Identifying Gene Knockout Strategies Using a Hybrid of Bees Algorithm and Flux Balance Analysis for in Silico Optimization of Microbial Strains

  • Yee Wen Choon
  • Mohd Saberi Mohamad
  • Safaai Deris
  • Chuii Khim Chong
  • Lian En Chai
  • Zuwairie Ibrahim
  • Sigeru Omatu
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 151)

Abstract

Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the local minima problem and to predict optimal sets of gene deletion for maximizing the growth rate of certain metabolite. This paper involves two case studies that consider the production of succinate and lactate as targets, by using E.coli as model organism. The results from this experiment are the list of knockout genes and the growth rate after the deletion. BAFBA shows better results compared to the other methods. The identified list suggests gene modifications over several pathways and may be useful in solving challenging genetic engineering problems.

Keywords

Evolutionary Programming Metabolic Engineering Bees Algorithm Gene Knockout Optimization 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Yee Wen Choon
    • 1
  • Mohd Saberi Mohamad
    • 1
  • Safaai Deris
    • 1
  • Chuii Khim Chong
    • 1
  • Lian En Chai
    • 1
  • Zuwairie Ibrahim
    • 2
  • Sigeru Omatu
    • 3
  1. 1.Artificial Intelligence and Bioinformatics Group, Faculty of Computer Science and Information SystemsUniversiti Teknologi MalaysiaSkudaiMalaysia
  2. 2.Department of Mechatronics and Robotics, Center for Artificial Intelligence and Robotics (CAIRO), Faculty of Electrical EngineeringUniversiti Teknologi MalaysiaSkudaiMalaysia
  3. 3.Department of Electronics, Information and Communication EngineeringOsaka Institute of TechnologyOsakaJapan

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