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)	2025: 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 – 2024: 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 Basic Section 39010:Science in plant genetics and breeding-related / Transformative Research Areas, Section (I) / Transformative Research Areas, Section (III) 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 / 機械学習 / 遺伝子発現 / RNA-seq / 倍数体 / 東アジア / パンコムギ / ゲノム解析 / 文化の伝播 … More / コムギ / 集団史 / 不和合性 / 自殖 / ゲノム重複 / 植物生殖 / 植物 … More Except Principal Investigator 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

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
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
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 2024 2023 2022 2021 2020 2019 2018 2017 2016

All Journal Article Presentation

[Journal Article] Small RNA-regulated dominance among polyploid subgenomes supports Haldane's sieve in evolution of self-compatibility.2023
- Author(s)
  Yew, C.-L., Tsuchimatsu, T., Shimizu-Inatsugi, R., Yasuda, S., Hatakeyama, M., Kakui, H., Ohta, T., Suwabe, K., Watanabe, M., Takayama, S., Shimizu, K. K.
- Journal Title
  
  Nature Commun.
  
  Volume: 14 Issue: 1 Pages: 7618-7618
- DOI
  10.1038/s41467-023-43275-2
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K18058, KAKENHI-PROJECT-22K21352, KAKENHI-PROJECT-23K23582, KAKENHI-PROJECT-21H05030, KAKENHI-PROJECT-20H02956
[Journal Article] Targeted single-cell gene induction by optimizing the dually regulated CRE/loxP system by a newly defined heat-shock promoter and the steroid hormone in Arabidopsis thaliana2023
- Author(s)
  Takumi Tomoi, Toshiaki Tameshige, Eriko Betsuyaku, Saki Hamada, Joe Sakamoto, Naoyuki Uchida, Keiko U Torii, Kentaro K Shimizu, Yosuke Tamada, Hiroko Urawa, Kiyotaka Okada, Hiroo Fukuda, Kiyoshi Tatematsu, Yasuhiro Kamei, Shigeyuki Betsuyaku
- Journal Title
  
  Frontiers in Plant Science
  
  Volume: in press Pages: 1171531-1171531
- DOI
  10.3389/fpls.2023.1171531
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20H02586, KAKENHI-PROJECT-20K20303, KAKENHI-PROJECT-21K19250, KAKENHI-PROJECT-22K05586, KAKENHI-PROJECT-23K23582, KAKENHI-PLANNED-23H03847, KAKENHI-PROJECT-20H05702, KAKENHI-PROJECT-21H02500, KAKENHI-PROJECT-23K26510
[Journal Article] UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 for Plant Survival in Sunlight under Field Conditions2023
- Author(s)
  Stockenhuber Reinhold、Akiyama Reiko、Tissot Nicolas、Milosavljevic Stefan、Yamazaki Misako、Wyler Michele、Arongaus Adriana B、Podolec Roman、Sato Yasuhiro、Widmer Alex、Ulm Roman、Shimizu Kentaro K
- Journal Title
  
  Plant And Cell Physiology
  
  Volume: 65 Issue: 1 Pages: 35-48
- DOI
  10.1093/pcp/pcad113
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Journal Article] Detecting frequency-dependent selection through the effects of genotype similarity on fitness components2023
- Author(s)
  Sato Yasuhiro、Takahashi Yuma、Xu Chongmeng、Shimizu Kentaro K
- Journal Title
  
  Evolution
  
  Volume: 77 Issue: 4 Pages: 1145-1157
- DOI
  10.1093/evolut/qpad028
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179, KAKENHI-PROJECT-20K15880
[Journal Article] Utility of commercial high‐resolution satellite imagery for monitoring general flowering in Sarawak, Borneo2023
- Author(s)
  Miura Tomoaki、Tokumoto Yuji、Nagai Shin、Shimizu Kentaro K.、Pungga Runi Anak Sylvester、Ichie Tomoaki
- Journal Title
  
