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Name: Mohd Saberi

Joined: Thursday 10 November 2011 08:49:00 (UTC)

Last seen: Wednesday 02 July 2014 06:44:25 (UTC)

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Location: Johor, Malaysia

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Field/Industry: Higher Education

Occupation/Role(s): Assoc. Professor (Bioinformatics Academic Program Coordinator)

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UNIVERSITI TEKNOLOGI MALAYSIA

 

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Blob A Method To Construct Gene Regulatory Networks To Es...

Created: 2013-06-10 06:56:01

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S.P. Chai, M.S. Mohamad. A Method To Construct Gene Regulatory Networks To Estimate and Calculate Time Delay. (2013). Jurnal Teknologi. Vol. 62, No. 1, pp. 25-31. UTM Press. Indexed by SCOPUS. 

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Blob Identifying Minimal Genomes and Essential Genes in M...

Created: 2013-05-31 03:04:59

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A.H.M. Salleh, M. S. Mohamad, S. Deris, R. M. Illias, “Identifying Minimal Genomes and Essential Genes in Metabolic Model Using Flux Balance Analysis”, The 5th Asian Conference on Intelligent Information and Database Systems (ACIIDS 2013), Istana Hotel, Kuala Lumpur, Malaysia, 18-20 March, 2013

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Blob Multiple Gene Sets for Cancer Classification Using G...

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K. Moorthy, M.S. Mohamad, S. Deris, “Multiple Gene Sets for Cancer Classification Using Gene Range Selection Based on Random Forest”, The 5th Asian Conference on Intelligent Information and Database Systems (ACIIDS 2013), Istana Hotel, Kuala Lumpur, Malaysia, 18–20 March, 2013. 

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Blob Using Bees Hill Flux Balance Analysis (BHFBA) for in...

Created: 2013-05-31 03:03:51

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Y. W. Choon, M. S. Mohamad, S. Deris, R. M. Illias, L. E. Chai, “Using Bees Hill Flux Balance Analysis (BHFBA) for in silico Microbial Strain Optimization”, The 5th Asian Conference on Intelligent Information and Database Systems (ACIIDS 2013), Istana Hotel, Kuala Lumpur, Malaysia, 18-20 March, 2013. 

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Blob A Hybrid of Artificial Bee Colony and Flux Balance A...

Created: 2013-05-31 03:03:16

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S.S Lee, Y.W. Choon, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, M.S. Mohamad, “A Hybrid of Artificial Bee Colony and Flux Balance Analysis for Identifying Optimum Knockout Strategies for Producing High Yields of Lactate in Echerichia Coli”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia, 27-28 February 2013. 

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Blob Identifying Gene Knockout Strategy Using Bees Hill F...

Created: 2013-05-31 03:02:36

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Y.W. Choon, M.S. Mohamad, S. Deris, R.M. Illias, L.E. Chai, C.K. Chong, “Identifying Gene Knockout Strategy Using Bees Hill Flux Balance Analysis (BHFBA) for Improving the Production of Ethanol in Bacillus Subtilis”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Prediction of Vanillin Production in Yeast Using a H...

Created: 2013-05-31 03:01:58

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L.H. Yin, Y.W. Choon, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, M.S. Mohamad, “Prediction of Vanillin Production in Yeast Using a Hybrid of Continuous Bees Algorithm and Flux Balance Analysis (CBAFBA)”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Inferring Gene Networks from Gene Expression Data Us...

Created: 2013-05-31 03:01:03

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M.A. Mutalib, L.E. Chai, C.K. Chong, Y.W. Choon, S. Deris, R.M. Illias, M.S. Mohamad, “Inferring Gene Networks from Gene Expression Data Using Dynamic Bayesian Network with Different Scoring Metric Approaches”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Using Particle Swarm Optimization for Estimating Kin...

Created: 2013-05-31 03:00:33

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S.T. Ng, C.K. Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S. Shamsir, M.S. Mohamad, “Using Particle Swarm Optimization for Estimating Kinetics Parameters on Essential Amino Acid Production of Arabidopsis Thaliana”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Using Ant Colony Optimization (ACO) on Kinetic Model...

