Shimizu Kentaro 清水健太郎

… Alternative Names

Researcher Number	10742629
Other IDs
Affiliation (Current)	2021: 横浜市立大学, 木原生物学研究所, 客員教授
Affiliation (based on the past Project Information) *help	2016 – 2020: 横浜市立大学, 木原生物学研究所, 客員教授 2016: チューリッヒ大学, 進化生物環境学研究所, 教授
Review Section/Research Field	Except Principal Investigator Biological Sciences / Applied biochemistry
Keywords	Principal Investigator トランスクリプトーム / 植物 Except Principal Investigator ゲノム / ハイブリッド / 異質倍数体 / 遺伝子発現 / 機械学習 / 交雑 / 遺伝子発現量 / ハイブリッドゲノム … More

季節性のない熱帯雨林での時系列トランスクリプトームによる環境認識・記憶の解析Principal Investigator
- Principal Investigator
  
  清水健太郎
- Project Period (FY)
  2018 – 2019
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Research Institution
  Yokohama City University
ハイブリッド新種ゲノムが有するオミクス適応能の包括的な解析Ongoing
- Principal Investigator
  
  瀬々潤
- Project Period (FY)
  2016 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Biological Sciences
- Research Institution
  National Institute of Advanced Industrial Science and Technology
Molecular dissection of correlative gene systems in plant sexual reproduction
- Principal Investigator
  
  TAKAYAMA Seiji
- Project Period (FY)
  2014 – 2016
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Applied biochemistry
- Research Institution
  The University of Tokyo
  Nara Institute of Science and Technology

All 2020 2019 2018 2017 2016

All Journal Article Presentation

[Journal Article] Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana2019
- Author(s)
  Sato Yasuhiro、Shimizu-Inatsugi Rie、Yamazaki Misako、Shimizu Kentaro K.*、Nagano Atsushi J.* (co-corresponding)
- Journal Title
  
  BMC Plant Biology
  
  Volume: 19 Pages: 163-163
- DOI
  10.1186/s12870-019-1705-2
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-18H04785
[Journal Article] Transcriptional Variation in Glucosinolate Biosynthetic Genes and Inducible Responses to Aphid Herbivory on Field-Grown Arabidopsis thaliana2019
- Author(s)
  Sato Yasuhiro、Tezuka Ayumi、Kashima Makoto、Deguchi Ayumi、Shimizu-Inatsugi Rie、Yamazaki Misako、Shimizu Kentaro K.*、Nagano Atsushi J.* (co-corresponding)
- Journal Title
  
  Frontiers in Genetics
  
  Volume: 10 Pages: 1-1
- DOI
  10.3389/fgene.2019.00787
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-18H04785
[Journal Article] Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica2018
- Author(s)
  Paape Timothy、Briskine Roman V.、Halstead-Nussloch Gwyneth、Lischer Heidi E. L.、Shimizu-Inatsugi Rie、Hatakeyama Masaomi、Tanaka Kenta、Nishiyama Tomoaki、Sabirov Renat、Sese Jun、Shimizu Kentaro K.
- Journal Title
  
  Nature Communications
  
  Volume: 9 Pages: 3909-3909
- DOI
  10.1038/s41467-018-06108-1
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-INTERNATIONAL-16K21727, KAKENHI-ORGANIZER-16H06464, KAKENHI-PLANNED-16H06469
[Journal Article] Homeolog expression quantification methods for allopolyploids2018
- Author(s)
  Tony C Y Kuo Masaomi Hatakeyama Toshiaki Tameshige Kentaro K Shimizu Jun Sese
- Journal Title
  
  Briefings in Bioinformatics
  
  Volume: bby121
- DOI
  10.1093/bib/bby121
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-16H06464, KAKENHI-PLANNED-16H06469, KAKENHI-PROJECT-17H06990, KAKENHI-PROJECT-16H06279
[Journal Article] Molecular basis of flowering under natural long-day conditions in Arabidopsis2018
- Author(s)
  Young Hun Song, Akane Kubota, Michael S. Kwon, Michael F. Covington, Nayoung Lee, Ella R. Taagen, Dianne Laboy Cintrテウn, Dae Yeon Hwang, Reiko Akiyama, Sarah K. Hodge, He Huang, Nhu H. Nguyen, Dmitri A. Nusinow, Andrew J. Millar, Kentaro K. Shimizu & Takato Imaizumi
- Journal Title
  
  Nature Plants
  
  Volume: 4 Pages: 824-835
- DOI
  10.1038/s41477-018-0253-3
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469, KAKENHI-PUBLICLY-18H04785
[Journal Article] Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica2017
- Author(s)
  Yew C-L, Kakui H, Shimizu KK
- Journal Title
  
