Design of Superior Cell Factories Based on Systems Wide Omics Analysis

  • Katsunori Yoshikawa
  • Chikara Furusawa
  • Takashi Hirasawa
  • Hiroshi Shimizu


The bioproduction industry is expanding towards sustainable production of energy, chemicals and materials requesting for superior, high-productivity cell factories. Recent advances in measurement technologies enable comprehensive analysis of cellular components, so-called “omics” analysis, which is expected to accelerate the construction of superior cell factories. As example, transcriptome analysis is widely used for genome-wide screening of candidate genes that may be manipulated to improve productivity. However, the massive amounts of data produced by this method, requests for smart approaches to narrow the selection of promising candidate genes as targets for higher productivity. In this chapter, we review several studies that demonstrate successful breeding based on omics data, and discuss how we can design experiments and screen for target genes to be manipulated for the development of superior cell factories.


Systems wide omics analysis Cell factory Genome Transcriptome Metabolome Proteome Fluxome Phenome Multi-omics analyses Fossil resources Biofuel Building block of chemicals Breeding Stress tolerance Metabolic engineering Systems metabolic engineering DNA microarray In silico simulation Genome-scale metabolic model Flux balance analysis Metabolic flux analysis Evolutionary engineering Adaptive evolution Next-generation sequencing technologies R programming language 


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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Katsunori Yoshikawa
    • 1
  • Chikara Furusawa
    • 1
  • Takashi Hirasawa
    • 1
  • Hiroshi Shimizu
    • 1
  1. 1.Department of Bioinformatic Engineering, Graduate School of Information Science and TechnologyOsaka UniversitySuitaJapan

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