Created: 2013-05-31 03:00:05

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N.F. Saidin, C.K Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S Shamsir, M.S. Mohamad, “Using Ant Colony Optimization (ACO) on Kinetic Modeling of the Acetoin Production in Lactococcus Lactis C7”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Inferring E. coli SOS Response Pathway from Gene Exp...

Created: 2013-05-31 02:59:33

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L.E. Chai, M.S. Mohamad, S.Deris, C.K. Chong, Y.W. Choon, “Inferring E. coli SOS Response Pathway from Gene Expression Data Using IST-DBN with Time Lag Estimation”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia, 27-28 February 2013. 

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Blob A Hybrid of SVM and SCAD with Group-specific Tuning ...

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M.F. Misman, W.H. Chan, M.S. Mohamad, S.Deris, “A Hybrid of SVM and SCAD with Group-specific Tuning Parameters in Identification of Informative Genes and Biological Pathways”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Identifying Gene Knockout Strategy Using Bees Hill F...

Created: 2013-05-31 02:58:12

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Y.W. Choon, C.K. Chong, L.E. Chai, M.S. Mohamad, S.Deris, R.M Illias, “Identifying Gene Knockout Strategy Using Bees Hill Flux Balance Analysis  (BHFBA) for Improving the Production of Succinic Acid and Glycerol in Saccharomyces cerevisiae”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob A Constraint and Rule In an Enhancement of Binary Pa...

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 M.S. Mohamad, S. Omatu, S. Deris, M. Yoshioka, “A Constraint and Rule In an Enhancement of Binary Particle Swarm Optimization To Select Informative Genes For Cancer Classification”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Multiclass Prediction for Cancer Microarray Data Usi...

Created: 2013-05-31 02:56:51

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K. Moorthy, M.S. Mohamad, S. Deris, “Multiclass Prediction for Cancer Microarray Data Using Various Variables Range Reduction Based On Random Forest”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Theronine Biosynthesis Pathway Simulation Using IBMD...

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C.K. Chong, Y.W. Choon, L.E. Chai, M.S. Mohamad, S.Deris, S. Shamsir, “Theronine Biosynthesis Pathway Simulation Using IBMDE With Parameter Estimation”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Modelling Gene Networks by a Dynamic Bayesian Networ...

Created: 2013-05-31 02:54:18

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 L.E. Chai, M.S. Mohamad, S.Deris, C.K. Chong, Y.W. Choon, “Modelling Gene Networks by a Dynamic Bayesian Network-based Model with Time Lag Estimation”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Parameter Estimation Using Improved Differential Evo...

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J.X. Yeoh, C.K. Chong, Y.W. Choon, L.E. Chai, M.S. Mohamad, S.Deris, R.M Illias, “Parameter Estimation Using Improved Differential Evolution (IDE) and Bacterial Foraging Algorithm to Model Tyrosine Production in Mus Musculus”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob A Two-Step Binary Particle Swarm Optimization Approa...

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Z.M. Yusof, A.F.Z. Abidin, A. Adam, K. Khalil, J.A.A Mukred, M.S Mohamad, Z. Ibrahim.  (2012). Vol 6, No.3, pp.771-776. .ICIC Express Letters (ICIC-EL). ICIC International. Indexed by SCOPUS.

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Blob A Pathway-Based Approach for Analyzing Microarray Da...

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C.H. Shi, M.S. Mohamad, S. Deris, Z. Ibrahim.  (2012). Vol 6, No.5, pp. 1253-1257. ICIC Express Letters (ICIC-EL). ICIC International. Indexed by SCOPUS.

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Blob “Aspartate Biosynthesis Pathway Simulation using an...

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C.K. Chong, M.S. Mohamad, S. Deris, M.S. Shamsir, Y.W. Choon, L.E. Chai, Universiti Malaysia Terengganu 11th International Annual Symposium on Sustainability Science and Management (UMTAS 2012), pp. 956-961, Universiti Malaysia Terengganu, Malaysia, 9-11 July 2012.

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Blob “Gene Knockout Strategies Identification by using a...