  J Plant Res
  
  Volume: 9 Pages: 1-10
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop2017
- Author(s)
  Hatakeyama M, Aluri S, Balachadran M, Sivarajan S R, Patrignani Andrea、Gr?ter Simon、Poveda Lucy、Shimizu-Inatsugi Rie、Baeten John、Francoijs Kees-Jan、Nataraja Karaba N、Reddy Yellodu AN, Phadnis S, Ravikumar RL, Schlapbach R, Sreeman SM, Shimizu KK
- Journal Title
  
  DNA Research
  
  Volume: 25 Pages: 39-47
- DOI
  10.1093/dnares/dsx036
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq.2017
- Author(s)
  Hirao AS, Onda Y, Shimizu-Inatsugi R, Sese J, Shimizu KK, Kenta T
- Journal Title
  
  American Journal of Molecular Biology
  
  Volume: 7 Pages: 1046-1053
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] The population genomic signature of environmental association and gene flow in an ecologically divergent tree speciesMetrosideros polymorpha(Myrtaceae)2017
- Author(s)
  Izuno A,Kitayama K, Onoda Y, Tsuji Y,Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y
- Journal Title
  
  Molecular Ecology
  
  Volume: 26 Pages: 1515-1532
- DOI
  10.1111/mec.14016
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469, KAKENHI-PROJECT-26711025, KAKENHI-PROJECT-15KK0255, KAKENHI-PROJECT-26221106, KAKENHI-ORGANIZER-16H06464
[Journal Article] Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology2017
- Author(s)
  Briskine RV, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK
- Journal Title
  
  Molecular Ecology Resources
  
  Volume: 未定
- DOI
  10.1111/1755-0998.12604
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae).2017
- Author(s)
  Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y
- Journal Title
  
  Mol Ecol
  
  Volume: 26 Pages: 1515-1532
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Reference-guided de novo assembly approach improves genome reconstruction for related species2017
- Author(s)
  Lischer HEL, Shimizu KK
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 18 Pages: 474-474
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity2017
- Author(s)
  Ang CC, O’brien MJ, Ng KKS, Lee PC, Hector A, Schmid B, Shimizu KK
- Journal Title
  
  Plant Ecology & Diversity
  
  Volume: 9 Pages: 459-469
- DOI
  10.1080/17550874.2016.1270363
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Positional bias in variant calls against draft reference assemblies2017
- Author(s)
  Briskine RV, Shimizu KK
- Journal Title
  
  BMC Genomics
  
  Volume: 18 Pages: 263-263
- DOI
  10.1186/s12864-017-3637-2
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Plant adaptive radiation mediated by polyploid plasticity in transcriptomes2017
- Author(s)
  Shimizu-Inatsugi R, Terada A, Hirose K, Kudos H, Sese J, Shimizu KK
- Journal Title
  
  Molecular Ecology
  
  Volume: 26 Pages: 193-207
- DOI
  10.1111/mec.13738
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.2016
- Author(s)
  Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Sll T, Schltterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krmer U, Koch MA, Nordborg M
- Journal Title
  
  Nature Genetics
  
  Volume: 48 Pages: 1077-1082
- DOI
  10.1038/ng.3617
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469, KAKENHI-PROJECT-15K18583
[Journal Article] Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica.2016
- Author(s)
  Paape T, Hatakeyama M, Shimizu-Inatsugi R, Cereghetti T, Onda Y, Kenta T, Sees J, Shimizu KK
- Journal Title
  
