Publications

Peer-reviewed papers

  • Akiyama K, Kurotani A, Iida K, Kuromori T, Shinozaki K, Sakurai T. RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. Plant Cell Physiol. 2014 Jan;55(1):e4. [PubMed]
  • Sakurai T, Mochida K, Yoshida T, Akiyama K, Ishitani M, Seki M, Shinozaki K. Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PLoS One. 2013 Sep 11;8(9):e74056. [PubMed]
  • Sakurai T, Yamada Y, Sawada Y, Matsuda F, Akiyama K, Shinozaki K, Hirai MY, Saito K. PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant Cell Physiol. 2013 Feb;54(2):e5. [PubMed]
  • Myouga F, Akiyama K, Tomonaga Y, Kato A, Sato Y, Kobayashi M, Nagata N, Sakurai T, Shinozaki K. The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins. Plant Cell Physiol. 2013 Feb;54(2):e2. [PubMed]
  • Sakurai T, Kondou Y, Akiyama K, Kurotani A, Higuchi M, Ichikawa T, Kuroda H, Kusano M, Mori M, Saitou T, Sakakibara H, Sugano S, Suzuki M, Takahashi H, Takahashi S, Takatsuji H, Yokotani N, Yoshizumi T, Saito K, Shinozaki K, Oda K, Hirochika H, Matsui M. RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol. 2011F eb;52(2):265-73. [PubMed]
  • Hirai MY, Sawada Y, Kanaya S, Kuromori T, Kobayashi M, Klausnitzer R, Hanada K, Akiyama K, Sakurai T, Saito K, Shinozaki K. Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources. J Plant Res. 2010 May;123(3):291-8. [PubMed]
  • Chikayama E, Sekiyama Y, Okamoto M, Nakanishi Y, Tsuboi Y, Akiyama K, Saito K, Shinozaki K, Kikuchi J. Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum. Anal Chem. 2010 Mar 1;82(5):1653-8. [PubMed]
  • Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH. sORF finder: a program package to identify small open reading frames with high coding potential. Bioinformatics. 2010 Feb 1;26(3):399-400. [PubMed]
  • Myouga F, Akiyama K, Motohashi R, Kuromori T, Ito T, Iizumi H, Ryusui R, Sakurai T, Shinozaki K. The Chloroplast Function Database: a large-scale collection of Arabidopsis Ds/Spm- or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis. Plant J. 2010 Feb 1;61(3):529-42. [PubMed]
  • Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K. PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol. 2008;8(3-4):339-45. [PubMed]
  • Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K. Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNAl ibrary. DNA Res. 2008 Dec;15(6):333-46. [PubMed]
  • Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J. 2008 Aug;55(3):526-42. [PubMed]
  • Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, Imura Y, Takabe H, Sakurai T, Akiyama K, Hirayama T, Okada K, Shinozaki K. A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J. 2006 Aug;47(4):640-51. [PubMed]
  • Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K. RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Res. 2005;12(4):247-56. [PubMed]
  • Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A, Toyoda T. A flexible representation of omic knowledge for thorough analysis ofmicroarray data. Plant Methods. 2006 Mar 2;2:5. [PubMed]
  • Oono Y, Seki M, Satou M, Iida K, Akiyama K, Sakurai T, Fujita M, Yamaguchi-Shinozaki K, Shinozaki K. Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays. Funct Integr Genomics. 2006 Jul;6(3):212-34. [PubMed]
  • Sakurai T, Satou M, Akiyama K, Iida K, Seki M, Kuromori T, Ito T, Konagaya A, Toyoda T, Shinozaki K. RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D647-50. [PubMed]
  • Takahashi S, Seki M, Ishida J, Satou M, Sakurai T, Narusaka M, Kamiya A, Nakajima M, Enju A, Akiyama K, Yamaguchi-Shinozaki K, Shinozaki K. Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray. Plant Mol Biol. 2004 Sep;56(1):29-55. PubMed
  • Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K. Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res. 2004 Sep 27;32(17):5096-103. [PubMed]
  • Kuromori T, Hirayama T, Kiyosue Y, Takabe H, Mizukado S, Sakurai T, Akiyama K, Kamiya A, Ito T, Shinozaki K. A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis. Plant J. 2004 Mar;37(6):897-905. [PubMed]
  • Seki M, Satou M, Sakurai T, Akiyama K, Iida K, Ishida J, Nakajima M, Enju A, Narusaka M, Fujita M, Oono Y, Kamei A, Yamaguchi-Shinozaki K, Shinozaki K. RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions. J Exp Bot. 2004 Jan;55(395):213-23. [PubMed]
  • Yamaguchi Y, Yoda H, Akiyama K, Sano H. Induction of transcripts encoding a novel seven-transmembrane protein during the hypersensitive response to tobacco mosaic virus infection in tobacco plants. Planta. 2003 Dec;218(2):249-53. [PubMed]
  • Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003 Oct 31;302(5646):842-6. [PubMed]
  • Oono Y, Seki M, Nanjo T, Narusaka M, Fujita M, Satoh R, Satou M, Sakurai T, Ishida J, Akiyama K, Iida K, Maruyama K, Satoh S, Yamaguchi-Shinozaki K, Shinozaki K. Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca 7000 full-length cDNA microarray. Plant J. 2003 Jun;34(6):868-87. [PubMed]
  • Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K. Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics. 2002 Nov;2(6):282-91. [PubMed]
  • Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J. 2002 Aug;31(3):279-92. [PubMed]
  • Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K. Functional annotation of a full-length Arabidopsis cDNA collection. Science. 2002 Apr 5;296(5565):141-5. [PubMed]

Reviews (in Japanese)

  • Seki M, Shinozaki K, Ishida J, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Iida K, Oono Y. [Arabidopsis functional genomics using full-length cDNAs]. Tanpakushitsu Kakusan Koso. 2003 Nov;48(14):1890-8. [PubMed]
  • Sakurai T, Satou M, Akiyama K, Seki M, Shinozaki K. [Bioinformatics].T anpakushitsu Kakusan Koso. 2002 Sep;47(12 Suppl):1500-5. [PubMed]

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