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Y.W. Choon, M.S. Mohamad , S. Deris, C.K. Chong, L.E. Chai, Universiti Malaysia Terengganu 11th International Annual Symposium on Sustainability Science and Management (UMTAS 2012), pp. 962-968, Universiti Malaysia Terengganu, Malaysia, 9-11 July 2012.

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Blob “The Emerging Field of Synthetic Biology: a Review”

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N. Habibi, S.Z.M. Hashim, C. A. Rodriguez, M.S.M. Mohamad, S.Deris, 2012 4th International Conference on Intelligent and Advanced Systems (ICIAS2012), pp.160-164, Kuala Lumpur Convention Centre, 12 – 14 June, 2012. Indexed by Scopus.

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Blob A Hybrid of Artificial Bee Colony and Flux Balance A...

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S.S Lee, Y.W. Choon, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, M.S. Mohamad. In A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 127-137. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3.

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Blob Identifying Gene Knockout Strategy Using Bees Hill F...

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Y.W. Choon, M.S. Mohamad, S. Deris, R.M. Illias, L.E. Chai, C.K. Chong. In A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 117-126. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3.

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Blob Prediction of Vanillin Production in Yeast Using a H...

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L.H. Yin, Y.W. Choon, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, M.S. Mohamad. In A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 101-116. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3.

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Blob Inferring Gene Networks from Gene Expression Data U...

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M.A. Mutalib, L.E. Chai, C.K. Chong, Y.W. Choon, S. Deris, R.M. Illias, M.S. Mohamad.In A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 77-86. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3.

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Blob Using Particle Swarm Optimization for Estimating Kin...

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S.T. Ng, C.K. Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S. Shamsir, M.S. Mohamad. In  A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 51-61. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3.

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Blob Using Ant Colony Optimization (ACO) on Kinetic Model...

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N.F. Saidin, C.K Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S Shamsir, M.S. Mohamad. In A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 25-35. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3.

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Blob Inferring E. coli SOS Response Pathway from Gene Exp...

Created: 2013-05-12 04:20:35

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L.E. Chai, M.S. Mohamad, S.Deris, C.K. Chong, Y.W. Choon.  In A.S Sidhu & S.K Dhillon (Eds.), Studies in Computational Intelligence: Adv. In Biomedical Infrastructure 2013, Vol. 477, pp. 5-14. Springer-Verlag Berlin / Heidelberg. 2013. ISBN: 978-3-642-37136-3. 

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Blob Identifying Minimal Genomes and Essential Genes in ...

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A.H.M. Salleh, M. S. Mohamad, S. Deris, R. M. Illias. In Intelligent Information and Database Systems. A. Selamat et al. (Eds.): ACIIDS 2013, Part 1, LNAI, Vol. 7802, pp. 414-423. Springer-Verlag Berlin / Heidelberg. 2013.  ISBN: 978-3-642-36545-4.

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Blob Multiple Gene Sets for Cancer Classification Using G...

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K. Moorthy, M.S. Mohamad, S. Deris. In Intelligent Information and Database Systems. A. Selamat et al. (Eds.): ACIIDS 2013, Part 1, LNAI, Vol. 7802, pp. 385-393. Springer-Verlag Berlin / Heidelberg. 2013.  ISBN: 978-3-642-36545-4.

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Blob Using Bees Hill Flux Balance Analysis (BHFBA) for in...

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Y. W. Choon, M. S. Mohamad, S. Deris, R. M. Illias, L. E. Chai. In Intelligent Information and Database Systems. A. Selamat et al. (Eds.): ACIIDS 2013, Part 1, LNAI, Vol. 7802, pp. 375-384. Springer-Verlag Berlin / Heidelberg. 2013.  ISBN: 978-3-642-36545-4.

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Blob Using Bayesian Networks To Construct Gene Regulatory...

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A.K. Tan, M.S. Mohamad.  (2012). Jurnal Teknologi. Vol. 58, pp. 1-6. UTM Press. Indexed by SCOPUS. 

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Blob Selecting a Small Subset of Informative Genes from G...

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M.S. Mohamad, S. Omatu, S. Deris, M. Yoshioka, Z. Ibrahim. (2012). International Journal of Innovative Computing, Information and Control. Vol. 8, No. 6, pp. 4285-4297. ICIC International. Indexed by ISI and SCOPUS. 

