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bonohulab

Welcome to bonohulab website. Toward data-driven genome breeding (digital breeding), we are developing data analysis infrastructure technology essential for genome editing, focusing on gene function analysis using bioinformatics called BioDX.

Bonohulab is also known as

  • Laboratory of Bio-DX, Genome Editing Innovation Center
  • Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life

in Hiroshima University. Very limitted number of students and postdocs can be accepted currently because there are not enough staffs to teach and space to accomodate. For coming FY2023, no additional members can be accepted as we have many applicants already.

Affiliation

Members

Research activities

Current research projects

  • Development of database technologies for genome editing
    • Development of the public data integration workflow for genome editing data analyses
    • Development of the functional annotation workflow from genomes and transcriptomes
  • Functional genomics by bioinformatic approach
    • Meta-analysis of stressed transcriptomes in the public databases
    • Comparative genomic analyses in Apis species
    • Deciphering cancer and aging-resistant mechanisms in Naked mole-rat from the analyses of genomes and transcriptomes
  • Developing and maitaining public databases in life science in Japan

Please refer Profiles of Faculty and Research Scholars for my activities provided in Hiroshima Univesity website.

Research projects involved so far

  • System development of functional annotation (formerly prediction) of genes
    • Gene Function Identification Tool (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, GGGenome(2011-2020)
  • Application of natural language processing method for life science
    • Allie (2007-2011)
    • Gendoo (2007-)
  • Index of public databases and construction of reference dataset
    • Reference Expression dataset (RefEx) (2010-)
    • DBCLS SRA (2011-)
    • All of gene expression (AOE) (2014-)

Time-course description about the projects

Database Center for Life Science (DBCLS) (2007-2020)

  • 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 an undergraduate student)

About Me

広島大学 大学院統合生命科学研究科 ゲノム情報科学研究室 / ゲノム編集イノベーションセンター プラチナバイオ共同研究講座 バイオDX研究室
a.k.a. bonohulab

Address:
〒739-0046 広島県東広島市鏡山3丁目10-23
広島大学イノベーションプラザ 2B01 (地図
2B01 Hiroshima University Innovation Plaza, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan