Ueda M, Hirano Y, Fukuhara H, Naka Y, Nakazawa M, Sakamoto T, Ogata Y, Tamada T

    Enzyme Microb Technol 雑誌   117   15 - 22   2018.10

  • Pathway-specific metabolome analysis with 18O2-labeled Medicago truncatula via a mass spectrometry-based approach Reviewed

    Kera K, Fine DD, Wherritt DJ, Nagashima Y, Shimada N, Ara T, Ogata Y, Sumner LW, Suzuki H

    Metabolomics 雑誌   14 ( 5 )   2018.05

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    Kind of work:Joint Work  

  • オミックスデータの解析・可視化の最先端技術:ConfeitoGUIplus

    尾形善之、鈴木秀幸

    植物の生長調節 雑誌   52 ( 2 )   2017.12

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    Kind of work:Joint Work  

  • Utilization of ConfeitoGUI, a toolkit to detect novel relationships from multivariate big data

    Ogata Y, Suzuki H

    Bioscience and Industry   75 ( 6 )   2017

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    Kind of work:Joint Work  

  • ConfeitoGUIplus for mutivariate analysis Reviewed

    Mannen K, Ogata Y, Suzuki H

    95 ( 7 )   2017

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    Kind of work:Joint Work  

  • Quantitative proteomic analysis of the response to zinc, magnesium, and calcium deficiency in specific cell types of Arabidopsis roots. Reviewed

    Fukao Y, Kobayashi M, Zargar SM, Kurata R, Fukui R, Mori IC, Ogata Y

    Proteomics 雑誌   4   2016.01

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    Kind of work:Joint Work  

  • Identification of putative target genes of bZIP19, a transcription factor essential for Arabidopsis adaptation to Zn deficiency in roots. Reviewed

    3. Inaba S, Kurata R, Kobayashi M, Yamagishi Y, Mori I, Ogata Y, Fukao Y

    Plant J 雑誌   117   4 - 10   2015.10

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    Kind of work:Joint Work  

  • A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. Reviewed

    4. Ikeue D, Schudoma C, Zhang W, Ogata Y, Sakamoto T, Kurata T, Furuhashi T, Kragler F, Aoki K

    Plant Methods 雑誌   11   2015.05

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    Kind of work:Joint Work  

  • Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation. Reviewed

    6. Suzuki M, Nakabayashi R, Ogata Y, Sakurai N, Tokimatsu T, Goto S, Suzuki M, Jasinski M, Martinola E, Otagaki S, Matsumoto S, Saito K, Shiratake K

    Plant Physiol 雑誌   168   47 - 59   2015.05

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    Kind of work:Joint Work  

  • Quantitative proteomics of Arabidopsis shoot microsomal proteins reveals a cross-talk between excess zinc and iron deficiency. Reviewed

    7. Zargar SM, Kurata R, Inaba S, Oikawa A, Fukui R, Ogata Y, Agrawal GK, Rakwal R, Fukao Y

    Proteomics 雑誌   15   1196 - 1201   2015.04

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    Kind of work:Joint Work  

  • Potential biomarkers of fatigue identified by plasma metabolome analysis in rats. Reviewed

    5. Kume S, Yamato M, Tamura Y, Jin G, Nakano M, Miyashige Y, Eguchi A, Ogata Y, Goda N, Iwai K, Yamano E, Watanabe Y, Soga T, Kataoka Y

    PLoS One 雑誌   10   2015.03

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    Kind of work:Joint Work  

  • Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis. Reviewed

    8. Zargar SM, Fujiwara M, Inaba S, Kobayashi M, Kurata R, Ogata Y, Fukao Y

    Plant Cell Rep 雑誌   34   157 - 166   2015.01

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    Kind of work:Joint Work  

  • Identification of laticifer-specific genes and their promoter regions from a natural rubber producing plant Hevea brasiliensis.

