All Stories

  1. Homeolog expression quantification methods for allopolyploids

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Professor Kentaro K. Shimizu

  2. Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

    Article • Nature Communications, September 2018, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  3. Molecular basis of flowering under natural long-day conditions in Arabidopsis

    Article • Nature Plants, September 2018, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  4. The Nagoya Protocol could backfire on the Global South

    Article • Nature Ecology & Evolution, May 2018, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  5. Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

    Article • May 2018, Cold Spring Harbor Laboratory Press

    Professor Kentaro K. Shimizu

  6. Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica

    Article • January 2018, Cold Spring Harbor Laboratory Press

    Professor Kentaro K. Shimizu

  7. Genomics meets remote sensing in global change studies: monitoring and predicting phenology, evolution and biodiversity

    Article • Current Opinion in Environmental Sustainability, December 2017, Elsevier

    Professor Kentaro K. Shimizu, Dr Debra Zuppinger-Dingley

  8. Integrative research efforts at the boundary of biodiversity and global change research

    Article • Current Opinion in Environmental Sustainability, December 2017, Elsevier

    Professor Kentaro K. Shimizu, Dr Debra Zuppinger-Dingley

  9. Reference-guided de novo assembly approach improves genome reconstruction for related species

    Article • BMC Bioinformatics, November 2017, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  10. Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica

    Article • Journal of Plant Research, October 2017, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  11. Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

    Article • DNA Research, September 2017, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  12. Duplicated pollen–pistil recognition loci control intraspecific unilateral incompatibility in Brassica rapa

    Article • Nature Plants, June 2017, Nature

    Professor Kentaro K. Shimizu

  13. Positional bias in variant calls against draft reference assemblies

    Article • BMC Genomics, March 2017, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  14. The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)

    Article • Molecular Ecology, February 2017, Wiley

    Professor Kentaro K. Shimizu

  15. Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica

    Article • Molecular Biology and Evolution, January 2017, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  16. Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

    Article • BMC Genomics, January 2017, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  17. Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity

    Article • Plant Ecology & Diversity, November 2016, Taylor & Francis

    Professor Kentaro K. Shimizu

  18. The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

    Article • Nature Plants, October 2016, Nature

    Professor Kentaro K. Shimizu

  19. Genome assembly and annotation of Arabidopsis halleri , a model for heavy metal hyperaccumulation and evolutionary ecology

    Article • Molecular Ecology Resources, October 2016, Wiley

    Professor Kentaro K. Shimizu

  20. Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri

    Article • Heredity, October 2016, Nature

    Professor Kentaro K. Shimizu

  21. Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

    Article • Molecular Ecology, August 2016, Wiley

    Professor Kentaro K. Shimizu

  22. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

    Article • Nature Genetics, July 2016, Nature

    Professor Kentaro K. Shimizu, Polina Yu Novikova, Professor Karol Marhold

  23. Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the AllotetraploidArabidopsis kamchatica

    Article • Molecular Biology and Evolution, July 2016, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  24. Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations

    Article • Journal of Plant Research, April 2016, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  25. Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

    Article • Nature Genetics, January 2016, Nature

    Professor Kentaro K. Shimizu

  26. Self-compatibility and selfing syndrome of Arabidopsis, C. elegans and others

    Article • Annual Review of Ecology Evolution and Systematics, December 2015, Annual Reviews

    Professor Kentaro K. Shimizu

  27. Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

    Article • Systematic and Applied Microbiology, July 2015, Elsevier

    Professor Kentaro K. Shimizu

  28. Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing

    Article • PLoS ONE, June 2015, PLOS

    Professor Kentaro K. Shimizu

  29. Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae)

    Article • PLoS ONE, June 2015, PLOS

    Professor Kentaro K. Shimizu

  30. Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae)

    Article • Annals of Botany, March 2015, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  31. Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia

    Article • Nature Plants, January 2015, Nature

    Professor Kentaro K. Shimizu

  32. Transcriptional Characteristics and Differences in Arabidopsis Stigmatic Papilla Cells Pre- and Post-Pollination

    Article • Plant and Cell Physiology, December 2014, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  33. Nitrogen as a key regulator of flowering inFagus crenata: understanding the physiological mechanism of masting by gene expression analysis

    Article • Ecology Letters, August 2014, Wiley

    Professor Kentaro K. Shimizu

  34. Efficient Purging of Deleterious Mutations in Plants with Haploid Selfing

    Article • Genome Biology and Evolution, May 2014, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  35. Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy

    Article • Annals of Botany, February 2014, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  36. Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

    Article • Nucleic Acids Research, January 2014, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  37. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

    Article • Molecular Ecology, October 2013, Wiley

    Professor Kentaro K. Shimizu

  38. Cell Type-Specific Transcriptome of Brassicaceae Stigmatic Papilla Cells From a Combination of Laser Microdissection and RNA Sequencing

    Article • Plant and Cell Physiology, September 2013, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  39. The More the Merrier: Recent Hybridization and Polyploidy in Cardamine

