Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae

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

doi:10.1007/978-3-642-40319-4_20

Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae

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

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

Abstract

Strains of Saccharomyces cerevisiae 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. Saccharomyces cerevisiae 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	Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops
Subtitle of host publication	DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers
Pages	223-233
Number of pages	11
DOIs	https://doi.org/10.1007/978-3-642-40319-4_20
Publication status	Published - 2013
Externally published	Yes
Event	17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013 - Gold Coast, QLD, Australia Duration: Apr 14 2013 → Apr 17 2013

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7867 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013
Country/Territory	Australia
City	Gold Coast, QLD
Period	4/14/13 → 4/17/13

Keywords

Bees algorithm
Flux balance analysis
Hill climbing
Microbial strains
Optimization

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-40319-4_20

Cite this

Choon, Y. W., Mohamad, M. S., Deris, S., Illias, R. M., Chai, L. E., & Chong, C. K. (2013). Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae. In Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers (pp. 223-233). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7867 LNAI). https://doi.org/10.1007/978-3-642-40319-4_20

Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae. / Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai et al.
Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. 2013. p. 223-233 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7867 LNAI).

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

Choon, YW, Mohamad, MS, Deris, S, Illias, RM, Chai, LE & Chong, CK 2013, Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae. in Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7867 LNAI, pp. 223-233, 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2013, Gold Coast, QLD, Australia, 4/14/13. https://doi.org/10.1007/978-3-642-40319-4_20

Choon YW, Mohamad MS, Deris S, Illias RM, Chai LE, Chong CK. Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae. In Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. 2013. p. 223-233. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-40319-4_20

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 succinic acid and glycerol in Saccharomyces cerevisiae. Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2013 International Workshops: DMApps, DANTH, QIMIE, BDM, CDA, CloudSD, Revised Selected Papers. 2013. pp. 223-233 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Identifying gene knockout strategy using Bees Hill Flux Balance Analysis (BHFBA) for improving the production of succinic acid and glycerol in Saccharomyces cerevisiae

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Keywords

ASJC Scopus subject areas

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