Atsushi Fukushima

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. doi request reprint DiffCorr: an R package to analyze and visualize differential correlations in biological networks
    Atsushi Fukushima
    RIKEN Plant Science Center, Kanagawa 230 0045, Japan
    Gene 518:209-14. 2013
  2. pmc Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches
    Atsushi Fukushima
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant Physiol 158:1487-502. 2012
  3. doi request reprint Comparative metabolomics charts the impact of genotype-dependent methionine accumulation in Arabidopsis thaliana
    Miyako Kusano
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Amino Acids 39:1013-21. 2010
  4. pmc Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana
    Miyako Kusano
    RIKEN Plant Science Center, 1 7 22, Yokohama, Kanagawa 230 0045, Japan
    BMC Syst Biol 1:53. 2007
  5. doi request reprint Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light
    Miyako Kusano
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Plant J 67:354-69. 2011
  6. pmc Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination
    Atsushi Fukushima
    RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Proc Natl Acad Sci U S A 106:7251-6. 2009
  7. pmc Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
    Atsushi Fukushima
    RIKEN Plant Science Center, Kanagawa 230 0045, Japan
    BMC Syst Biol 5:1. 2011
  8. doi request reprint Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis
    Miyako Kusano
    RIKEN Plant Science Center, Tsurumi, Yokohama 230 0045, Japan
    Mol Plant 5:442-51. 2012
  9. doi request reprint Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism
    Doris Albinsky
    RIKEN Plant Science Center, Tsurumi ku, Yokohama, Japan
    Mol Plant 3:125-42. 2010
  10. pmc SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana
    Atsushi Fukushima
    RIKEN Plant Science Center, 1 7 22 Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 15:367-74. 2008

Detail Information

Publications19

  1. doi request reprint DiffCorr: an R package to analyze and visualize differential correlations in biological networks
    Atsushi Fukushima
    RIKEN Plant Science Center, Kanagawa 230 0045, Japan
    Gene 518:209-14. 2013
    ..The package can be downloaded from the following website: http://diffcorr.sourceforge.net/...
  2. pmc Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches
    Atsushi Fukushima
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant Physiol 158:1487-502. 2012
    ..The approaches and results reported here will be useful to prioritize candidate genes for further functional genomics studies of tomato metabolism...
  3. doi request reprint Comparative metabolomics charts the impact of genotype-dependent methionine accumulation in Arabidopsis thaliana
    Miyako Kusano
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Amino Acids 39:1013-21. 2010
    ..The findings suggest that our metabolomics approach not only can reveal the impact of Met over-accumulation on metabolism, but also may provide clues to identify crucial pathways for regulation of metabolism in plants...
  4. pmc Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana
    Miyako Kusano
    RIKEN Plant Science Center, 1 7 22, Yokohama, Kanagawa 230 0045, Japan
    BMC Syst Biol 1:53. 2007
    ..We investigated the metabolic network between wild-type and 2 mutant (methionine-over accumulation 1 [mto1] and transparent testa4 [tt4]) plants regarding the alteration of metabolite accumulation in Arabidopsis thaliana...
  5. doi request reprint Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light
    Miyako Kusano
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Plant J 67:354-69. 2011
    ....
  6. pmc Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination
    Atsushi Fukushima
    RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Proc Natl Acad Sci U S A 106:7251-6. 2009
    ..These findings indicated that mitochondrial functions are coupled with the circadian system in plants...
  7. pmc Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
    Atsushi Fukushima
    RIKEN Plant Science Center, Kanagawa 230 0045, Japan
    BMC Syst Biol 5:1. 2011
    ....
  8. doi request reprint Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis
    Miyako Kusano
    RIKEN Plant Science Center, Tsurumi, Yokohama 230 0045, Japan
    Mol Plant 5:442-51. 2012
    ..Exploring metabolomic traits is a powerful way to follow rice genetic traces and breeding history...
  9. doi request reprint Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism
    Doris Albinsky
    RIKEN Plant Science Center, Tsurumi ku, Yokohama, Japan
    Mol Plant 3:125-42. 2010
    ..Thus, the combination of a metabolomics-based screening method and a gain-of-function approach is useful for rapid characterization of novel genes in both Arabidopsis and rice...
  10. pmc SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana
    Atsushi Fukushima
    RIKEN Plant Science Center, 1 7 22 Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 15:367-74. 2008
    ..In our SVD analysis on Arabidopsis data set, array experiments that contributed most as the principal components included stamen development, germinating seed and stress responses on leaf...
  11. pmc Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment
    Miyako Kusano
    RIKEN Plant Science Center, Yokohama, Japan
    PLoS ONE 6:e16989. 2011
    ..We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms...
  12. doi request reprint Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice
    Miyako Kusano
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Plant J 66:456-66. 2011
    ..These results demonstrated a crucial function of OsGS1;1 in coordinating the global metabolic network in rice plants grown using ammonium as the nitrogen source...
  13. doi request reprint Metabolomic approaches toward understanding nitrogen metabolism in plants
    Miyako Kusano
    RIKEN Plant Science Center, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
    J Exp Bot 62:1439-53. 2011
    ..Examples are used to illustrate the application of metabolomic techniques to the model plants Arabidopsis and rice, as well as other crops and vegetables...
  14. pmc Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
    Henning Redestig
    Metabolomics Research Group, RIKEN Plant Science Center, 1 7 22 Tsurumi ku, Suehiro cho, Yokohama, Kanagawa, 230 0045, Japan
    BMC Bioinformatics 11:214. 2010
    ..Connecting identifiers of analytes found in experimental data with the identifiers of their parent metabolites in public databases can therefore be very laborious...
  15. pmc Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana
    Keiko Yonekura-Sakakibara
    RIKEN Plant Science Center, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Plant J 69:154-67. 2012
    ..These data suggest major routes from cyanidin 3-O-glucoside to the most highly modified cyanidin in the potential intricate anthocyanin modification pathways in Arabidopsis...
  16. doi request reprint Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data
    Henning Redestig
    RIKEN Plant Science Center, Tsurumi ku, Suehiro cho, 1 7 22 Yokohama, Kanagawa, 230 0045, Japan
    Anal Chem 81:7974-80. 2009
    ..Our method is applicable to data from randomized and designed experiments that use ISs to monitor the systematic error...
  17. doi request reprint Integrated omics approaches in plant systems biology
    Atsushi Fukushima
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Curr Opin Chem Biol 13:532-8. 2009
    ..Further prospects for using metabolomics and the key points to be addressed are discussed. This could be a valuable strategy for a systems-level understanding of plant systems...
  18. pmc Current challenges and future potential of tomato breeding using omics approaches
    Miyako Kusano
    RIKEN Plant Science Center, 1 7 22 Suehiro, Tsurumi, Yokohama, Kanagawa 230 0045, Japan Kihara Institute for Biological Research, Yokohama City University, 641 12 Maioka, Totsuka, Yokohama, Kanagawa 244 0813, Japan
    Breed Sci 63:31-41. 2013
    ..Key applications of omics approaches are also presented as case examples to improve economically important traits for tomato breeding...
  19. ncbi request reprint Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice
    Miyako Kusano
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    J Chromatogr B Analyt Technol Biomed Life Sci 855:71-9. 2007
    ..Our method of combining 1D- and GC x GC-TOF/MS is useful for the metabolic phenotyping of natural variants in rice for further studies in breeding programs...