    9. Aoki Y, Takahashi S, Takayama D, Ogata Y, Sakurai N, Suzuki H, Asawatreratanakul K, Wititsuwannakul D, Wititsuwannakul R, Shibata D, Koyama T, Nakayama T

    Plant Sci 雑誌   225   1 - 8   2014.08

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    Kind of work:Joint Work  

  • Quantitative transcriptional changes associated with chlorosis severity in mosaic leaves of tobacco plants infected with Cucumber mosaic virus. Reviewed

    12. Mochizuki T, Ogata Y, Hirata Y, Ohki ST

    Mol Plant Biol 雑誌   15   242 - 254   2014.04

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    Kind of work:Joint Work  

  • Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. Reviewed

    11. Sakurai N, Ara T, Enomoto M, Motegi T, Morishita Y, Kurabayashi A, Iijima Y, Ogata Y, Nakajima D, Suzuki H, Shibata D

    Biomed Res Int 雑誌   2014   2014.04

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    Kind of work:Joint Work  

  • Cellulose digestion and metabolism induced biocatalytic transitions in anaerobic microbial ecosystems. Reviewed

    13. Yamazawa A, Iikura T, Morioka Y, Shino A, Ogata Y, Date Y, Kikuchi J

    Metabolites 雑誌   4   36 - 52   2013.12

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    Kind of work:Joint Work  

  • Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the Arabidopsis unfolded protein response. Reviewed

    14. Mishiba K, Nagashima Y, Suzuki E, Hayashi N, Ogata Y, Shimada Y, Koizumi N

    Proc Natl Acad Sci USA 雑誌   110   5713 - 5718   2013.04

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    Kind of work:Joint Work  

  • Functional genomics of tomato in a post-genome-sequencing phase. Reviewed

    Aoki K, Ogata Y, Igarashi K, Yano K, Nagasaki H, Kaminuma E, Toyoda A

    Breed Science 雑誌   63   14 - 20   2013.03

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    Kind of work:Joint Work  

  • Construction and analysis of EST libraries of the trans-polyisoprene producting plant, Eucommia ulmoides Oliver Reviewed

    N. Suzuki, H. Uefuji, T. Nishikawa, Y. Mukai, A. Yamashita, M. Hattori, N. Ogasawara, T. Bamba, E.I. Fukusaki, A. Kobayashi, Y. Ogata, N. Sakurai, H. Suzuki, D. Shibata, Y. Nakazawa

    Planta 雑誌   2012.06

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    Kind of work:Joint Work  

  • Development of KaPPA-View4 for omics studies on Jatropha and a database system KaPPA-Loader for construction of local omics databases Reviewed

    N. Sakurai, Y. Ogata, T. Ara, R. Sano, N. Akimoto, A. Hiruta, H. Suzuki, M. Kajikawa, U. Widyastuti, S. Suharsono, A. Yokota, K. Akashi, J. Kikuchi, D. Shibata

    Plant Biotechnol. 雑誌 Japanese Society for Plant Cell and Molecular Biology   29   131 - 135   2012.05

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    Kind of work:Joint Work  

  • Identification and characterization of ANAC042 a transcription factor family gene involved in the regulation of camalexin biosynthesis in Arabidopsis Reviewed

    H. Saga, T. Ogawa, K. Kai, H. Suzuki, Y. Ogata, N. Sakurai, D. Shibata, D. Ohta

    Mol. Plant Microbe Interact. 雑誌   25   684 - 696   2012.05

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    Kind of work:Joint Work  

  • ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach Reviewed

    Y. Ogata, E. Chikayama, Y. Morioka, R.C. Everroad, A. Shino, A. Matsushima, H. Haruna, S. Moriya, T. Toyoda, J. Kikuchi

    PLoS One 雑誌   7   2012.02

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    Kind of work:Joint Work  

  • Plant expressed sequence tags database: practical uses and the improvement of their searches using network module analysis Reviewed

    Y. Ogata, H. Suzuki

    Plant Biotechnol. 雑誌 Japanese Society for Plant Cell and Molecular Biology   28   351 - 360   2011.09

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    Kind of work:Joint Work  

  • ECOMICS: Ecosystem trans-OMICS tools and methodds for complex environmental samples and datasets Reviewed