  Ecological Research
  
  Volume: Early View Issue: 3 Pages: 386-402
- DOI
  10.1111/1440-1703.12382
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K12352, KAKENHI-PLANNED-22H05179
[Journal Article] A low-coverage 3′ RNA-seq to detect homeolog expression in polyploid wheat2023
- Author(s)
  Sun Jianqiang、Okada Moeko、Tameshige Toshiaki、Shimizu-Inatsugi Rie、Akiyama Reiko、Nagano Atsushi?J、Sese Jun、Shimizu Kentaro?K
- Journal Title
  
  NAR Genomics and Bioinformatics
  
  Volume: 5 Issue: 3
- DOI
  10.1093/nargab/lqad067
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K18156, KAKENHI-PROJECT-22K05586, KAKENHI-PROJECT-23K23582, KAKENHI-PROJECT-23H00386
[Journal Article] Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation2023
- Author(s)
  Akiyama Reiko、Goto Takao、Tameshige Toshiaki、Sugisaka Jiro、Kuroki Ken、Sun Jianqiang、Akita Junichi、Hatakeyama Masaomi、Kudoh Hiroshi、Kenta Tanaka、Tonouchi Aya、Shimahara Yuki、Sese Jun、Kutsuna Natsumaro、Shimizu-Inatsugi Rie、Shimizu Kentaro K.
- Journal Title
  
  Nature Communications
  
  Volume: 14 Issue: 1 Pages: 5792-5792
- DOI
  10.1038/s41467-023-41260-3
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K21352, KAKENHI-PROJECT-22K05586, KAKENHI-PROJECT-23K23582, KAKENHI-PROJECT-21H04977
[Journal Article] A global analysis of matches and mismatches between human genetic and linguistic histories2022
- Author(s)
  Barbieri Chiara、Blasi Dami?n E.、Arango-Isaza Epifan?a、Sotiropoulos Alexandros G.、Hammarstr?m Harald、Wichmann S?ren、Greenhill Simon J.、Gray Russell D.、Forkel Robert、Bickel Balthasar、Shimizu Kentaro K.
- Journal Title
  
  Proceedings of the National Academy of Sciences
  
  Volume: 119 Issue: 47
- DOI
  10.1073/pnas.2122084119
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-21H05366
[Journal Article] Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade2022
- Author(s)
  Sotiropoulos、Arango-Isaza、Ban、Barbieri 、Bourras 、Cowger 、Czembor、Ben-David、Dinoor、Ellwood、Graf、Hatta、Helguera、Sanchez-Martin、McDonald, Morgounov、Muller、Shamanin、Shimizu、Yoshihira、Zbinden、Keller、Wicker
- Journal Title
  
  Nature Communications
  
  Volume: 13 Issue: 1 Pages: 4315-4315
- DOI
  10.1038/s41467-022-31975-0
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-21H05366
[Journal Article] Polyploidy before and after domestication of crop species2022
- Author(s)
  Akagi Takashi、Jung Katharina、Masuda Kanae、Shimizu Kentaro K.
- Journal Title
  
  Current Opinion in Plant Biology
  
  Volume: 69 Pages: 102255-102255
- DOI
  10.1016/j.pbi.2022.102255
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05173, KAKENHI-PLANNED-22H05179, KAKENHI-PUBLICLY-21H05366, KAKENHI-PROJECT-23K23582
[Journal Article] Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?2022
- Author(s)
  Shimizu Kentaro K.
- Journal Title
  
