Keiichi Mochida

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. ncbi Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags
    Yasunari Ogihara
    Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Maioka cho 641 12, Yokohama 244 0813, Japan
    Plant J 33:1001-11. 2003
  2. ncbi SSR-based linkage map with new markers using an intraspecific population of common wheat
    Atsushi Torada
    Hokkaido Green Bio Institute, Higashi 5 Kita 15, 069 1317 Naganuma, Hokkaido, Japan
    Theor Appl Genet 112:1042-51. 2006
  3. ncbi Genome-wide analysis for identification of salt-responsive genes in common wheat
    Kanako Kawaura
    Kihara Institute for Biological Research, Yokohama City University, Maioka cho 641 12, Totsuka ku, Yokohama, Japan
    Funct Integr Genomics 8:277-86. 2008
  4. pmc Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean
    Lam Son Phan Tran
    RIKEN Plant Science Center, Signaling Pathway Research Unit, Tsurumi, Yokohama, Japan
    Plant Signal Behav 5:255-7. 2010
  5. pmc Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 17:303-24. 2010
  6. pmc TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 20:151-62. 2013
  7. pmc Advances in omics and bioinformatics tools for systems analyses of plant functions
    Keiichi Mochida
    RIKEN Biomass Engineering Program, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 52:2017-38. 2011
  8. pmc Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila
    Teruaki Taji
    Faculty of Applied Bioscience, Tokyo University of Agriculture, 1 1 1 Sakuragaoka, Setagaya Ku, Tokyo 156 8502, Japan
    BMC Plant Biol 8:115. 2008
  9. pmc Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns
    Kanako Kawaura
    Kihara Institute for Biological Research, Yokohama City University, Maioka cho 641 12, Yokohama 244 0813, Japan
    BMC Genomics 10:271. 2009
  10. pmc Correlation exploration of metabolic and genomic diversity in rice
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22, Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    BMC Genomics 10:568. 2009