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Blob Protein Secondary Structure Prediction Using Optima...

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C.Y. Fai, R. Hassan, M. S. Mohamad.(2012). International Journal of BioSciences and Technology (IJBSBT). Vol. 4, No. 2, pp. 35–44. Science & Engineering Research Support Society. Indexed by SCOPUS. 

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Blob Metabolic Pathway Extraction Using Combined Probabil...

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A. H. M. Salleh, M.S. Mohamad. (2012). International Journal of BioSciences and Technology (IJBSBT). Vol. 4, No. 2, pp. 1–10. Science & Engineering Research Support Society. Indexed by SCOPUS.

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Blob Multivariate Analysis of Gene Expression Data and Mi...

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K. Moorthy, M.S. Mohamad, S. Deris, Z. Ibrahim. (2012). Vol 6, No.5, pp.1335-1339. ICIC Express Letters (ICIC-EL). ICIC International. Indexed by SCOPUS.

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Blob Investigation on Different Learning Techniques for W...

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M.I. Shapiai, Z. Ibrahim, S. Sudin, M.S. Mohamad, M. Khalid.  (2012). Vol 6, No.3, pp. 705-710. ICIC Express Letters (ICIC-EL). ICIC International. Indexed by SCOPUS.

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Blob An Image Registration Technique To Enhance PCB Insp...

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I. Ibrahim, S.A.R.S.A Bakar, M.M. Mokji, K. Khalil, Z.M. Yusof, J.A.A. Mukred, M.S. Mohamad, Z. Ibrahim. (2012). Vol 6, No.3, pp. 717-712. ICIC Express Letters (ICIC-EL). ICIC International. Indexed by SCOPUS.

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Blob DNA Sequence Design for DNA Computation based on Bin...

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Z. Ibrahim, N.K. Khalid, S. Buyamin, J. Abdulla, A. Mukred, Z.M. Yusof, K. Khalil, M.F.M. Saaid, N. Mokhtar, J. Watada, A. Engelbrecht. (2012). International Journal of Innovative Computing, Information and Control. Vol. 8, No. 5(B), pp. 3341-3450. ICIC International. Indexed by ISI and SCOPUS. 

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Blob Random Forest for Gene Selection and Microarray Data...

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K. Moorthy, M.S. Mohamad.  Communications in Computer and Information Science. Vol. 295, pp. 174-183. Springer-Verlag Berlin / Heidelberg. 2012. ISBN:   978-3-642-32825-1. Indexed by SCOPUS.

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Blob A Hybrid of SVM and SCAD with Group-specific Tuning ...

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M.F. Misman, M.S. Mohamad, S. Deris, R.N.M.R. Mohamad, S.Z.M. Hashim, S. Omatu. Advances in Intelligent and Soft-Computing. Vol. 151,  pp. 387-394. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-28764-0. Indexed by ISI and SCOPUS.

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Blob Inferring Gene Regulatory Networks from Gene Expres...

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L.E. Chai, M.S. Mohamad, S. Deris, C.K. Chong, Y.W. Choon, Z. Ibrahim, S. Omatu. Advances in Intelligent and Soft-Computing. Vol. 151, pp. 379-386. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-28764-0. Indexed by ISI and SCOPUS.

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Blob Identifying Gene Knockout Strategies Using a Hybrid...

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Y.W. Choon, M.S. Mohamad, S. Deris, C.K. Chong, L.E. Chai, Z. Ibrahim, S. Omatu.Advances in Intelligent and Soft-Computing. Vol. 151, pp. 371-378. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-28764-0. Indexed by ISI and SCOPUS.

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Blob Parameter Estimation for Simulation of Glycolysis Pa...

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C.K. Chong, M.S. Mohamad, S. Deris, Y.W. Choon, L.E. Chai.  Communications in Computer and Information Science. Vol. 295, pp. 352-355. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-32825-1. Indexed by SCOPUS.  

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Blob Using an Improved Differential Evolution Algorithm ...