    J. Kikuchi, Y. Ogata, K. Shinozaki

    J. Ecosys. Ecograph. 雑誌 OMICS Publishing Group   S2   S2 - 001   2011.08

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    Kind of work:Joint Work  

  • Analysis of expressed sequence tags in developing secondary xylem and shoot of Acacia mangium Reviewed

    S. Suzuki, K. Suda, N. Sakurai, Y. Ogata, T. Hattori, H. Suzuki, D. Shibata, T. Umezawa

    J. Wood Sci. 雑誌 The Japan Wood Research Society   57   40 - 46   2011.01

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    Kind of work:Joint Work  

  • KaPPA-View4: the metabolic pathway database for representation and analysis of correlation networks of genes expressions and metabolite accumulations and omics data Reviewed

    N. Sakurai, T. Ara, Y. Ogata, R. Sano, T. Ono, K. Sugiyama, A. Hiruta, F. Fujii, K. Yamazaki, K. Yano, K. Aoki, A. Aharoni, K. Hamada, K. Yokoyama, S. Kawamura, H. Otsuka, T. Tokimatsu, M. Kanehisa, H. Suzuki, K. Saito, D. Shibata

    Nucleic Acids Res. 雑誌 Oxford Journals   39   D677 - D684   2011.01

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    Kind of work:Joint Work  

  • Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module Reviewed

    S. Ozaki, Y. Ogata, K. Suda, A. Kurabayashi, T. Suzuki, N. Yamamoto, Y. Iijima, T. Tsugane, T. Fujii, C. Konishi, S. Inai, S. Bunsupa, M. Yamazaki, D. Shibata, K. Aoki

    DNA Res. 雑誌 Kazusa DNA Research Institute   17   105 - 116   2010.04

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    Kind of work:Joint Work  

  • A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress tolerance Reviewed

    Y. Ogata, H. Suzuki, D. Shibata

    J. Wood Sci. 雑誌 The Japan Wood Research Society   55   395 - 400   2009.12

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    Kind of work:Joint Work  

  • A gene co-expression database for understanding biologcial processes in soybean Reviewed

    Y. Ogata, H. Suzuki, D. Shibata

    Plant Biotechnol. 雑誌 Japanese Society for Plant Cell and Molecular Biology   26   503 - 507   2009.12

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    Kind of work:Joint Work  

  • Practical network approaches and biologic interpretations of co-expression analysis in plants Reviewed

    Y. Ogata, D. Shibata

    Plant Biotechnol. 雑誌 Japanese Society for Plant Cell and Molecular Biology   26   3 - 8   2009.03

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    Kind of work:Joint Work  

  • Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics Reviewed

    K. Urano, K. Maruyama, Y. Ogata, Y. Morishita, M. Takeda, N. Sakurai, H. Suzuki, K. Saito, D. Shibata, M. Kobayashi, K. Yamaguchi-Shinozaki, K. Shinozaki

    Plant J. 雑誌 John Wiley & Sons, Inc.   57   1065 - 1078   2009.01

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    Kind of work:Joint Work  

  • Over-expression of transcription associated factor gene co-expressed with the genes of mevalonate pathway, upstream of isoprenoid biosynthesis, in Arabidopsis cultured cells Reviewed

    R. Sano, Y. Ogata, H. Suzuki, Y. Ogawa, T. Dansako, N. Sakurai, K. Okazaki, K. Aoki, K. Saito, D. Shibata

    Plant Biotechnol. 雑誌 Japanese Society for Plant Cell and Molecular Biology   25   583 - 587   2008.12

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    Kind of work:Joint Work  

  • Metabolite annotations based on the integration of mass spectral information Reviewed

    Y. Iijima, Y. Nakamura, Y. Ogata, K. Tanaka, N. Sakurai, K. Suda, T. Suzuki, H. Suzuki, K. Okazaki, M. Kitayama, S. Kanaya, K. Aoki, D. Shibata

    Plant J. 雑誌 John Wiley & Sons, Inc.   54   949 - 962   2008.06

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    Kind of work:Joint Work  

  • Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry Reviewed

    H. Suzuki, R. Sasaki, Y. Ogata, Y. Nakamura, N. Sakurai, M. Kitajima, H. Takayama, S. Kanaya, K. Aoki, D. Shibata, K. Saito