Collaborators

Detail Information

Publications36

  1. ncbi Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags
    Yasunari Ogihara
    Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Maioka cho 641 12, Yokohama 244 0813, Japan
    Plant J 33:1001-11. 2003
    ..This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants...
  2. ncbi SSR-based linkage map with new markers using an intraspecific population of common wheat
    Atsushi Torada
    Hokkaido Green Bio Institute, Higashi 5 Kita 15, 069 1317 Naganuma, Hokkaido, Japan
    Theor Appl Genet 112:1042-51. 2006
    ..Moreover, the new SSR markers will contribute to the enrichment of molecular marker resources in common wheat...
  3. ncbi Genome-wide analysis for identification of salt-responsive genes in common wheat
    Kanako Kawaura
    Kihara Institute for Biological Research, Yokohama City University, Maioka cho 641 12, Totsuka ku, Yokohama, Japan
    Funct Integr Genomics 8:277-86. 2008
    ..Among them, only a few TFs show high sequence homologies to genes in rice. These investigations suggest that salt-responsive genes identified by this study are candidates for salt-stress tolerance uniquely in wheat...
  4. pmc Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean
    Lam Son Phan Tran
    RIKEN Plant Science Center, Signaling Pathway Research Unit, Tsurumi, Yokohama, Japan
    Plant Signal Behav 5:255-7. 2010
    ....
  5. pmc Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 17:303-24. 2010
    ..In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms...
  6. pmc TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 20:151-62. 2013
    ....
  7. pmc Advances in omics and bioinformatics tools for systems analyses of plant functions
    Keiichi Mochida
    RIKEN Biomass Engineering Program, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 52:2017-38. 2011
    ..From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances...
  8. pmc Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila
    Teruaki Taji
    Faculty of Applied Bioscience, Tokyo University of Agriculture, 1 1 1 Sakuragaoka, Setagaya Ku, Tokyo 156 8502, Japan
    BMC Plant Biol 8:115. 2008
    ..Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance...
  9. pmc Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns
    Kanako Kawaura
    Kihara Institute for Biological Research, Yokohama City University, Maioka cho 641 12, Yokohama 244 0813, Japan
    BMC Genomics 10:271. 2009
    ..This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals...
  10. pmc Correlation exploration of metabolic and genomic diversity in rice
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22, Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    BMC Genomics 10:568. 2009
    ..To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions...
  11. pmc Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops
    Keiichi Mochida
    RIKEN Biomass Engineering Program, Yokohama 230 0045, Japan
    Plant Cell Physiol 52:785-803. 2011
    ..Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/...
  12. doi LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors
    Keiichi Mochida
    Plant Science Center, Gene Discovery Research Group, RIKEN, Yokohama 230 0045 Japan
    Bioinformatics 26:290-1. 2010
    ..LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in agriculturally important legumes...
  13. pmc In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 16:353-69. 2009
    ..This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean...
  14. ncbi A case of fatal emphysematous pyelonephritis presenting as lower limb gaseous gangrene
    B Balicco
    Department of Anesthesia and Intensive Care, San Marco Polyclinic, Zingonia, Bergamo, Italy
    Minerva Anestesiol 75:665-8. 2009
    ..Intensivists should reasonably suspect it whenever diabetic patients develop septic conditions and signs of gas collection in the abdomen, pelvis, retroperitoneal space or even in the lower limbs...
  15. pmc In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 18:321-32. 2011
    ....
  16. pmc TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
    Keiichi Mochida
    Plant Science Center, RIKEN, Yokohama 230 0045, Japan
    BMC Plant Biol 8:72. 2008
    ....
  17. pmc Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress
    Dung Tien Le
    Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi, Japan
    DNA Res 18:263-76. 2011
    ..Our systematic analysis has identified excellent tissue-specific and/or dehydration-responsive candidate GmNAC genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans...
  18. pmc TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics
    Keiichi Mochida
    Plant Science Center, RIKEN, Yokohama 230 0045, Japan
    Plant Physiol 150:1135-46. 2009
    ..This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/...
  19. pmc Genome-wide discovery and information resource development of DNA polymorphisms in cassava
    Tetsuya Sakurai
    RIKEN Center for Sustainable Resource Science, Tsurumi ku, Yokohama, Kanagawa, Japan
    PLoS ONE 8:e74056. 2013
    ..All data on the discovered DNA polymorphisms were organized into the Cassava Online Archive database, which is available at http://cassava.psc.riken.jp/. ..
  20. pmc Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library
    Taishi Umezawa
    Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3 1 1, Tsukuba, Ibaraki 305 0074, Japan
    DNA Res 15:333-46. 2008
    ..A large set of soybean full-length cDNA clones reported in this study will serve as a useful resource for gene discovery from soybean and will also aid a precise annotation of the soybean genome...
  21. pmc The auxin response factor transcription factor family in soybean: genome-wide identification and expression analyses during development and water stress
