Koh Aoki

Summary

Affiliation: Kazusa DNA Research Institute
Country: Japan

Publications

  1. pmc Destination-selective long-distance movement of phloem proteins
    Koh Aoki
    Plant Science Center, RIKEN, Institute of Physical and Chemical Research, Tsurumi, Yokohama 230 0045, Japan
    Plant Cell 17:1801-14. 2005
  2. ncbi request reprint [Long distance movement of protein and RNA: regulation of phloem traffic]
    Koh Aoki
    Tanpakushitsu Kakusan Koso 51:237-48. 2006
  3. pmc Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
    Koh Aoki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Japan
    BMC Genomics 11:210. 2010
  4. pmc Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
    Soichi Ozaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu 292 0818, Japan
    DNA Res 17:105-16. 2010
  5. doi request reprint An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values
    Nozomu Sakurai
    Department of Biotechnology Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    Bioinformatics 29:290-1. 2013
  6. pmc KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes
    Yoshiyuki Ogata
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Plant Cell Physiol 50:173-7. 2009
  7. ncbi request reprint Cryopreservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells
    Yoichi Ogawa
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Cryo Letters 29:427-36. 2008
  8. doi request reprint Efficient and high-throughput vector construction and Agrobacterium-mediated transformation of Arabidopsis thaliana suspension-cultured cells for functional genomics
    Yoichi Ogawa
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Plant Cell Physiol 49:242-50. 2008
  9. pmc High-throughput cryopreservation of plant cell cultures for functional genomics
    Yoichi Ogawa
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Plant Cell Physiol 53:943-52. 2012
  10. pmc Metabolite annotations based on the integration of mass spectral information
    Yoko Iijima
    Kazusa DNA Research Institute, Kazusa Kamatari 2 6 7, Kisarazu 292 0818, Japan
    Plant J 54:949-62. 2008

