Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis

Yee Wen Choon; Mohd Saberi Mohamad; Safaai Deris; Rosli M. Illias; Lian En Chai; Chuii Khim Chong

doi:10.1007/978-3-642-37137-0_12

Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis

Yee Wen Choon, Mohd Saberi Mohamad, Safaai Deris, Rosli M. Illias, Lian En Chai, Chuii Khim Chong

Research output: Chapter in Book/Report/Conference proceeding › Chapter

3 Citations (Scopus)

Abstract

Bacillus subtilis strains can be manipulated to improve product yield and growth characteristics. Optimization algorithms are developed to identify the effects of gene knockout on the results. However, this process is often faced the problem of being trapped in local minima and slow convergence due to repetitive iterations of algorithm. In this paper, we proposed Bees Hill Flux Balance Analysis (BHFBA) which is a hybrid of Bees Algorithm, Hill Climbing Algorithm and Flux Balance Analysis to solve the problems and improve the performance in predicting optimal sets of gene deletion for maximizing the growth rate and production yield of desired metabolite. Bacillus subtilis is the model organism in this paper. The list of knockout genes, growth rate and production yield after the deletion are the results from the experiments. BHFBA performed better in term of computational time, stability and production yield.

Original language	English
Title of host publication	Advances in Biomedical Infrastructure 2013
Subtitle of host publication	Proceedings of International Symposium on Biomedical Data Infrastructure (BDI 2013)
Publisher	Springer Verlag
Pages	117-126
Number of pages	10
ISBN (Print)	9783642371363
DOIs	https://doi.org/10.1007/978-3-642-37137-0_12
Publication status	Published - 2013
Externally published	Yes

Publication series

Name	Studies in Computational Intelligence
Volume	477
ISSN (Print)	1860-949X

Keywords

Bacillus subtilis
Bees algorithm
Flux balance analysis
Hill climbing
Optimization

ASJC Scopus subject areas

Artificial Intelligence

Access to Document

10.1007/978-3-642-37137-0_12

Cite this

Choon, Y. W., Mohamad, M. S., Deris, S., Illias, R. M., En Chai, L., & Chong, C. K. (2013). Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis. In Advances in Biomedical Infrastructure 2013: Proceedings of International Symposium on Biomedical Data Infrastructure (BDI 2013) (pp. 117-126). (Studies in Computational Intelligence; Vol. 477). Springer Verlag. https://doi.org/10.1007/978-3-642-37137-0_12

Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis. / Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai et al.
Advances in Biomedical Infrastructure 2013: Proceedings of International Symposium on Biomedical Data Infrastructure (BDI 2013). Springer Verlag, 2013. p. 117-126 (Studies in Computational Intelligence; Vol. 477).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Choon, YW, Mohamad, MS, Deris, S, Illias, RM, En Chai, L & Chong, CK 2013, Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis. in Advances in Biomedical Infrastructure 2013: Proceedings of International Symposium on Biomedical Data Infrastructure (BDI 2013). Studies in Computational Intelligence, vol. 477, Springer Verlag, pp. 117-126. https://doi.org/10.1007/978-3-642-37137-0_12

Choon YW, Mohamad MS, Deris S, Illias RM, En Chai L, Chong CK. Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis. In Advances in Biomedical Infrastructure 2013: Proceedings of International Symposium on Biomedical Data Infrastructure (BDI 2013). Springer Verlag. 2013. p. 117-126. (Studies in Computational Intelligence). doi: 10.1007/978-3-642-37137-0_12

Choon, Yee Wen ; Mohamad, Mohd Saberi ; Deris, Safaai et al. / Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis. Advances in Biomedical Infrastructure 2013: Proceedings of International Symposium on Biomedical Data Infrastructure (BDI 2013). Springer Verlag, 2013. pp. 117-126 (Studies in Computational Intelligence).

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Identifying gene knockout strategy using bees hill flux balance analysis (BHFBA) for improving the production of ethanol in bacillus subtilis

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