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C.K. Chong, M.S. Mohamad, S. Deris, M.S. Shamsir, A. Abdullah, Y.W. Choon, L.E. Chai, S. Omatu.Advances in Intelligent and Soft Computing. Vol. 151, pp. 709-716. Springer-Verlag Berlin / Heidelberg. 2012.  ISBN: 978-3-642-28764-0. Indexed by ISI and SCOPUS

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Blob Optimized Local Protein Structure with Support Vecto...

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C.Y. Fai, R. Hassan, M. S. Mohamad. Communications in Computer and Information Science. Vol. 295, pp. 333-342. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-32825-1. Indexed by SCOPUS.

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Blob Optimized Local Protein Structure with Support Vecto...

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 C.Y. Fai, R. Hassan, M. S. Mohamad. Communications in Computer and Information Science. Vol. 295, pp. 333-342. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-32825-1. Indexed by SCOPUS.

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Blob A New Hybrid Firefly Algorithm for Complex and Nonli...

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A.Abdullah, S. Deris, M. S. Mohamad, S.Z.M. Hashim.  Advances in Intelligent and Soft Computing. Vol. 151, pp. 673-680. Springer-Verlag Berlin / Heidelberg. 2012. ISBN: 978-3-642-28764-0. Indexed by ISI and SCOPUS.

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Blob Reconstructing Metabolic Networks - A Review. Advanc...

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Y.W. Choon, M.S. Mohamad.  Vol. 1, pp. 26-40. UTM Press. 2011. ISBN: 978-983-52-0822-5.

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Blob Automation of DNA Computing Readout Method Based on...

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M.F.M. Saaid, S. Sudin, I. Ibrahim, Z.M. Yusof, K. Khalil, J.A.A. Mukred, M.S. Mohamad, N. Mokhtar, Z. Ibrahim, J. Watada. (2012). International Journal of Innovative Computing, Information and Control. Vol. 8, No. 3(A), pp. 1907-1916. ICIC International. Indexed by ISI and SCOPUS.

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Blob An Improved Swarm Optimization for Parameter Estima...

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A. Abdullah, S. Deris, M.S. Mohamad, S. Anwar. (2013). PLoS ONE, Vol. 8, No. 4, pp. e61258. PLoS. Indexed by ISI and SCOPUS.

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Blob Validation of Hierarchical Gene Clusters Using Repea...

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L.F. Tee, M.S. Mohamad, S. Deris, A.A.M. Faudzi, M.S.A. Latiff, R. Sallehuddin. (2013). Jurnal Teknologi. Vol. 6. No. 1, pp. 7-12. UTM Press. Index by Scopus. 

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Blob Validation of Hierarchical Gene Clusters Using Repea...

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 L.F. Tee, M.S. Mohamad, S. Deris, A.A.M. Faudzi, M.S.A. Latiff, R. Sallehuddin. (2013). Jurnal Teknologi. Vol. 6. No. 1, pp. 7-12. UTM Press. Index by Scopus. 

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Blob A Review of Computational Approaches for In Silico M...

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W. H. Chan, M. S. Mohamad, S. Deris and R. M. Illias.  (2013). Current Bioinformatics. Vol. 8, No. 2, pp. 253-258. Bentham Science Publishers. Indexed by ISI and SCOPUS.

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Blob A New Hybrid Bee Evolution Algorithm for parameter E...

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A. Abdullah, S. Deris, M.S Mohamad. (2013) ICIC Express Letter Part B: Application, Vol 4 (1), p. 1-6. ICIC International.

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Blob Using A Dynamic Bayesian Network-based Model for Inf...

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 Largely due to the technological advances in bioinformatics, researchers are now garnering interests in inferring gene regulatory networks (GRNs) from gene expression data which is otherwise unfeasible in the past. This is because of the need of researchers to uncover the potentially vast information and understand the dynamic behavior of the GRNs. In this regard, dynamic Bayesian network (DBN) has been broadly utilized for the inference of GRNs thanks to its ability to handle time-seri...

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Blob Aspartate Biosynthesis Pathway Simulation Using an I...

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 An improved Differential Evolution algorithm (IDE) is proposed in this paper. It is aimed at enhancing its efficiency in estimating the relevant kinetic parameters for metabolic pathway data to simulate aspartate biosynthesis pathway for plant model Arabidopsis. Metabolic pathway data are anticipated to be of vital help in the development of effectual tools in parameter estimation and kinetic modeling platforms. However, a number of computation algorithms face difficulty, produces low a...