    Phytochemistry 雑誌 Elsevier Ltd.   69   99 - 111   2008.01

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    Kind of work:Joint Work  

  • Approaches for extracting practical information from gene co-expression networks in plant biology Reviewed

    K. Aoki, Y. Ogata, D. Shibata

    Plant Cell Physiol. 雑誌 The Japanese Society of Plant Physiologists   48   381 - 390   2007.03

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    Kind of work:Joint Work  

  • Introduction and virification of a novel method for measuring wood fiber length using a single cross section in Acacia mangium Reviewed

    K. Honjo, Y. Ogata, M. Fujita

    Trees 雑誌 Springer Verlag   20   356 - 362   2006.06

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    Kind of work:Joint Work  

  • 木部細胞形態の定量的画像処理のための環境設定(第2報)フィルムスキャナによる超広領域画像の非顕微鏡的サンプリングの試み Reviewed

    尾形善之、門川朋樹、藤田稔

    木材学会誌 雑誌 日本木材学会   48   341 - 347   2003.09

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    Kind of work:Joint Work  

  • Asynchronous wood formation in young Acacia mangium planted in Malaysia Reviewed

    Y. Ogata, T. Nobuchi, M. Fujita, M.H. Sahri

    J. Wood Sci. 雑誌 The Japan Wood Research Society   48   89 - 94   2002.04

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    Kind of work:Joint Work  

  • Growth rings and tree growth in young para rubber trees from Peninsular Malaysia Reviewed

    Y. Ogata, T. Nobuchi, M. Fujita

    IAWA J. 雑誌 International Association of Wood Anatomists   22   43 - 56   2001.03

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    Kind of work:Joint Work  

  • An analysis of the seasonality of wood formation in cinnamon trees and eucalyptuses by knife-cutting method Reviewed

    Y. Ogata, T. Nobuchi, M. Fujita

    Bull. Kyoto Univ. For. 雑誌 Kyoto University   68   116 - 126   1996.12

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    Kind of work:Joint Work  

  • Seasonal characteristics of wood formation in Hopea odorata and Shorea henryana Reviewed

    T. Nobuchi, Y. Ogata, S. Siripatanadilok

    IAWA J. 雑誌 International Association of Wood Anatomists   16   361 - 369   1995.12

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    Kind of work:Joint Work  

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Books and Other Publications

  • 未利用バイオクスの活用技術と事業性評価.(バイオマス利用の設計図入手を目指した物質・情報資源の探索)

    菊地淳、尾形善之( Role: Joint author)

    サイエンス&テクノロジー株式会社  2010.09 

  • Bioinformatics tools to discover co-expressed genes in plants

    Y. Ogata, N. Sakurai, N.J. Provart, D. Steinhauser, L. Krall( Role: Joint author)

    VILEY-VCH Verlag  2008.06 

  • Growth rings and tree growth in young para rubber trees from Peninsular Malaysia

    Y. Ogata, T. Nobuchi, M. Fujita( Role: Joint author)

    UPM Press  2008.04 

  • Seasonal characteristics of wood formation in Hopea odorata and Shorea henryana

    T. Nobuchi, Y. Ogata, S. Siripatanadilok( Role: Joint author)

    UPM Press  2008.04 

Presentations

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Works

  • Ucorn DB

    2024.01
    -
    Now

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    Work type:Database science  

  • Vcorn SARS-CoV-2

    2020.04
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    Now

  • Gcorn fungi

    2019.12
    -
    Now

  • Gcorn plant

    2019.11
    -
    Now

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    Work type:Database science  

  • ConfeitoGUI

    Ogata, Yoshiyuki

    2015.09
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    Now

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    Work type:Software  

    A toolkit for grouping in a size-sensitive manner based on correlation network analysis

Industrial Property Rights

  • 相関ネットワーク解析プログラム

    鈴木秀幸、萬年一斗、柴田大輔、尾形善之

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    property_type:Patent 

    Patent/Registration no:特許第6318334号 

Outline of collaborative research (seeds)