  Current Opinion in Plant Biology
  
  Volume: 69 Pages: 102292-102292
- DOI
  10.1016/j.pbi.2022.102292
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-22H05179, KAKENHI-PROJECT-23K23582
[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
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-16H06469, KAKENHI-PLANNED-21H05314
[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] Effects of Allopolyploidization on Homoeologous Gene Expression under Cold Treatment in Synthetic Hexaploid Wheat2024
- Author(s)
  Moeko Okada, Jianquiang Sun, Toshiaki Tameshige, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Shigeo Takumi, Jun Sese, Kentaro K. Shimizu
- Organizer
  KAAB international symposium, Niigata, 2024-03-26
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Robustness of polyploid species in natura studied by genomics and machine learning2023
- Author(s)
  Kentaro K. Shimizu
- Organizer
  Joint Kickoff Symposium for Key-Molecule-Network in Plant Reproduction (KEPLR) and CRISPit, Tokyo, Japan, 2023-06-04
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] コムギの栽培化に伴って花粉数は変わるのか？2023
- Author(s)
  角井宏行, Naoto-Benjamin Hamaya, 岡田萌子, Katharina Jung, 聶紀魯, Thomas Wicker, Beat Keller, 清水健太郎, 那須田周平
- Organizer
  第18回ムギ類研究会，滋賀 2023-12-23
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Robustness of polyploid species: evolutionary genomic studies using Arabidopsis kamchatica and wheat2023
- Author(s)
  Kentaro K. Shimizu
- Organizer
  Symposium Genome duplication at the intersection of biodiversity and crop sciences, Fribourg, Switzerland, 10.07.2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Pairing homoeologous 2欠失変異体を利用したパンコムギへの異種染色体断片導入2023
- Author(s)
  田渕雅啓, 岡田萌子, 道川麻美, 井上喜博, 西村和紗, 水野信之, 清水健太郎, 小林史典, 宅見薫雄, 吉田健太郎
- Organizer
  日本育種学会第144回講演会, 神戸大学, 2023-09-17
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Robustness of allopolyploid species in natura: genome shock or gradual evolution?2023
- Author(s)
  Kentaro K. Shimizu
- Organizer
  Polyploidy 2023, Palm Coast, Florida, USA, 2023-05-10
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Effects of allopolyploidization on homoeologous gene expression changes and environmental response in hexaploid wheat.2023
- Author(s)
  Moeko Okada, J. Sun, T. Tameshige, M. Hatakeyama, R. Shimizu-Inatsugi, S. Takumi, J. Sese, K. K. Shimizu
- Organizer
  Plant and Animal Genome Conference 30, San Diego, USA, 2023-01-16
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Effects of allopolyploidization on homoeologous gene expression changes and environmental response in hexaploid wheat2023
- Author(s)
  Moeko Okada, Jianqiang Sun, Toshiaki Tameshige, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Shigeo Takumi, Jun Sese, Kentaro K. Shimizu
- Organizer
  30th Plant and Animal Genome Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] 異質倍数体化が相同遺伝子発現パターンに及ぼす影響2023
- Author(s)
  岡田萌子, 孫建強、爲重才覚、畠山剛臣、清水(稲継)理恵、宅見薫雄、瀬々潤、清水健太郎
- Organizer
  第18回ムギ類研究会，滋賀 2023-12-23
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] 大規模トランスクリプトームから見た野外環境下におけるパンコムギの季節性遺伝子発現2023
- Author(s)
  Toshiaki Tameshige, Jianqiang Sun, Reiko Akiyama, Jiro Sugisaka, Yoko Kamiya, Atsushi Nagano, Rie Shimizu-Inatsugi, Jun Sese, Kentaro Shimizu
- Organizer
  日本植物学会第87回大会，札幌 2023-09-08
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Unravelling the Genetic Architecture of Male Reproductive Traits in Asian Bread Wheat (Triticum aestivum L.).2023
- Author(s)
  Naoto-Benjamin Hamaya, Hiroyuki Kakui, Jilu Nie, Moeko Okada, Thomas Wicker, Beat Keller, Shuhei Nasuda, Kentaro K. Shimizu
- Organizer
  30th Plant and Animal Genome Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] Unravelling the Genetic Architecture of Male Reproductive Traits in Asian Bread Wheat (Triticum aestivum L.)2023
- Author(s)
  Naoto-Benjamin Hamaya, Hiroyuki Kakui, Jilu Nie, Moeko Okada, Thomas Wicker, Beat Keller, Shuhei Nasuda, Kentaro K. Shimizu
- Organizer
  30th Plant and Animal Genome Conference, San Diego, USA. 2023/1/13-18
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] パンコムギの気孔密度多様性とパターン形成理論2023
- Author(s)
  爲重才覚・杉阪次郎・竹中祥太朗・黒木健・新田みゆき・那須田周平・清水健太郎
- Organizer
  第18回ムギ類研究会，滋賀 2023-12-23
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Environmental robustness of Arabidopsis allopolyploid species2023
- Author(s)
  Kentaro K. Shimizu
- Organizer
  第46回日本分子生物学会、神戸・zoom 2023-11-20
- Invited
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] コムギ NAM 集団の茎立ち期における UAV によるハイスループットフェノタイピングおよび UAV から得られた形質と収量関連形質との関連2023
- Author(s)
  吉岡俊輔, 黒木健, 新田みゆき, 聶紀魯, 石井昌範, 角井宏行, 岡田萌子, 竹中祥太郎, 清水健太郎, 岩田洋佳, 郭威, 那須田周平
- Organizer
  日本育種学会第144回講演会, 神戸大学, 2023-09-16
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Time-series field phenotyping system PlantServation using machine learning revealed seasonal pigment fluctuation trends in diploid and polyploid Arabidopsis2023