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Blob Gene Knockout Strategies Identification by Using a H...

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 By optimizing microbial strains it is possible to improve product yield or improve growth characteristics. Microbial strains can be optimized through genetic engineering. It is proven that through genetic engineering it is able to obtain the desirable phenotypes. However, it is difficult to predict the effects of genetic modifications on the resulting phenotype due to the complexity of the networks. Optimization algorithms are implemented in previous works in order to identify the effec...

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Blob Parameter Estimation for Simulation of Glycolysis Pa...

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 An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data to simulate glycolysis pathway for Saccharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testifying to be supreme to the others estimation algorithms. The outcomes from this study promote estimating ...

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Blob Identifying Metabolic Pathway within Microarray Gene...

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 Extracting metabolic pathway that dictates a specific biological response is currently one of the important disciplines in metabolic system biology research. Previous methods have successfully identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structure is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identifying the significant pathwa...

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Blob Random Forest for Gene Selection and Microarray Data...

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 A random forest method has been selected to perform both gene selection and classification of the microarray data. The goal of this research is to develop and improve the random forest gene selection method. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. In this research, ten datasets that consists of different classes are used, which are Adenocarcinoma, ...

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Blob Optimized Local Protein Structure with Support Vecto...

Created: 2012-07-24 04:21:20

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 Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact through complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental ...

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Blob Prediction of Protein Residue Contact Using Support ...

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 Prediction of protein residue contact is one of the important twodimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or noncontacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy of ...

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Blob Metabolic Pathway Extraction Using Combined Probabil...

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 Extracting metabolic pathway from microarray gene expression data that dictates a specific biological response is currently one of the important disciplines in system biology research. However due to the complexity of the global metabolic network and the importance to maintain the biological structure, this has become a greater challenge. Previous methods have successfully identified those pathways but without concerning the genetic effect and relationship of the genes, representation o...

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Blob Protein secondary structure prediction using optimal...

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 Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. The importance of understanding protein structure has fueled the development of protein structure databases and prediction tools. The main objective of this research is to optimize local protein str...

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Blob Prediction of Protein Residue Contact Using Support ...

Created: 2012-05-11 02:44:49

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 Prediction of protein residue contact is one of the important two-dimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or noncontacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy o...

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Blob Predicting Protein Secondary Structure with Neural N...

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 Protein secondary structure prediction has benefited largely from the improvements in machine learning techniques. A novel neural network classifier based on the Dempster-Shafer theory has been introduced by Denoeux. It demonstrated favourable performance in some artificial and real world problems when compared against methods such as Support Vector Machines and Kernel Fisher Discriminants. However, it has not been used for protein secondary structure prediction. In this work, we examin...

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Blob Pathway-Based Microarray Analysis for Defining Stati...

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 In this reiew, we have discussed about approaches in pathway based microarray analysis. Commonly, there are two approaches in pathway based analysis, Enrichment Score and Supervised Machine Learning. These pathway based approaches usually aim to statistically define significant pathways that related to phenotypes of interest. Firstly we discussed an overview of pathway based microarray analysis and its general flow processes in scoring the pathways, the methods applied in both a...

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Blob Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-05-11 02:28:43 | Last updated: 2012-05-11 02:28:44

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 An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data which is used to simulate glycolysis pathway for Satcharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testified to be better than the other estimation algorithms. The outcomes from this study promot...

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Blob Optimized Local Protein Structure with Support Vecto...

Created: 2012-05-11 02:27:24

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 Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact 1fo1sngh complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental...

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Blob One-Class Classifier to Predict Protein-Protein Inte...

Created: 2012-05-11 02:25:30

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 Protein-protein interactions are important in a wide range of biological processes. The development of drugs that target such interactions is a very active research field. Hence predicting protein-protein interactions represent an important challenge in bioinformatics research. Machine learning techniques have been applied to predict protein-protein interactions. Most of these techniques address this problem as a binary classification problem. While it is easy to get a dataset of...