  • Gene homology analysis

  • Omics analysis in various organisms

Grant-in-Aid for Scientific Research

  • 都市緑地の植生を環境DNAメタバーコーディング法で把握するための基礎的研究

    Grant-in-Aid for Scientific Research(C)  2024

  • 都市緑地の植生を環境DNAメタバーコーディング法で把握するための基礎的研究

    2021

Charge of on-campus class subject

  • 応用生物科学概論

    2024   Weekly class   Undergraduate

  • 生物統計学演習

    2024   Weekly class   Undergraduate

  • バイオインフォマティクス特論

    2024   Weekly class   Graduate school

  • 機能ゲノム科学特論

    2024   Weekly class   Graduate school

  • 応用生物科学特論

    2024   Weekly class   Graduate school

  • 応用生物科学研究実験2A

    2024   Intensive lecture   Graduate school

  • 応用生物科学研究実験1A

    2024   Intensive lecture   Graduate school

  • 応用生物科学ゼミナール2A

    2024   Intensive lecture   Graduate school

  • 応用生物科学ゼミナール1A

    2024   Intensive lecture   Graduate school

  • 応用生物科学特別研究実験3A

    2024   Intensive lecture   Graduate school

  • 応用生物科学特別研究実験2A

    2024   Intensive lecture   Graduate school

  • 応用生物科学特別研究実験1A

    2024   Intensive lecture   Graduate school

  • 生物統計学演習

    2023   Weekly class   Undergraduate

  • 応用生物科学特別研究実験2A

    2023   Intensive lecture   Graduate school

  • 応用生物科学特別研究実験1A

    2023   Intensive lecture   Graduate school

  • バイオインフォマティクス特論

    2023   Weekly class   Graduate school

  • 機能ゲノム科学特論

    2023   Weekly class   Graduate school

  • 応用生物科学特論

    2023   Weekly class   Graduate school

  • 応用生物科学研究実験2A

    2023   Intensive lecture   Graduate school

  • 応用生物科学研究実験1A

    2023   Intensive lecture   Graduate school

  • 植物バイオサイエンス卒業研究

    2023   Intensive lecture   Undergraduate

  • 初年次ゼミナール

    2023   Weekly class   Graduate school

  • 植物バイオサイエンス演習

    2023   Intensive lecture   Undergraduate

  • 植物科学英語

    2023   Intensive lecture   Undergraduate

  • 応用生物科学特別研究実験3B

    2023   Intensive lecture   Graduate school

  • 応用生物科学研究プレゼンテーション

    2023   Intensive lecture   Graduate school

  • バイオインフォマティクス演習

    2023   Weekly class   Undergraduate

  • Introduction to Plant Biotechnology

    2021    

  • First Year Seminar

    2021    

  • Topics in Life, Environment, and Advanced Sciences

    2021    

  • Topics in Bioinformatics

    2021    

  • Topics in Economic Botany

    2021    

  • Biometry

    2021    

  • Laboratory : Basic Plant Biotechnology

    2021   Practical Training  

  • Research program in Plant Bioscience

    2021    

  • Special Practice in Plant Bioscience

    2021    

  • Basic genomics

    2021    

  • ICT Practice for Plant Bioscience

    2021    

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Charge of off-campus class subject

  • 情報処理演習

    Institution:Osaka Prefecture University

  • バイオインフォマティクス特論

    Institution:Osaka Prefecture University

  • Topics of Bioinformatics

    Institution:Osaka Prefecture University

  • Data Processing in Bioscience

    Institution:Osaka Prefecture University

  • Biostatistics

    Institution:Osaka Prefecture University

  • 生物統計学

    Institution:Osaka Prefecture University

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Number of papers published by graduate students

  • 2023

    Number of undergraduate student / college student presentations:Number of graduate students presentations:1

  • 2022

    Number of undergraduate student / college student presentations:Number of graduate students presentations:1

  • 2021

    Number of undergraduate student / college student presentations:Number of graduate students presentations:2