Skip to content

Instantly share code, notes, and snippets.

@bonohu

bonohu/ResearchActivities.md

Last active November 30, 2017 06:02
Show Gist options
  • Save bonohu/467a34db53230de6521e8d231d108699 to your computer and use it in GitHub Desktop.
Save bonohu/467a34db53230de6521e8d231d108699 to your computer and use it in GitHub Desktop.
Download ZIP
Research Activities
Raw
ResearchActivities.md

Research Activities

Main theme: Reverse engineering of signaling network controlling metabolic pathways

Research Organization of Information and Systems(ROIS), Database Center for Life Science(DBCLS)

  • Make sense of public transcriptome database 　　-　AOE(All of Expression): the integration of gene expression data 　　- RefEx: Constructing and maintaining Reference Expression data set　
  • 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)　
  • Sequence analysis pipeline 　　- KAIKO functional annotation pipeline　

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(ICR)

  • 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)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment