Research projects

Interest: Reverse engineering of signaling network controlling energy metabolisms in an omic scale.

Expertise: Data-driven approach, especially for the utilization of public databases.

List of research projects involved

System development of functional annotation (formerly prediction) of genes

  • GFIT (1996-2000)
  • Functional annotation of mouse (FANTOM) (2000-2003)
  • Kaiko annotation pipeline (2010-)

Computational analysis of transcription factor binding sites (ChIP-on-chip, ChIPseq)

  • SayaMatcher (2003-2007)
  • GGRNA (2011-2012)
  • GGGenome(2012-)

Application of natural language processing method for life science

  • Allie (2007-2011)
  • Gendoo (2007-)

Index of public databases and construction of reference dataset

  • RefEx (2010-)
  • DBCLS SRA (2011-)
  • AOE (2014-)

Time-course description about the projects

Database Center for Life Science (DBCLS) (2007-)

  • Functional annotation of public transcriptome data
    • RefEx: reference expression dataset for functional analysis of genes of interest
    • AOE (All of Expression): index of public gene expression data
      • Collaboration with DDBJ Genomic Expression Archive (GEA)
  • Systematic analysis of transcriptomic sequences
    • KAIKO functional annotation pipeline -> unannotated insects
    • RNA-seq Workflow for insects making use of Transcriptome Shotgun Assembly (TSA) database
  • Constructing and maintaining educational materials for Japanese
    • TogoTV: Tutorial movies for databases and web tools for life science (mostly in Japanese)
    • AJACS: Off-line tutorial series in database and web tools
      • MotDB: Tutorial website for life science (Japanese only)

Saitama Medical University, Research Center for Genomic Medicine (RCGM) (2003-2007)

  • Deciphering hypoxic signaling networks in eukaryotes fully 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
    • Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements

RIKEN Genomic Sciences Center (GSC) (2000-2003)

  • 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) (1995-2000)

  • 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 (1994-1995)

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

Written by Dr Bono in research on 月 24 12月 2018.