    Chien Van Ha
    1Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 20:511-24. 2013
    ....
  22. pmc Genomics and bioinformatics resources for crop improvement
    Keiichi Mochida
    RIKEN Plant Science Center, Yokohama, 230 0045 Japan
    Plant Cell Physiol 51:497-523. 2010
    ..We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology...
  23. pmc Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop
    Yoshinori Utsumi
    Plant Genomic Network Research Team, RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa, Japan
    DNA Res 19:335-45. 2012
    ..These results demonstrate that our microarray is a useful tool for analysing the cassava transcriptome and that it is applicable for various cassava genotypes...
  24. pmc Genome-wide expression profiling of soybean two-component system genes in soybean root and shoot tissues under dehydration stress
    Dung Tien Le
    Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama, Japan
    DNA Res 18:17-29. 2011
    ....
  25. pmc Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources
    Keiichi Mochida
    Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi ku, Yokohama, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Totsuka ku, Yokohama, Kanagawa, Japan
    PLoS ONE 8:e75265. 2013
    ..The database represents a "one-stop" information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops. ..
  26. doi Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals
    Jordan A Ramilowski
    RIKEN Center for Life Science Technologies Division of Genomic Technologies, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 54:697-710. 2013
    ....
  27. doi Functional genomics of soybean for improvement of productivity in adverse conditions
    Lam Son Phan Tran
    RIKEN Plant Science Center, Tsurumi, Yokohama 230 0045, Japan
    Funct Integr Genomics 10:447-62. 2010
    ..Soybean functional genomics, therefore, will ultimately enable us to develop new soybean varieties with improved productivity under adverse conditions by genetic engineering...
  28. pmc Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants
    Hirofumi Nakagami
    RIKEN Plant Science Center, Tsurumi ku, Yokohama 230 0045, Japan
    Plant Physiol 153:1161-74. 2010
    ..We also assessed the phosphorylation sites on nucleotide-binding leucine-rich repeat proteins and identified novel conserved phosphorylation sites that may regulate this class of proteins...
  29. pmc A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis
    Yozo Okazaki
    RIKEN Plant Science Center, Tsurumi ku, Yokohama 230 0045, Japan
    Plant Cell 21:892-909. 2009
    ..A comparative genomics study on UGP3 homologs across different plant species suggested the structural and functional conservation of the proteins and, thus, a committing role for UGP3 in sulfolipid synthesis...
  30. ncbi A platform for functional prediction and comparative analyses of transcription factors of legumes and beyond
    Lam Son Phan Tran
    RIKEN Plant Science Center, Signaling Pathway Research Unit, 1 7 22, Suehiro cho, Tsurumi, Yokohama Japan
    Plant Signal Behav 5:550-2. 2010
    ..LegumeTFDB provides an important user-friendly public resource for comparative genomics and understanding of transcriptional regulation in three important legumes and beyond. ..
  31. pmc Unlocking Triticeae genomics to sustainably feed the future
    Keiichi Mochida
    Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 54:1931-50. 2013
    ..In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae...
  32. ncbi Confocal analysis of chromosome behavior in wheat x maize zygotes
    Keiichi Mochida
    Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Yokohama, Japan
    Genome 47:199-205. 2004
    ..These results suggest that factors on the kinetochores of maize chromosomes that are required to control chromosome movement are deficient in the zygotic cell cycle...
  33. ncbi Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat
    Keiichi Mochida
    Nagahama Institute of Bio Science and Technology, Shiga, 526 0829, Japan
    Mol Genet Genomics 276:304-12. 2006
    ..Then, the method was applied to screen genes in response to abiotic stresses such as drought and ABA treatments. In silico selection of screened genes from virtual display should provide a powerful tool for functional plant genomics...
  34. ncbi Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags
    Yasunari Ogihara
    Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Maioka cho 641 12, Totsuka ku, Yokohama 244 0813, Japan
    Genes Genet Syst 79:227-32. 2004
    ..Forty-three genes (3.5% of wheat cDNAs homologous to those of rice) possessed distinct GC-content in the 5 -UTR region, suggesting different breeding behaviors of wheat and rice...
  35. pmc Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat
    Naoki Shitsukawa
    Department of Bioscience, Fukui Prefectural University, Fukui, Japan
    Plant Cell 19:1723-37. 2007
    ..Consequently, of the three WLHS1 homoeologs, only WLHS1-D functions in hexaploid wheat. This is a situation where three homoeologs are differentially regulated by genetic and epigenetic mechanisms...
  36. pmc Expression profile of two storage-protein gene families in hexaploid wheat revealed by large-scale analysis of expressed sequence tags
    Kanako Kawaura
    Laboratory of Genetic Engineering, Kyoto Prefectural University and Kyoto Prefectural Institute of Agricultural Biotechnology, Shimogamo, Kyoto 606 8522, Japan
    Plant Physiol 139:1870-80. 2005
    ..These lines of evidence suggest that expression of the two storage-protein genes is independently regulated, and that the alpha/beta-gliadin genes possess novel regulation systems in addition to the prolamin box...