• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.22-26
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• 2002

There are a number of ways in which environmental microbiology and microbial ecology will benefit from DNA micro array technology. These include community genome arrays, SSU rDNA arrays, environmental functional gene arrays, population biology arrays, and there are clearly more different applications of microarray technology that can be applied to relevant problems in environmental microbiology. Two types of the applications, bacterial identification chip and functional gene detection chip, will be presented. For the bacterial identification chip, a new approach employing random genome fragments that eliminates the disadvantages of traditional DNA-DNA hybridization is proposed to identify and type bacteria based on genomic DNA-DNA similarity. Bacterial genomes are fragmented randomly, and representative fragments are spotted on a glass slide and then hybridized to test genomes. Resulting hybridization profiles are used in statistical procedures to identify test strains. Second, the direct binding version of microarray with a different array design and hybridization scheme is proposed to quantify target genes in environmental samples. Reference DNA was employed to normalize variations in spot size and hybridization. The approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.30 no.3C
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• pp.112-118
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• 2005

In this paper, we propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by the template matching method. The proposed measure is obtained by binary-thresholding over the whole template region and taking the number of white pixels inside the spotted area. This measure is compared with the normalized covariance in terms of the classification ability of the successfulness of the locating markers. The proposed measure is evaluated for the scanned images of HPV DNA microarrays where the marker locating is a critical issue because of the small number of spots. The targeting spots of HPV DNA chips are designed for genotyping 22 types of the human papilloma virus(HPV). The proposed measure is proven to give more discriminative response reducing the miss cases of the successful marker locating.

• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1667-1670
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• 2004

In DNA microarray produced by DNA-deposition technology, DNA-immobilization and -hybridization yields on a solid support are most important factors for its accuracy and sensitivity. We have developed a dendrimeric support using silylated aldehyde slides and polyamidoamine (PAMAM) dendrimers. An oligonucleotide array was prepared through a crosslinking between the dendrimeric support and an oligonucleotide. Both DNAimmobilization and -hybridization yields on the solid support increased by the modification with the dendrimers. The increase of the immobilization and hybridization efficiency seems to result from a threedimensional arrangement of the attached oligonucleotide. Therefore, our dendrimeric support may provide a simple and efficient solution to the preparation of DNA microarrays with high-density DNA-deposition and high hybridization efficiency.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.29-34
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• 2005

DNA microarray becomes a major tool for the investigation of global gene expression in all aspects of cancer and biomedical research. DNA microarray experiment generates enormous amounts of data and they are meaningful only in the context of a detailed description of microarrays, biomaterials, and conditions under which they were generated. MicroArray Gene Expression Data (MGED) society has established microarray standard for structured management of these diverse and large amount data. MGED MAGE-OM (MicroArray Gene Expression Object Model) is an object oriented data model, which attempts to define standard objects for gene expression. To assess the relevance of DNA microarray analysis of cancer research it is required to combine clinical and genomics data. MAGE-OM, however, does not have an appropriate structure to describe clinical information of cancer. For systematic integration of gene expression and clinical data, we create a new model, Cancer Genomics Object Model.

• BMB Reports
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• v.35 no.5
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• pp.532-535
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• 2002

To establish a method to evaluate the quality of the printed microarray and DNA fragments' immobilization. The target gene fragments that were made with the restriction display PCR (RD-PCR) technique were printed on a superamine modified glass slide, then immobilized with UV cross-linking and heat. This chip was hybridized with universal primers that were labeled with cy3-dUTP, as well as cDNA that was labeled with cy3-dCTP, as the conventional protocol. Most of the target gene fragments on the chip showed positive signals, but the negative control showed no signal, and vice versa. We established a method that enables an effective evaluation of the quality of the microarrays.

• Genomics & Informatics
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• v.1 no.1
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• pp.20-24
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• 2003

The analysis of DNA microarry data is one of the most important things for functional genomics research. The matrix representation of microarray data and its successive 'optimal' incisional hyperplanes is a useful platform for developing optimization algorithms to determine the optimal partitioning of pairwise proximity matrix representing completely connected and weighted graph. We developed Deterministic Annealing (DA) approach to determine the successive optimal binary partitioning. DA algorithm demonstrated good performance with the ability to find the 'globally optimal' binary partitions. In addition, the objects that have not been clustered at small non­zero temperature, are considered to be very sensitive to even small randomness, and can be used to estimate the reliability of the clustering.

• 한국생물공학회:학술대회논문집
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• 2003.10a
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• pp.153-158
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• 2003

The genome-wide program of gene expression during the cell division cycle response to serum free media in chinese hamster ovary(CHO) cells was characterized using cDNA microarrays. Many transcripts of genes showed variation during the cell cycle. Characterization is critical step toward understanding the basic cell cycle processes and serum-free media role in CHO cells

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2005.04a
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• pp.37-37
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• 2005

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.59-60
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• 2000

The past few years have seen a dramatic increase in gene expression data on the basis of DNA microarrays or DNA chips. Going beyond a generic view on the genome, microarray data are able to distinguish between gene populations in different tissues of the same organism and in different states of cells belonging to the same tissue. This affords a cell-wide view of the metabolic and regulatory processes under different conditions, building an effective basis for new diagnoses and therapies of diseases. In this talk we present machine learning techniques for effective mining of DNA microarray data. A brief introduction to the research field of machine learning from the computer science and artificial intelligence point of view is followed by a review of recently-developed learning algorithms applied to the analysis of DNA chip gene expression data. Emphasis is put on graphical models, such as Bayesian networks, latent variable models, and generative topographic mapping. Finally, we report on our own results of applying these learning methods to two important problems: the identification of cell cycle-regulated genes and the discovery of cancer classes by gene expression monitoring. The data sets are provided by the competition CAMDA-2000, the Critical Assessment of Techniques for Microarray Data Mining.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.04a
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• pp.47-48
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• 2003

The development of cDNA microarray has permitted the analysis of thousands of genes simultaneously. cDNA microarray has been used to analyze gene expression profiles during developmental stage in both single and multicellular organisms. Two significant factors contributing to the limitation of the development of cDNA microarray in the Bombyx mori are the shortage of accessible repositories of cDNA clones and ESTs and the relative scarcity of facilities to produce microarrays and analyze the data generated. (omitted)