2009

1. DAGViz: a directed acyclic graph browser that supports analysis of Gene Ontology annotation.
   Yano K, Aoki K, Suzuki H, Shibata D. (2009)
   Plant Biotechnol. 26(1): 9-13.


2. Practical network approaches and biologic interpretations of co-expression analyses in plants.
   Ogata Y, Shibata D. (2009)
   Plant Biotechnol. 26(1): 3-7.


3. The prediction of local modular structures in a co-expression network based on gene expression datasets.
   Ogata Y, Sakurai N, Suzuki H, Aoki K, Saito K, Shibata D. (2009)
   Genome Inform. 23(1): 117-27.


4. A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses.
   Ogata Y, Suzuki H, Shibata D. (2009)
   Journal of Wood Science. 55(6): 395-400.


5. A gene co-expression database for understanding biological processes in soybean.
   Ogata Y, Suzuki H, Shibata D. (2009)
   Plant Biotechnol. 26(5): 503-7.


6. Improvement of the quantitative differential metabolome pipeline for gas chromatography-mass spectrometry data by automated reliable peak selection.
   Ara T, Sakurai N, TangeY, Morishita Y, Suzuki H, Aoki K, Saito K, Shibata D. (2009)
   Plant Biotechnol. 26(5): 445-9.


7. Application of metabolomics to improve tomato fruit productivity and quality.
   Iijima Y, Aoki K. (2009)
   J. Japan. Soc. Hort. Sci. 78(1): 14-22.


8. Involvement of ethylene in the accumulation of esculeoside A during fruit ripening of tomato (Solanum lycopersicum).
   Iijima Y, Fujiwara Y, Tokita T, Ikeda T, Nohara T, Aoki K, Shibata D. (2009)
   J. Agric. Food Chem. 57(8): 3247-52.


9. Pathway engineering of Brassica napus seeds using multiple key enzyme genes involved in ketocarotenoid formation.
   Fujisawa M, Takita E, Harada H, Sakurai N, Suzuki H, Ohyama K, Shibata D, Misawa N. (2009)
   J. Exp. Bot. 60(4): 1319-32.


10. Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A.
    Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, Fujita M, Yoshiwara K, Matsukura S, Morishita Y, Sasaki R, Suzuki H, Saito K, Shibata D, Shinozaki K, Yamaguchi-Shinozaki K. (2009)
    Plant Physiol. 150(4): 1972-80.


11. Functional genomics of the Dof transcription factor family genes in suspension-cultured cells of Arabidopsis thaliana.
    Tsujimoto Inui Y, Naito Y, Sakurai N, Suzuki H, Sasaki R, Takahashi H, Ohtsuki N, Nakano T, Yanagisawa S, Shibata D, Uchimiya H, Shinshi H, Suzuki K. (2009)
    Plant Biotechnol. 26(1): 15-28.


12. Simple functional analysis of key genes involved in astaxanthin biosynthesis using Arabidopsis cultured cells.
    Harada H, Fujisawa M, Teramoto M, Sakurai N, Suzuki H, Shibata D, Misawa N. (2009)
    Plant Biotechnol. 26(1): 81-92.


13. Expressed sequence tags from rhizomes of Glycyrrhiza uralensis.
    Sudo H, Seki H, Sakurai N, Suzuki H, Shibata D, Toyoda A, Totoki Y, Sakaki Y, Iida O, Shibata T, Kojoma M, Muranaka T, Saito K. (2009)
    Plant Biotechnol. 26(1): 105-7.


14. Establishment of the Evaluation System of Salt Tolerance on Transgenic Woody Plants in the Special Netted-house.
    Yu X, Kikuchi A, Matsunaga E, Morishita Y, Nanto K, Sakurai N, Suzuki H, Shibata D, Shimada T, Watanabe KN. (2009)
    Plant Biotechnol. 26(1): 135-41.


15. ARTRA: a new database of the Arabidopsis transcriptome and gene-specific sequences for microarray probes and RNAi triggers.
    Ohba T, Suzuki K, Oura T, Ando T, Noda H, Sakurai N, Suzuki H, Shibata D, Asada K, Kato I. (2009)
    Plant Biotechnol. 26(1): 161-5.


16. An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites.
    Oishi T, Tanaka K, Hashimoto T, Shinbo Y, Jumtee K, Bamba T, Fukusaki E, Suzuki H, Shibata D, Takahashi H, Asahi H, Kurokawa K, Nakamura Y, Hirai A, Nakamura K, Altaf-Ul-Amin Md, Kanaya S. (2009)
    Plant Biotechnol. 26(1): 167-74.


17. Metabolomics for the characterization of cytochromes P450-dependent fatty acid hydroxylation reactions in Arabidopsis.
    Kai K, Hashidzume H, Yoshimura Y, Suzuki H, Sakurai N, Shibata D, Ohta D. (2009)
    Plant Biotechnol. 26(1): 175-82.


18. Over-expression of Arabidopsis FT gene reduces juvenile phase and induces early flowering in ornamental gentian plants.
    Nakatsuka T, Abe Y, Kakizaki Y, Kubota A, Shimada N, Nishihara M. (2009)
    Euphytica. 168(1): 113-9.


19. Identification of gentian cultivars using SCAR markers based on intron-length polymorphisms of flavonoid biosynthetic genes.
    Shimada N, Nakatsuka T, Nakano Y, Kakizaki Y, Abe Y, Hikage T, Nishihara M. (2009)
    Scientia Horticulturae. 119(3): 292-6.


20. Jasmonic acid control of GLABRA3 links inducible defense and trichome patterning in Arabidopsis.
    Yoshida Y, Sano R, Wada T, Takabayashi J, Okada K. (2009)
    Development. 136(6): 1039-48.


21. Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in Arabidopsis thaliana.
    Zhao CR, Ikka T, Sawaki Y, Kobayashi Y, Suzuki Y, Hibino T, Sato S, Sakurai N, Shibata D, Koyama H. (2009)
    BMC Plant Biol. 9: 32.


22. STOP1 regulates multiple genes that protect arabidopsis from proton and aluminum toxicities.
    Sawaki Y, Iuchi S, Kobayashi Y, Ikka T, Sakurai N, Fujita M, Shinozaki K, Shibata D, Kobayashi M, Koyama H. (2009)
    Plant Physiol. 150(1): 281-94.


23. Aliphatic aldehyde reductase activity related to the formation of volatile alcohols in Vietnamese coriander leaves.
    Quynh CT, Iijima Y, Morimitsu Y, Kubota K. (2009)
    Biosci Biotechnol Biochem. 73(3): 641-7.


24. KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes.
    Ogata Y, Sakurai N, Aoki K, Suzuki H, Okazaki K, Saito K, Shibata D. (2009)
    Plant Cell Physiol. 50(1): 173-7


25. Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics.
    Urano K, Maruyama K, Ogata Y, Morishita Y, Takeda M, Sakurai N, Suzuki H, Saito K, Shibata D, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K. (2009)
    Plant J. 57(6): 1065-78