Collaborators

Detail Information

Publications22

  1. pmc Destination-selective long-distance movement of phloem proteins
    Koh Aoki
    Plant Science Center, RIKEN, Institute of Physical and Chemical Research, Tsurumi, Yokohama 230 0045, Japan
    Plant Cell 17:1801-14. 2005
    ....
  2. ncbi request reprint [Long distance movement of protein and RNA: regulation of phloem traffic]
    Koh Aoki
    Tanpakushitsu Kakusan Koso 51:237-48. 2006
  3. pmc Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
    Koh Aoki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Japan
    BMC Genomics 11:210. 2010
    ....
  4. pmc Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
    Soichi Ozaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu 292 0818, Japan
    DNA Res 17:105-16. 2010
    ..This result demonstrates that coexpression modules, at least the ones identified in this study, represent actual transcriptional coordination between genes, and can facilitate the inference of tomato gene function...
  5. doi request reprint An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values
    Nozomu Sakurai
    Department of Biotechnology Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    Bioinformatics 29:290-1. 2013
    ..Availability and implementation: Available for free at http://webs2.kazusa.or.jp/mfsearcher. The web service is implemented in Java, MySQL, Apache and Tomcat, with all major browsers supported...
  6. pmc KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes
    Yoshiyuki Ogata
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Plant Cell Physiol 50:173-7. 2009
    ..It can assist plant biologists in accessing omics information for plant biology. The KAGIANA tool is freely available at http://pmnedo.kazusa.or.jp/kagiana/...
  7. ncbi request reprint Cryopreservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells
    Yoichi Ogawa
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Cryo Letters 29:427-36. 2008
    ..These results indicate that cryopreservation of T87 cells is useful for comprehensive metabolomics research and for the large scale collection of transformed cultured cell lines for functional genomics research...
  8. doi request reprint Efficient and high-throughput vector construction and Agrobacterium-mediated transformation of Arabidopsis thaliana suspension-cultured cells for functional genomics
    Yoichi Ogawa
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Plant Cell Physiol 49:242-50. 2008
    ....
  9. pmc High-throughput cryopreservation of plant cell cultures for functional genomics
    Yoichi Ogawa
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Plant Cell Physiol 53:943-52. 2012
    ..The simplicity of the protocol will accelerate the pace of research in functional plant genomics...
  10. pmc Metabolite annotations based on the integration of mass spectral information
    Yoko Iijima
    Kazusa DNA Research Institute, Kazusa Kamatari 2 6 7, Kisarazu 292 0818, Japan
    Plant J 54:949-62. 2008
    ....
  11. ncbi request reprint Molecular characterization of His-Asp phosphorelay signaling factors in maize leaves: implications of the signal divergence by cytokinin-inducible response regulators in the cytosol and the nuclei
    Yasuharu Asakura
    Plant Science Center, RIKEN Institute of Physical and Chemical Research, 1 7 22, Suehiro, Tsurumi, Yokohama 230 0045, Japan
    Plant Mol Biol 52:331-41. 2003
    ....
  12. ncbi request reprint The prediction of local modular structures in a co-expression network based on gene expression datasets
    Yoshiyuki Ogata
    Department of Biotechnology Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari Kisarazu, Chiba 292 0818, Japan
    Genome Inform 23:117-27. 2009
    ..It is also applicable to a large dataset of gene expression profiles, which is difficult to calculate in a mass...
  13. ncbi request reprint AtIPT3 is a key determinant of nitrate-dependent cytokinin biosynthesis in Arabidopsis
    Kentaro Takei
    Plant Science Center, RIKEN Institute of Physical and Chemical Research, Suehiro 1 7 22, Tsurumi, Yokohama, 230 0045 Japan
    Plant Cell Physiol 45:1053-62. 2004
    ..These results suggest that nitrogen availability differentially regulates expression of AtIPT3 and AtIPT5, and that AtIPT3 is a key determinant of cytokinin biosynthesis in response to rapid changes in the availability of NO(3)(-)...
  14. ncbi request reprint Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry
    Hideyuki Suzuki
    Kazusa DNA Research Institute, Kazusa Kamatari 2 6 7, Kisarazu 292 0818, Japan
    Phytochemistry 69:99-111. 2008
    ..Developmental changes in the flavonoid profiles demonstrated that kaempferol glycosides increased promptly after germination. In contrast, quercetin glycosides, predominant flavonoids in the seeds, were not detectable in growing leaves...
  15. ncbi request reprint Approaches for extracting practical information from gene co-expression networks in plant biology
    Koh Aoki
    Kazusa DNA Research Institute, Kazusa Kamatari 2 6 7, Kisarazu, 292 0818, Japan
    Plant Cell Physiol 48:381-90. 2007
    ..Co-expression network analysis is a powerful approach for data-driven hypothesis construction and gene prioritization, and provides novel insights into the system-level understanding of plant cellular processes...
  16. pmc KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
    Nozomu Sakurai
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Nucleic Acids Res 39:D677-84. 2011
    ..kazusa.or.jp/kpv4-kegg/). At present, gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available...
  17. pmc Genome-wide SNP genotyping to infer the effects on gene functions in tomato
    Hideki Hirakawa
    1 Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 20:221-33. 2013
    ..The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database (http://plant1.kazusa.or.jp/tomato/)...
  18. doi request reprint Involvement of ethylene in the accumulation of esculeoside A during fruit ripening of tomato (Solanum lycopersicum)
    Yoko Iijima
    Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    J Agric Food Chem 57:3247-52. 2009
    ....
  19. pmc Functional genomics of tomato in a post-genome-sequencing phase
    Koh Aoki
    Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1 1 Gakuen, Naka, Sakai, Osaka 599 8531, Japan Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Breed Sci 63:14-20. 2013
    ..Finally, we describe the current status of efforts to resequence S. lycopersicum cultivars to demonstrate how resequencing can allow the use of intraspecific genomic diversity for detailed phenotyping and breeding...
  20. pmc In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut
    Kenta Shirasawa
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    BMC Plant Biol 12:80. 2012
    ..Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers...
  21. pmc A subclass of plant heat shock cognate 70 chaperones carries a motif that facilitates trafficking through plasmodesmata
    Koh Aoki
    Section of Plant Biology, Division of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 99:16342-7. 2002
    ..These results are discussed in terms of the roles likely played by this subclass of Hsc70 chaperones in the trafficking of non-cell-autonomous proteins...
  22. ncbi request reprint Identification and characterization of a gene encoding drought-inducible protein localizing in the bundle sheath cell of sugarcane
    Bambang Sugiharto
    Research Center for Molecular Biology, University of Jember, Jl Kalimantan III 23, Jember, 68121, Indonesia
    Plant Cell Physiol 43:350-4. 2002
    ..These results suggest that SoDip22 functions to adapt to drought stress in the bundle sheath cell, and that the signaling pathway for the induction is, at least in a part, mediated by ABA...