- Author(s)
  Toshiaki Tameshige, Reiko Akiyama, Takao Goto, Jiro Sugisaka, Ken Kuroki, Jianqiang Sun, Junichi Akita, Masaomi Hatakeyama, Hiroshi Kudoh, Tanaka Kenta, Aya Tonouchi, Yuki Shimahara, Jun Sese, Natsumaro Kutsuna, Rie Shimizu-Inatsugi, Kentaro K Shimizu
- Organizer
  The 33rd International Conference on Arabidopsis Research (ICAR2023), Chiba, Japan, 2023-06-07
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Effects of allopolyploidization on homoeologous gene expression changes and environmental response in hexaploid wheat2023
- Author(s)
  Moeko Okada, Jianqiang Sun, Toshiaki Tameshige, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Shigeo Takumi, Jun Sese, Kentaro K. Shimizu
- Organizer
  30th Plant and Animal Genome Conference, San Diego, USA. 2023/1/13-18
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] RNA-seq-based bulked segregant analysis of the causal U-genome gene for hybrid incompatibility between tetraploid wheat and wild wheat relative Aegilops umbellulata2022
- Author(s)
  Moeko Okada, Kentaro Yoshida, Kentaro K. Shimizu, Shigeo Takumi
- Organizer
  The 26th International Conference on Sexual Plant Reproduction, Prague, Czech Republic, 2022-06-21
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] 倍数体種の頑健性2022
- Author(s)
  清水健太郎
- Organizer
  第141回育種学会
- Invited
- Data Source
  KAKENHI-PUBLICLY-21H05366
[Presentation] Polyploid Arabidopsis inherit parental traits in natura as shown by deep-learning and soil analyses2022
- Author(s)
  Kentaro K. Shimizu
- Organizer
  Congress of the European Society for Evolutionary Biology, Prague, Czech, 2022-08-19
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] パンコムギのnested association mapping (NAM)集団のGRAS-Diマーカーによるコンセンサスマップの構築2022
- Author(s)
  聶紀魯・新田みゆき・竹中祥太朗・岡田萌子・清水健太郎・那須田周平
- Organizer
  第17回ムギ類研究会、つくば、2022-12-16
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Aegilops umbellulata Zhuk. で観察されたうどんこ病菌に対する侵入後抵抗性の遺伝解析2022
- Author(s)
  河村凌, 岡田萌子, 小村翔也, 清水健太郎, 西村和紗, 井上喜博, 吉田健太郎
- Organizer
  第17回ムギ類研究会，茨城 2022-12-16
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] Identification and analysis of candidate genes regulating pollen number in A. thaliana2022
- Author(s)
  Naoto-Benjamin Hamaya, Hiroyuki Kakui, Afif Hedhly, Ana Marcela Florez-Rueda, Masaomi Hatakeyama, Misako Yamazaki, Ueli Grossniklaus, Kentaro K. Shimizu
- Organizer
  26th International Conference on Sexual Plant Reproduction
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] Pollen number is regulated by REDUCED POLLEN NUMBER1 encoding ribosome assembly factor and is characterized by an enriched selection signal among traits related to selfing syndrome in Arabidopsis thaliana2022
- Author(s)
  Kentaro K. Shimizu, Hiroyuki Kakui, Takashi Tsuchimatsu, Misako Yamazaki, Masaomi Hatakeyama, Lucas Mohn, Thomas Stテ、dler, Michael Lenhard, Magnus Nordborg
- Organizer
  26th International Conference on Sexual Plant Reproduction
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] Polyploid Arabidopsis inherit parental traits in natura as shown by deep-learning and soil analyses2022
- Author(s)
  Kentaro Shimizu, Reiko Akiyama, Takao Goto, Toshiaki Tameshige, Ken Kuroki, Jiro Sugisaka, Tim Paape, Gwyneth Halstead-Nussloch, Jianqiang Sun, Aya Tonouchi, Yuki Shimahara, Hiroshi Kuodh, Tanaka Kenta, Junichi Akita, Jun Sese, Rie Shimizu-Inatsugi, Natsumaro Kutsuna
- Organizer
  Congress of the European Society for Evolutionary Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] Machine learning of image and transcriptome data of Arabidopsis and wheat polyploid plants in natura2022
- Author(s)
  Kentaro K. Shimizu
- Organizer
  SwissPLANT 2022, Meiringen, Switzerland, 2022-06-15
- Data Source
  KAKENHI-PROJECT-23K23582
[Presentation] RNA-seq-based bulked segregant analysis of the causal U-genome gene for hybrid incompatibility between tetraploid wheat and wild wheat relative Aegilops umbellulat2022
- Author(s)
  Moeko Okada, Kentaro Yoshida, Kentato K. Shimizu, Shigeo Takumi.
- Organizer
  26th International Conference on Sexual Plant Reproduction
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] A global analysis of matches and mismatches between human genetic and linguistic histories by assemblying the "GELATO" database2022
- Author(s)
  Kentaro K. Shimizu
- Organizer
  Joint Conference on Language Evolution
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-21H05366
[Presentation] Brassica rapaの系統間一側性不和合性を支配するUI遺伝子座のゲノム構造比較解析2022
- Author(s)
  高田美信, 清水元樹, 鈴木剛, 渡辺正夫
- Organizer
  第17回東北育種研究集会
- Data Source
  KAKENHI-PLANNED-22H05179
[Presentation] Wheat2022
- Author(s)
  Kentaro K. Shimizu
- Organizer
  ILCAA Joint Research Project "Studies in Asian and African Geolinguistics"
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-21H05366
[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: 3 results
3. 渡辺正夫 (90240522)

