Shimizu Kentaro 清水健太郎

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SHIMIZU Kentaro 清水健太郎

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Researcher Number	10742629
Other IDs
Affiliation (Current)	2023: 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 – 2023: 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	Principal Investigator Transformative Research Areas, Section (III) / Transformative Research Areas, Section (I) / Basic Section 39010:Science in plant genetics and breeding-related Except Principal Investigator Transformative Research Areas, Section (III) / Applied biochemistry / Biological Sciences
Keywords	Principal Investigator ゲノム / トランスクリプトーム / 不和合性 / 自殖 / 植物生殖 / 東アジア / パンコムギ / ゲノム解析 / 機械学習 / 遺伝子発現 / 植物 … More Except Principal Investigator … More ゲノム / 異分野技術融合 / 国際活動支援 / 異分野コア技術群支援 / ゲノム動態 / 繁殖適応戦略 / 両性花 / シロイヌナズナ / 全ゲノム関連解析 / 有性生殖 / 植物 / 発現解析 / GWAS / バイオインフォマティクス / ハイブリッドゲノム / 遺伝子発現量 / 交雑 / 機械学習 / 遺伝子発現 / 異質倍数体 / ハイブリッド Less

パンコムギの品種間シス制御の違いを利用した新規対立遺伝子の単離Principal Investigator
- Principal Investigator
  
  清水健太郎
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 39010:Science in plant genetics and breeding-related
- Research Institution
  Yokohama City University
Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations
- Principal Investigator
  
  赤木剛士
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Okayama University
受粉時における自殖性と他殖性の質的・量的バランスを制御する分子機構と選択圧Principal Investigator
- Principal Investigator
  
  清水健太郎
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Yokohama City University
The study of diffusion and altitudinal adaptation of East Asian wheat by integrating genome science and archaeologyPrincipal Investigator
- Principal Investigator
  
  清水健太郎
- Project Period (FY)
  2021 – 2022
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (I)
- Research Institution
  Yokohama City University
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
Comprehensive analysis of omics adaptability in hybrid species
- Principal Investigator
  
  Sese Jun
- 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
  Humanome Lab., Inc.
  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 2021 2020 2019 2018 2017 2016

All Journal Article Presentation

[Journal Article] ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw2021
- Author(s)
  Milosavljevic Stefan、Kuo Tony、Decarli Samuele、Mohn Lucas、Sese Jun、Shimizu Kentaro K.、Shimizu-Inatsugi Rie、Robinson Mark D.
- Journal Title
  
  BMC Genomics
  
  Volume: 22 Issue: 1 Pages: 547-547
- DOI
  10.1186/s12864-021-07845-2
- Data Source
  KAKENHI-PLANNED-16H06469
[Journal Article] The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests2021
- Author(s)
  Ng Kevin Siong、Kobayashi MJ.、Fawcett JA.、Hatakeyama M、Paape T、Ng CH、Ang CC、Tnah LH、Lee CT、Nishiyama T、Sese J、O’Brien MJ.、Copetti D、Isa Mohd NM、Ong RC、Putra M、Siregar IZ.、Indrioko S、Kosugi Y、Izuno A、Isagi Y、Lee SL, Shimizu KK.
- Journal Title
  
  Communications Biology
  
  Volume: 4 Issue: 1 Pages: 1166-1166
- DOI
  10.1038/s42003-021-02682-1
- Data Source
  KAKENHI-PLANNED-16H06469
[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 Issue: 1 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 Issue: 1 Pages: 3909-3909
- DOI
  10.1038/s41467-018-06108-1
- NAID
  120007128243
- 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)
  Kuo Tony C Y、Hatakeyama Masaomi、Tameshige Toshiaki、Shimizu Kentaro K、Sese Jun
- Journal Title
  
  Briefings in Bioinformatics
  
  Volume: bby121 Issue: 2 Pages: 395-407
- 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 Issue: 10 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 Issue: 1 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 species Metrosideros 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 Issue: 6 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 Issue: 5 Pages: 1025-1036
- 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 Issue: 5-6 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 Issue: 1 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 Issue: 1 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 polymorphism2016
- 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 Issue: 9 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 kamchatica2016
- 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 Issue: 11 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] Time-course image analysis of Arabidopsis thaliana and its wild relatives in fluctuating field conditions using machine learning2021
- Author(s)
  Reiko Akiyama, Takao Goto, Toshiaki Tameshige, Jiro Sugisaka, Rie Shimizu-Inatsugi, Jianqiang Sun, Junichi Akita, Natsumaro Kutsuna, Jun Sese, Kentaro K. Shimizu
- Organizer
  Patterns in Nature and Plant Sciences; PSC SYMPOSIUM 2021
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469
[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. FUJII Sota (90716713)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
2. 孫建強 (90838624)

# of Collaborated Projects: 2 results

# of Collaborated Products: 1 results
3. 渡辺正夫 (90240522)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
4. Sese Jun (40361539)

# of Collaborated Projects: 1 results

# of Collaborated Products: 9 results
5. TAKAYAMA Seiji (70273836)

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 赤木剛士 (50611919)

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# of Collaborated Products: 0 results
10. 木下哲 (60342630)

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11. 伊藤寿朗 (90517096)

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12. 榊原恵子 (90590000)

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13. 奥田哲弘 (90727702)

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14. 井澤毅 (10263443)

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15. 白澤健太 (60527026)

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# of Collaborated Products: 0 results
16. 内田誠一 (70315125)

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17. 越阪部晃永 (70632107)

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18. 草野修平 (80759291)

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19. 遠藤真咲 (40546371)

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20. 小田原瑛美子 (40802054)

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21. 櫻庭俊 (90647380)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results

Shimizu Kentaro 清水 健太郎

SHIMIZU Kentaro 清水 健太郎

Research Projects

Research Products

Co-Researchers

パンコムギの品種間シス制御の違いを利用した新規対立遺伝子の単離Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

受粉時における自殖性と他殖性の質的・量的バランスを制御する分子機構と選択圧Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

The study of diffusion and altitudinal adaptation of East Asian wheat by integrating genome science and archaeologyPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

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

Comprehensive analysis of omics adaptability in hybrid species

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] ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests2021

Author(s)

Journal Title

DOI

Data Source

[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

NAID

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

Shimizu Kentaro 清水健太郎

SHIMIZU Kentaro 清水健太郎