    Article • The Plant Cell, September 2013, American Society of Plant Biologists (ASPB)

    Professor Kentaro K. Shimizu, Professor Karol Marhold

  40. Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility

    Article • Journal of Evolutionary Biology, August 2013, Wiley

    Professor Kentaro K. Shimizu

  41. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

    Article • Nature Genetics, July 2013, Nature

    Professor Kentaro K. Shimizu

  42. Selection Is No More Efficient in Haploid than in Diploid Life Stages of an Angiosperm and a Moss

    Article • Molecular Biology and Evolution, May 2013, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  43. Mass flowering of the tropical tree S horea beccariana was preceded by expression changes in flowering and drought‐responsive genes

    Article • Molecular Ecology, May 2013, Wiley

    Professor Kentaro K. Shimizu

  44. Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus

    Article • Scientific Reports, March 2013, Nature

    Professor Kentaro K. Shimizu

  45. Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica

    Article • PLoS Genetics, July 2012, PLOS

    Professor Kentaro K. Shimizu

  46. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

    Article • Mobile DNA, January 2012, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  47. In Situ Enzyme Activity in the Dissolved and Particulate Fraction of the Fluid from Four Pitcher Plant Species of the Genus Nepenthes

    Article • PLoS ONE, September 2011, PLOS

    Professor Kentaro K. Shimizu

  48. Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation

    Article • Gene, September 2011, Elsevier

    Professor Kentaro K. Shimizu

  49. Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

    Article • Annals of Botany, August 2011, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  50. Coexistence of Trichome Variation in a Natural Plant Population: A Combined Study Using Ecological and Candidate Gene Approaches

    Article • PLoS ONE, July 2011, PLOS

    Professor Kentaro K. Shimizu

  51. Challenges in studies on flowering time: interfaces between phenological research and the molecular network of flowering genes

    Article • Ecological Research, May 2011, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  52. Using knockout mutants to reveal the growth costs of defensive traits

    Article • Proceedings of the Royal Society B Biological Sciences, January 2011, Royal Society Publishing

    Professor Kentaro K. Shimizu

  53. Potential Application of Pollen Genotyping for Evolutionary Genetic and Genomic Studies: Linkage/Recombination Analysis and Haplotype Sequencing

    Article • January 2011, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  54. Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment

    Article • Proceedings of the National Academy of Sciences, June 2010, Proceedings of the National Academy of Sciences

    Professor Kentaro K. Shimizu

  55. Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

    Article • Nature, April 2010, Nature

    Professor Kentaro K. Shimizu

  56. Diversity at the Mla Powdery Mildew Resistance Locus from Cultivated Barley Reveals Sites of Positive Selection

    Article • Molecular Plant-Microbe Interactions, April 2010, Scientific Societies

    Professor Kentaro K. Shimizu

  57. The allopolyploidArabidopsis kamchaticaoriginated from multiple individuals ofArabidopsis lyrataandArabidopsis halleri

    Article • Molecular Ecology, October 2009, Wiley

    Professor Karol Marhold, Professor Kentaro K. Shimizu

  58. MAA3 (MAGATAMA3) Helicase Gene is Required for Female Gametophyte Development and Pollen Tube Guidance in Arabidopsis thaliana

    Article • Plant and Cell Physiology, October 2008, Oxford University Press (OUP)

    Professor Kentaro K. Shimizu

  59. Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis

    Article • PLoS Genetics, April 2008, PLOS

    Professor Kentaro K. Shimizu

  60. Independent origins of self-compatibility in Arabidopsis thaliana

    Article • Molecular Ecology, December 2007, Wiley

    Professor Kentaro K. Shimizu

  61. Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene

    Article • Molecular Phylogenetics and Evolution, June 2006, Elsevier

    Professor Karol Marhold, Professor Kentaro K. Shimizu

  62. Evolutionary and Ecological Genomics of Arabidopsis

    Article • PLANT PHYSIOLOGY, May 2005, American Society of Plant Biologists (ASPB)

    Professor Kentaro K. Shimizu

  63. Ecology meets molecular genetics in Arabidopsis

    Article • Population Ecology, December 2002, Springer Science + Business Media

    Professor Kentaro K. Shimizu

  64. Multiple factors contribute to outcrossing in a tropical emergent Dipterocarpus tempehes, including a new pollen-tube guidance mechanism for self-incompatibility

    Article • American Journal of Botany, January 2002, Botanical Society of America

    Professor Kentaro K. Shimizu

  65. Faculty of 1000 evaluation for Male-female communication triggers calcium signatures during fertilization in Arabidopsis.

    Article • Faculty of 1000, Ltd.

    Professor Kentaro K. Shimizu

  66. Faculty of 1000 evaluation for Live imaging of calcium spikes during double fertilization in Arabidopsis.

    Article • Faculty of 1000, Ltd.

    Professor Kentaro K. Shimizu

  67. Faculty of 1000 evaluation for Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis.

    Article • Faculty of 1000, Ltd.

    Professor Kentaro K. Shimizu