# of Collaborated Projects: 2 results

# of Collaborated Products: 2 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)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
10. 木下哲 (60342630)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. 伊藤寿朗 (90517096)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. 榊原恵子 (90590000)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 奥田哲弘 (90727702)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
14. 井澤毅 (10263443)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
15. 白澤健太 (60527026)

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 草野修平 (80759291)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
18. 遠藤真咲 (40546371)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
19. 小田原瑛美子 (40802054)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
20. 櫻庭俊 (90647380)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
21. 越阪部晃永 (70632107)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
22. ICHIE Tomoaki

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
23. 亀井保博

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
24. 永井信

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
25. 徳本雄史

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
26. 永野惇

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
27. 工藤洋

# 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

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

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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

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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

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

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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

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Comprehensive analysis of omics adaptability in hybrid species

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Molecular dissection of correlative gene systems in plant sexual reproduction

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[Journal Article] Small RNA-regulated dominance among polyploid subgenomes supports Haldane's sieve in evolution of self-compatibility.2023

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[Journal Article] Targeted single-cell gene induction by optimizing the dually regulated CRE/loxP system by a newly defined heat-shock promoter and the steroid hormone in Arabidopsis thaliana2023

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[Journal Article] UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 for Plant Survival in Sunlight under Field Conditions2023

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[Journal Article] Detecting frequency-dependent selection through the effects of genotype similarity on fitness components2023

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[Journal Article] Utility of commercial high‐resolution satellite imagery for monitoring general flowering in Sarawak, Borneo2023

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[Journal Article] A low-coverage 3′ RNA-seq to detect homeolog expression in polyploid wheat2023

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[Journal Article] Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation2023

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Shimizu Kentaro 清水健太郎

SHIMIZU Kentaro 清水健太郎