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

Created: 2012-07-24 04:51:56

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-07-24 04:49:23

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

Created: 2012-07-24 04:48:16

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 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...

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 eScience-WF-Motifs-Consolidated-DataSet

Created: 2012-07-18 23:58:01

Credits: User pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The spreadsheet containing data consolidated by domain. Also contains al the charts that are generated over consolidated data.

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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Blob eSCience-WF-Motifs-Wings-DataSet

Created: 2012-07-18 23:56:30

Credits: User pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

  The Dataset containing Wings workflows that are manually analyzed for the detection of motifs

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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