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Blob Multi-Objective Optimization Using Genetic Algorithm...

Created: 2012-05-11 02:23:50

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 Microarray technology has been increasingly used in cancer research because of its potential for measuring expression levels of thousands of genes simultaneously in tissue samples. It is used to collect the information from tissue samples regarding gene expression differences that could be useful for cancer classification. However, this classification task faces many challenges due to availability of a smaller number of samples compared to the huge number of genes, and many of ...

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Blob Intelligent Hybrid Algorithm using Constraint-Based ...

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 Almost all hospital has its own nurses and still use the old fashion manual way of managing nurse scheduling in daily business. Nurse scheduling problem represents a difficult class of multi-objective optimisation problems consisting of a number of interfering objectives between the hospitals and individual nurses. Nurse scheduling consists of assignment of shifts and holidays to nurses for each day on the time horizon, taking into consideration a variety of conflicting interests or obj...

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Blob Inferring Gene Regulatory Networks from Gene Express...

Created: 2012-05-11 02:20:28

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 Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the ...

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Blob Identifying Metabolic Pathway within Microarray Gene...

Created: 2012-05-11 02:18:43 | Last updated: 2012-05-11 02:18:44

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 Extracting metabolic pathway that dictates a specific biological response is cunently one of the important disciplines in metabolic system biology research. Previous methods have successfirlly identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structw€ is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identi&ing the significant...

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Blob Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:16:43

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 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 lo...

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Blob Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:15:08 | Last updated: 2012-05-11 02:15:09

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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 lo...

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Blob Genetic Algorithms Wrapper Approach to Select Inform...

Created: 2012-05-11 02:13:44

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 Constantly improving gene expression technology offer the ability to measure the expression levels of thousand of genes in parallel. Gene expression data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. Key issues that need to be addressed under such circumstances are the efficient selection of minimum number of genes that contribute to a disease from the thousands of genes measured on microarrays that are inherently noisy. ...

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Blob Feature Selection Method Using Genetic Algorithm for...

Created: 2012-05-11 02:10:56

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Practical pattern classification problems require selection of a subset of attributes or features to represent the patterns to be classified. The feature selection process is very important which selects the informative features for used classification process. This is due to the fact that performance of the classifier is sensitive to the choice of the features used to construct the good classifier from small or high dimension data that are inherently noisy. In this paper, we propose an...

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Blob Distributed Data Partitioning Interface for Homogene...

Created: 2012-05-11 02:09:31

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The effort required to write efficient parallel programmes or to parallelize existing sequential algorithms remains daunting. This is true even for regularly structured problems. Much of the work takes place when partitioning and distributing workloads over processors in a distributed computing environment. To alleviate this task, we present a data parallel interface called Distributed Data Partitioning Interface (DDPI). Its simple interface permits parallel implementation even by users...

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Blob Bioinformatics: A Tool for Bio-Knowledge Generation ...

Created: 2012-05-11 02:08:16

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 With the knowledge-based economy (KBE) emerging as a new paradigm, it becomes important that economic actors acquire new knowledge and technology. This will stimulate innovation and contribute further growth and development. In the knowledge-based economy, it is not tangible capital but intangible and innovations that determine international competitiveness, productivity growth and worker’s status in the labour market. This intangible capital and innovation are supplied by knowled...

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Blob Automation of DNA Computing Readout Method Based on ...

Created: 2012-05-11 02:05:16

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Preaiausly, an eutornatian of a DNA mmputing rcodad methd far the HamiJtoni,an Path Prcblen (EPP) hos been implementd bosed on, LightCgcler Sgstem. In this stud,y, a simiJar reoilmrt approach is implemented baseil on DNA Engine Opticon 2 System. The rcadott appmaeh consists of tuo steps: rcnl-time arnplification in vitro us'i,ng TaqMowbaseil rcal-time PCR, followed by on in sili,co phase. The in silico phase consists of a d,ata clwtering algorithm and an information processing to e...

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Blob Applying Filter Approach and Genetic Algorithm Wrapp...

Created: 2012-05-11 02:02:28

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Gene expression microarray data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. One problem arising from this data is how to select a small subset of genes from thousands of genes and much fewer samples that are inherently noisy. This research deals with finding a small subset of informative genes from the gene expression data which maximize the classification accuracy and minimize the running time. This paper proposed a mo...