  Molecular Biology and Evolution
  
  Volume: 33 Pages: 2781-2800
- DOI
  10.1093/molbev/msw141
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469, KAKENHI-PROJECT-15H02670
[Presentation] Effects of rainfall exclusion on tropical emergent tree in Southeast Asian tropics2020
- Author(s)
  Yuji Tokumoto, Masaki J Kobayashi, Masaomi Hatakeyama, Yuta Inoue, Yayoi Takeuchi, Bibian Anak Michael Diway, Daisuke Todaka, Tomonori Kume, Tomo'omi Kumagai, Tomoaki Ichie, Tohru Nakashizuka, Michiko Nakagawa, Shoko Sakai, Kentaro K. Shimizu
- Organizer
  World Biodiversity Forum 2020, Davos Congress Centre, Davos, Switzerland
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-18H04785
[Presentation] Comparative molecular phenology of tropical plants in South-easi Asia2020
- Author(s)
  Chongmeng Xu, Yuji Tokumoto, Kentaro K. Shimizu
- Organizer
  World Biodiversity Forum 2020, Davos Congress Centre, Davos, Switzerland
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-18H04785
[Presentation] Genomics for global change studies2019
- Author(s)
  Kentaro K. Shimizu
- Organizer
  Global Change and Biodiversity: Integrating the impact of earth and world drivers across scales, Monte Verita, Switzerland
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-18H04785
[Presentation] Gene functions in natura - approaches using machine learning and mutants to analyze phenome, transcriptome and ecological data in naturally fluctuating environments2018
- Author(s)
  Kentaro K. Shimizu
- Organizer
  The 41th Annual Meeting of the Molecular Biology Society of Japan, Yokoham
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-18H04785
[Presentation] A single dominant mutateon conferred self-compatibility in allotetraploid Arabidopsis kamchatica2017
- Author(s)
  Yew C.L., Tsuchimatsu T., Shimizu-Inatsugi R., Shimizu K.K.
- Organizer
  Zurich-Basel Plant Science Center PSC symposium,
- Data Source
  KAKENHI-PLANNED-16H06469
[Presentation] Multiple hybrid de novo genome assembly of finger millet2017
- Author(s)
  Hatakeyama M., Aluri S., Patrignani A., Grter S., Poveda L., Schlapbach R., Shimizu-Inatsugi R., Shimizu K.K., Baeten J.B., Francoijs K.-J., Balachadran M.T., Sivarajan SR, Nataraja K.N., Ravikumar R.L., Reddy Y.A.N., Sreeman SM
- Organizer
  Zurich-Basel Plant Science Center PSC symposium
- Data Source
  KAKENHI-PLANNED-16H06469
[Presentation] A dominant mutation conferred self-compatibility in allotetraploid A.kamuchatica2017
- Author(s)
  Yew C.L., Tsuchimatsu T., Shimizu-Inatsugi R., Shimizu K.K.
- Organizer
  Symposium on “Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution”
- Data Source
  KAKENHI-PLANNED-16H06469
[Presentation] Identification of a gene controlling pollen number by a GWAS and CRISPR mutants2017
- Author(s)
  Kakui H., Tsuchimatsu T., Yamazaki M., Marona C., Tsutsui H., Hedhly A., Meng D., Sato Y., Stadler T., Grossniklaus U., Kanaoka M., Lenhard M., Nordborg M., Shimizu K
- Organizer
  Symposium on “Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution”
- Data Source
  KAKENHI-PLANNED-16H06469

1. TAKAYAMA Seiji (70273836)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
2. WADA Yuko (50379541)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. FUJII Sota (90716713)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. MURASE Koji (50467693)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. TSUCHIMATSU Takashi (60740107)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
6. 瀬々潤 (40361539)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results
7. 孫建強 (90838624)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. KITAYAMA Kanehiro

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
9. ISAGI Yuji

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
10. IZUNO Ayako

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. Nagano Atushi J.

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. TSUJI Hiroyuki

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 爲重才覚

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 小野田雄介

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
15. 工藤洋

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
16. 田中章司郎

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
17. 恩田義彦

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Shimizu Kentaro 清水 健太郎

SHIMIZU Kentaro 清水 健太郎

Research Projects

Research Products

Co-Researchers

季節性のない熱帯雨林での時系列トランスクリプトームによる環境認識・記憶の解析Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Institution

ハイブリッド新種ゲノムが有するオミクス適応能の包括的な解析Ongoing

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Molecular dissection of correlative gene systems in plant sexual reproduction

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Journal Article] Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana2019

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Transcriptional Variation in Glucosinolate Biosynthetic Genes and Inducible Responses to Aphid Herbivory on Field-Grown Arabidopsis thaliana2019

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Homeolog expression quantification methods for allopolyploids2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Molecular basis of flowering under natural long-day conditions in Arabidopsis2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica2017

Author(s)

Journal Title

Data Source

[Journal Article] Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop2017

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq.2017

Author(s)

Journal Title

Data Source

[Journal Article] The population genomic signature of environmental association and gene flow in an ecologically divergent tree speciesMetrosideros polymorpha(Myrtaceae)2017

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology2017

Author(s)

Journal Title

DOI

Data Source

[Journal Article] The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae).2017

Author(s)

Journal Title

Data Source

[Journal Article] Reference-guided de novo assembly approach improves genome reconstruction for related species2017

Author(s)

Journal Title

Data Source

[Journal Article] Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity2017

Author(s)

Shimizu Kentaro 清水健太郎

SHIMIZU Kentaro 清水健太郎