• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2003.09a
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• pp.595-598
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• 2003

A new classifier is constructed by using a generalized regression neural network (GRNN) in conjunction with a random generator (RC). The RG played a role of generating a number of sets of random spreads given a range for gaussian functions in the pattern layer, The range experimentally varied from 0.4 to 1.4. The DNA sequences consisted 4 types of promoters. The performance of classifier is examined in terms of total classification sensitivity (TCS), and individual classification sensitivity (ICS). for comparisons, another GRNN classifier was constructed and optimized in conventional way. Compared GRNN, the RG-GRNN demonstrated much improved TCS along with better ICS on average.

• 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.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.30 no.10 s.253
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• pp.1261-1268
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• 2006

This paper reports low-cost microreactor $(10{\mu}{\ell})$ biochip for the DNA PCR (polymerase chain reaction). The microbiochip $(20mm{\times}28mm)$ is a hybrid type which is composed of PDMS (polydimethylsiloxane) layer with serpentine micochannel $(360{\mu}m{\times}100{\mu}m)$ chamber and glass substrate integrated with microheater and thermal microsensor. Undesirable bubble is usually created during sample loading to PMDS-based microchip because of hydrophobic chip surface. Created bubbles interrupt stable biochemical reaction. We designed improved microreactor chamber using microfluidic simulation. The designed reactor has a coner-rounded serpentine channel architecture, which enables stable injection into hydrophobic surface using micropipette only. Reactor temperature needed to PCR reaction is controlled within ${\pm}0.5^{\circ}C$ by PID controller of LabVIEW software. It is experimentally confirmed that SRY gene PCR by the fabricated microreactor chip is performed for less than 54 min.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2003.05a
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• pp.311-312
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• 2003

Microarray를 해석하는데 있어서 방해가 되는 요인에는 여러 가지가 있을 수 있다. 예를 들면 probe DNA의 농도, spotting 시의 습도, spot의 크기 및 모양, slide blocking 과정, lab리ing technique, hybri야zation 온도와 시간 그리고 background signal 등이 그것이다(Hegde et at., 2000). 본 연구에서는 전보에서 선정된 rhabdovirus의 96개 probe로 실제 oligonucleotide chip을 만들어 spot의 모양이나 크기에 관계되는 spotting 조건을 확립하고, slide blocking과 slide washing에 따른 background signal을 낮추기 위한 과정을 도입하였다. (중략)

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2007.11a
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• pp.149-152
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• 2007

본 논문은 바이오 인포메틱스의 분야를 간단히 소개하고 기능유전체학에서 microarray 실험에 대한 통계적 방법론을 살펴보고자 한다. 또한 DNA chip 설계와 생물학적 특정에 대해 살펴보고 각 분야에서 적용되는 통계적 방법을 연구분석 해보고자 한다.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.834-834
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• 2005

• Korean Journal of Agricultural Science
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• v.30 no.1
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• pp.76-88
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• 2003

This study exploits the robot system which is necessary in gene study, bio-technology industry. As well, it can achieve the job of DNA chip manufacturing whose use rate has been increased recently. The robot consists of DNA spotting device for spotting DNA on the silylated slide and well plate, bed for fixing well-plate, washing & drying device of washing and drying the pin part of DNA spotting device, distillation-water vessel, and discharge vessel of wash water. We made the term of sticking DNA to the pin on well plate to be 15 seconds. The spot size of DNA was set to be 0.28 mm on the average by bringing the slide into contact with pin for 1 second. At this rate, if DNA is spotted in the minimum space possible of about 0.32mm, it can stick about 8,100 DNA spots on the well plate. Analyzing the procedure: Movement starts. Pin washes, dries, and smears DNA on the well plate. Spots DNA onto 12 chips takes 2 minutes and 50 seconds.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.3
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• pp.1687-1689
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• 2013

We performed a case-control study to investigate whether SNPs of CHIP might affect the development of IA in Chinese Han nationality. We believe we are the first to have screened IA patients for mutations in the CHIP gene to determine the association with these variants. The study group comprised 224 Chinese Han nationality patients with at least one intracranial aneurysm and 238 unrelated healthy Han nationality controls. Genomic DNA was isolated from blood leukocytes. The entire coding regions of CHIP were genotyped by PCR amplification and DNA sequencing. Differences in genotype and allele frequencies between patients and controls were tested by the chi-square method. Genotype and allele frequencies of the SNP rs116166850 was demonstrated to be in Hardy-Weinberg equilibrium. No significant difference in genotype or allele frequencies between case and control groups was detected at the SNP. Our data do not support the hypothesis of a major role for the CHIP gene in IA development in the Chinese Han population.

• Clinical and Experimental Pediatrics
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• v.48 no.7
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• pp.779-788
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• 2005

Purpose : Echinacea, a traditional plant medicine has been used as immune-stimulant. Recent studies have revealed that extract of Echinacea has immunostimulatory effects on human blood mononuclear cells. This study was designed for the purpose of screening the genes associated with immunologic effects of Echinacea on monocytes and dendritic cells using a cDNA microarray chip. Methods : $CD14^+$ monocyte cells were cultured for one day with Echinacea extract(final concentration : $50{\mu}g/mL$) in experiment 1, but were cultured without Echinacea in experiment 2. The gene expression of these cultured monocytes was analyzed using the cDNA microarray chip. Dendritic cells produced from $CD14^+$ monocyte were cultured for five days with GM-CSF and IL-4, and then cultured for one day with Echinacea in experiment 3, but were done without Echinacea in experiment 4. Results : In experiments 1 and 2, there were 17 significantly expressed genes with average expression ratios above 2.5, including interferon gamma-inducible protein 30(IFI 30), CDC(cell-division-cylcle)-like kinase 2(CLK 2), syndecan binding protein(syntenin), superoxide dismutase 2, etc. In experiments 3 and 4, there were 24 gene, with significantly expressed genes were 24 genes, which were insulin-like growth factor 2(somatomedin A), methyl-CpG binding domain protein 3, IFI 30, small inducible cytokine subfamily A, member 22, etc. The genes encoding CD44, IFI 30, mannose receptor C type 1(MRC 1), chemokine receptor 7(CCR 7), CLK 2, syntenin and cytochrome C oxidase subunit VIII were significantly expressed in both monocytes and dendritic cells cultured with Echinacea. Conclusion : This study employed a cDNA microarray chip to elicit the immune-associated gene profile; the expression was enhanced by Echinacea in CD14+ monocytes and dendritic cells. Thus we laid the basis for the quantitative and functional analysis of genes induced by Echinacea in monocytes and monocyte-derived dendritic cells.