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Blob An Iterative GASVM-Based Method: Gene Selection and ...

Created: 2012-05-11 02:00:37

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Microarray technology has provided biologists with the ability to measure the expression levels of thousands of genes in a single experiment. One of the urgent issues in the use of microarray data is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult due to many irrelevant genes, noisy genes, and the availability of the small number of samples compared to the huge number of genes (hi...

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Blob An Improved Binary Particle Swarm Optimisation for G...

Created: 2012-05-11 01:58:19

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The application of microarray data for cancer classification has recently gained in popularity. The main problem that needs to be addressed is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult because of the availability of the small number of samples compared to the huge number of genes, many irrelevant genes, and noisy genes. Therefore, this paper proposes an improved binary parti...

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Blob An Image Registration Technique To Enhance PCB Inspe...

Created: 2012-05-11 01:56:19

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 is well k*atm that renl PCB inuge inipieetio* bwal 0n rclerential ap: proaches foces misalignment problems in detecting delects betwecn a template imoge arul a ilefectiae image. Hence, o reliable image registrtion techniqre is needed to aligt, these two irnages per{utly. Henre, a rqistrution trch*irye uhich inaryorvtes affme trcnsformotion anil bi-cubic interynlation has been prcposed. Etperimental rcsults haae shown that this regishation techniqte is suitoble to be employei to obt...

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Blob A Two-Step Binary Particle Swarm Optimization Approa...

Created: 2012-05-11 01:52:33 | Last updated: 2012-05-11 01:52:34

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Manipitetibn of wdre itzing, buffer sizing, and futffer inseriiai atu a few techniques that con be used to i,mproae tfune d,eloy 'in aery lorge su,le intqrction (VLSI) circuit routing- Thi* paper enhances an eri,sting approach, which is based on Particl,e Swarrn Optimization (PSO) fur sofuing rcuting poblem in VLil circaits. A hoo-step Binary Particle Swarm Optimizatdon (BPSO) apprcach, which is based on BPSO, is chosen in thi^s stuily to improue time ilelay through finding the bes...

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Blob A Study of Network-based Approach for Cancer Classif...

Created: 2012-05-11 01:49:20 | Last updated: 2012-05-11 01:49:21

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The advent of high-throughput techniques such as microarray data enabled researchers to elucidate process in a cell that fruitfully useful for pathological and medical. For such opportunities, microarray gene expression data have been explored and applied for various types of studies e.g. gene association, gene classification and construction of gene network. Unfortunately, since gene expression data naturally have a few of samples and thousands of genes, this leads to a biologi...

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Blob A Parallelizing Interface for K-Means Type Clusterin...

Created: 2012-05-11 01:46:24

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The k-means clustering algorithm and neural network batch training becomes computationally intensive when the manipulated data is large. One way to reduce the computational demand of such techniques is to execute them in a concurrent manner. Unfortunately, the effort required to implement these techniques in a distributed computing environment remains daunting. Much of the work takes place when partitioning and distributing workloads over processors in the distributed computing environm...

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Blob A New Hybrid Firefly Algorithm for Complex and Nonli...

Created: 2012-05-11 01:44:17 | Last updated: 2012-05-11 01:44:18

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 Global optimization methods play an important role to solve many real-world problems. However, the implementation of single methods is excessively preventive for high dimensionality and nonlinear problems, especially in term of the accuracy of finding best solutions and convergence speed performance. In recent years, hybrid optimization methods have shown potential achievements to overcome such challenges. In this paper, a new hybrid optimization method called Hybrid Evolutionary ...

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Blob A Hybrid of SVM and SCAD with Group-specific Tuning ...

Created: 2012-05-11 01:39:36

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The incorporation of pathway data into the microarray analysis had lead to a new era in advance understanding of biological processes. However, this advancement is limited by the two issues in quality of pathway data. First, the pathway data are usually made from the biological context free, when it comes to a specific cellular process (e.g. lung cancer development), it can be that only several genes within pathways are responsible for the corresponding cellular process. Second, p...

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