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Blob Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-07-24 04:46:49

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-07-24 04:45:28

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-07-24 04:44:00

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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 ...

Created: 2012-07-24 04:19:46

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-07-04 06:59:13

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-07-04 06:55:38

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-05-11 02:34:20

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-05-11 02:33:00

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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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