Research Activities

Main theme: Reverse engineering of signaling network controlling metabolic pathways

Database Center for Life Science (DBCLS)

  • Functional annotation of public transcriptome data
    • AOE (All of Expression):  index of public gene expression data
      • Collaboration with DDBJ Omics aRchive (DOR)
    • RefEx: reference expression dataset for functional analysis of genes of interest
  • Constructing and maintaining educational materials for Japanese
    • TogoTV: Tutorial movies for databases and web tools for lifescience (mostly in Japanese)
    • MotDB: Tutorial website for LSDB (Japanese only)
    • AJACS: Off-line tutorial series in database and web tools
  • Sequence analysis pipeline
    • KAIKO functional annotation pipeline
      • Application of GFIT method to functional annotation of insect
    • Transcriptome Sequence Assembly
      • Construction of ‘UniGene’-type resource from RNA-seq reads

Saitama Medical University, Research Center for Genomic Medicine (RCGM)

  • Deciphering hypoxic signaling networks in eukaryotes fully(fooly?) utilizing genomic resources
    • Comparative genomic approach for identifying conserved core networks
      • C.elegans and mammalian cells
  • Computational research environment for integrated analysis of genomic data
    • SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements. Bono HU  (2005)
  • Pathway analysis of cancer cells
    • The study of metabolic pathways in tumors based on the transcriptome. Bono H and Okazaki Y (2005)
  • Collaborations
    • Genome Network project
    • Finding nuclear receptor response elements in mammalian genomes
      • Peroxisome Proliferator Activated Receptors (PPAR)
      • Andorogen Receptor (AR)
        • Identification and functional analysis of consensus androgen response elements in human prostate cancer cells Horie-Inoue K,Bono H, Okazaki Y and Inoue S (2004)
        • Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements Horie-Inoue K, Takayama K, Bono H, Ouchi Y, Okazaki Y and Inoue S (2006)

RIKEN Genomic Sciences Center (GSC)

  • Transcriptome analysis of RIKEN cDNA microarrays
    • 20k vs mouse 49 tissues
    • 60k vs mouse 20 tissues
  • Functional annotation of mouse (FANTOM)

Kyoto University, Institute for Chemical Research (KUICR)

  • Analysis of amino acid synthesis pathway in the complete genomes utilizing KEGG
  • Analysis of bacterial two-component (His-Asp phosphorelay) signaling pathway in the complete genome sequences

The University of Tokyo

  • Cloning one subtype of gamma subunit of hetero trimeric G-protein (as under graduate student)
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