Shimizu Lab. Graduate School of Information Science and Technology,Osaka University

Japanese Page

Welcome to Shimizu Lab.

11/29/2013 Press Release: Satoshi Ono, Hiroshi Shimizu, Chikara Furusawa, "FastPros: Screening of reaction knockout strategies for metabolic engineering," Bioinformatics

We are studying metabolic engineering integrated by bioinformatics data.
Main subjects in our lab are

  • Modification of metabolic pathway for biochemicals
  • Creation of stress tolerant cells for bioprocesses
  • Understanding of organisms as systems
Especially,
  • Screening of useful genes based on transcriptome analysis
  • Conferring stress tolerance based on comprehensive phenotype data
  • Prediction of metabolic flux profiles by genome scale metabolic model
  • Precise metabolic flux estimation with metabolomics data
  • Dynamic analysis of gene expression in metabolic pathway
  • Comprehensive phenotypic/Gentic analysis of stress tolerant microoranigams obtained by experimental evolution.

The bioprocesses for production of biochemicals has advantage, regarding with environment-concious processes. It is highly desired to improve metabolic pathways for maximizing cellular potential in bioproduction. After finishing genome sequencing and elucidation of principal metabolic pathways, rational design of improvement of metabolic pathways and systematic analyses of omics data should be established. In the cells muti-hierarchical network such as gene, protein, metabolite networks exist and elements in the networks are interacting each other. It is well known that there are many cases to fail improvement of productivity and production yield for the targeted product even the gene directly related to synthetic reaction is modified. We are trying to omics data of expression of gene, protein and metabolic fluxes and to establish design of cell factory of your targeted product.