• Journal of the Institute of Electronics Engineers of Korea TC
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• v.46 no.2
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• pp.27-37
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• 2009

Sensor nodes forming a sensor network have limited energy capacity such as small batteries and when these nodes are placed in a specific field, it is important to research minimizing sensor nodes' energy consumption because of difficulty in supplying additional energy for the sensor nodes. Clustering has been in the limelight as one of efficient techniques to reduce sensor nodes' energy consumption in sensor networks. However, energy saving results can vary greatly depending on election of cluster heads, the number and size of clusters and the distance among the sensor nodes. /This research has an aim to find the optimal set of clusters which can reduce sensor nodes' energy consumption. We use a Genetic Algorithm(GA), a stochastic search technique used in computing, to find optimal solutions. GA performs searching through evolution processes to find optimal clusters in terms of energy efficiency. Our results show that GA is more efficient than LEACH which is a clustering algorithm without evolution processes. The two-dimensional GA (2D-GA) proposed in this research can perform more efficient gene evolution than one-dimensional GA(1D-GA)by giving unique location information to each node existing in chromosomes. As a result, the 2D-GA can find rapidly and effectively optimal clusters to maximize lifetime of the sensor networks.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.12
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• pp.2283-2288
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• 2006

As development in technology of bioinformatics recently makes it possible to operate micro-level experiments, we can observe the expression pattern of total genome through on chip and analyze the interactions of thousands of genes at the same time. Thus, DNA microarray technology presents the new directions of understandings for complex organisms. Therefore, it is required how to analyze the enormous gene information obtained through this technology effectively. In this thesis, We used sample data of bioinformatics core group in harvard university. It designed and implemented system that evaluate accuracy after dividing in class of two using Bayesian algorithm, ASA, of feature extraction method through normalization process, reducing or removing of noise that occupy by various factor in microarray experiment. It was represented accuracy of 98.23% after Lowess normalization.

• The Journal of the Korea Contents Association
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• v.10 no.10
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• pp.102-110
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• 2010

Alternative splicing is an important process in gene expression. Alternative Splicing can lead to mutations and diseases. Most studies detect alternatively spliced genes with ESTs (Expressed Sequence Tags). However, reliance on ESTs might have some weaknesses in predicting alternative splicing. ESTs have been stored in the libraries. The EST libraries are often not clearly organized and annotated. We can pick erroneous ESTs. It is also difficult to predict whether or not alternative splicing exists for those genes where ESTs are not available. To address these issues and to improve the quality of detection and prediction for alternative splicing, we propose the One-leaf One-node Tree Algorithm that uses pre-mRNAs. It is achieved by codons, three nucleotides, as attributes for each chromosome in Arabidopsis thaliana. The proposed decision tree shows that alternative and normal splicing have different splicing patterns according to triplet nucleotides in each chromosome. Based on the patterns, alternative splicing of unlabeled genes can also be predicted.

• Genomics & Informatics
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• v.4 no.2
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• pp.71-76
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• 2006

We have investigated biological responses to radiofrequency (RF) radiation in in vitro and in vivo models. By measuring the levels of heat shock proteins as well as the activation of mitogen activated protein kinases (MAPKs), we could not detect any differences upon RF exposure. In this study, we used more sensitive method to find the molecular responses to RF radiation. Jurkat, human T-Iymphocyte cells were exposed to 1763 MHz RF radiation at an average specific absorption rate (SAR) of 10 W/kg for one hour and harvested immediately (R0) or after five hours (R5). From the profiles of 30,000 genes, we selected 68 differentially expressed genes among sham (S), R0 and R5 groups using a random-variance F-test. Especially 45 annotated genes were related to metabolism, apoptosis or transcription regulation. Based on support vector machine (SVM) algorithm, we designed prediction model using 68 genes to discriminate three groups. Our prediction model could predict the target class of 19 among 20 examples exactly (95% accuracy). From these data, we could select the 68 biomarkers to predict the RF radiation exposure with high accuracy, which might need to be validated in in vivo models.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.95-98
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• 2006

Recent proteomic studies of protein domains require high-throughput and systematic approaches. Since most experiments using protein domains, the modules of protein-protein interactions, require gene cloning, the first experimental step should be retrieving DNA sequences of domain encoding regions from databases. For a large scale proteomic research, however, it is a laborious task to extract a large number of domain sequences manually from several inter-linked databases. We present a new methodology to retrieve DNA sequences of domain encoding regions through automatic database cross-referencing. To extract protein domain encoding regions, it traverses several inter-connected database with validation process. And we applied this method to retrieve all the EGF domain encoding DNA sequences of homo sapiens. This new algorithm was implemented using Python library PAMIE, which enables to cross-reference across distinct databases automatically.

• Journal of the Korean Institute of Intelligent Systems
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• v.17 no.2
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• pp.167-172
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• 2007

Long gene sequences and their products have been studied by many methods. The use of DNA(Deoxyribonucleic acid) microarray technology has resulted in an enormous amount of data, which has been difficult to analyze using typical research methods. This paper proposes that mass data be analyzed using division clustering with the K-means clustering algorithm. To demonstrate the superiority of the proposed method, it was used to analyze the microarray data from rice DNA. The results were compared to those of the existing K-meansmethod establishing that the proposed method is more useful in spite of the effective reduction of performance time.

• Journal of information and communication convergence engineering
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• v.9 no.5
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• pp.615-618
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• 2011

Living cells generate the cell cycle or apoptosis, depending on the course will be repeated. If an error occurs during this period of life in order to maintain the cells in the peripheral cells find the error portion. These cellular functions were applied to the system to simulate the circuit. Circuit implementation of the present study was constructed the redundant structure in order to found the error quickly. Self-repairing of digital systems as an advanced form of fault-tolerance has been increasingly receiving attention according as digital systems have been more and more complex and speed-up especially for urgent systems or those working on extreme environments such as deep sea and outer space. Simulating the process of cell differentiation algorithm was confirmed by the FPGA on the counter circuit. If an error occurs on the circuit where the error was quickly locate and repair. In this paper, we propose a novel self-repair architecture for fast and robust fault-recovery that can easily apply to real, complex digital systems. These Self-Repairing Algorithms make it possible for the application digital systems to be alive even though in very noisy and extreme environments.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2000.10a
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• pp.328-332
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• 2000

As DNA sequences have been known through the Genome project the techniques for dealing with molecule-level gene information are being made researches briskly. It is also urgent to develop new computer algorithms for making databases and analyzing it efficiently considering the vastness of the information for known sequences. In this respect, this paper studies the association rule search algorithms for finding out the characteristics shown by means of the association between promoter sequences and genes, which is one of the important research areas in molecular biology. This paper treat biological data, while previous search algorithms used transaction data. So, we design a transformed association nile algorithm that covers data types and biological properties. These research results will contribute to reducing the time and the cost for biological experiments by minimizing their candidates.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.28 no.7C
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• pp.712-718
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• 2003

C.elegans are often used to study of function of gene, but it is difficult for human observation to distinguish the mutants of C.elegans. To solve this problem, the system, which can classify the mutant types automatically using the computer vision, is now studying. Tn previous work［1］, we described the preprocessing method for automated-classification system. In this paper, we introduce shape features, which can be extracted from an acquisition image. We divide the feature into two categories, which are related to size and posture of the worm, and each feature is described mathematically We validate the shape information experimentally. And we use hierarchical clustering algorithm for classification. It reveals that 4 mutants of the worm, which are used in experiment, can be classified with over 90% of success rate.

• Genomics & Informatics
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• v.3 no.3
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• pp.53-62
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• 2005

MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.