• KIEE International Transactions on Electrophysics and Applications
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• 제11C권3호
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• pp.85-90
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• 2001

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and other application area. So, the improvement of DNA detection system is very important for the determination of this hybridization reaction. In this study, we report the characterization of the probe and target oligonucleotide hybridization reaction using the evanescent field microscopy. First, we have fabricated DNA chip microarray. The particles which were immobilized oligonucleotides were arranged by the random fluidic self-assembly on the pattern chips, using hydrophobic interaction. Second, we have detected DNA hybridization reaction using evanescent field microscopy. The 5'-biotinylated probe oligonucleotides were immobilized on the surface of DNA chip microarray and the hybridization reaction with the Rhodamine conjugated target oligonucleotide was excited fluorescence generated on the evanescent field microscopy. In the foundation of this result, we could be employed as the basis of a probe olidonucleotide, capable of detecting the target oligonucleotide and monitoring it in a large analyte concentration range and various mismatching condition.

• 한국환경독성학회:학술대회논문집
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• 한국환경독성학회 2000년도 추계심포지움 및 학술발표회:바이오모니터링 기법을 이용한 환경위해성 평가
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• pp.54-54
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• 2000

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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• pp.745-746
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• 2001

Transcriptome analysis was performed for the production of recombinant protein in E. coli using DNA microarray containing 2,850 genes including all functionally known and putative ones. Changes in transcriptome were analyzed qualitatively and quantitatively to provide their physiological and metabolic meanings.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2003년도 춘계 학술발표회 논문집
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• pp.177-182
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• 2003

• Journal of Microbiology and Biotechnology
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• 제16권11호
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• pp.1773-1777
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• 2006

We evaluated the usefulness of DNA microarray as a comparative genomics tool, and tested the validity of the cutoff values for defining absent genes in test genomes. Three genome-sequenced E. coli strains (K-12, EDL933, and CFT073) were subjected to comparative genomic hybridization with DNA microarrays covering almost all ORFs of the reference strain K-12, and the microarray results were compared with the results obtained from in silico analyses of genome sequences. For defining the K-12 ORFs absent in test genomes (reference strain-specific ORFs), we applied and evaluated the cutoff level of -1. The average sequence similarity between ORFs, to which corresponding spots showed a log-ratio of>-1, was $96.9{\pm}4.8$. The numbers of spots showing a log-ratio of <-1 (P<0.05, t-test) were 90 (2.5%) and 417 (10.6%) for the EDL933 genome and the CFT073 genome, respectively. Frequency of false negatives (FN) was ca. 0.2, and the cutoff level of -1.3 was required to achieve the FN of 0.1. The average sequence similarity of the false negative ORFs was $77.8{\pm}14.8$, indicating that the majority of the false negatives were caused by highly divergent genes. We concluded that the microarray is useful for identifying missing or divergent ORFs in closely related prokaryotic genomes.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.71-76
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• 2006

Comparative genomic hybridization (CGH) is a technique for studying chromosomal changes in cancer. As cancerous cells multiply, they can undergo dramatic chromosomal changes, including chromosome loss, duplication, and the translocation of DNA from one chromosome to another. Chromosome aberrations have previously been detected using optical imaging of whole chromosomes, a technique with limited sensitivity, resolution, quantification, and throughput. Efforts in recent years to use microarrays to overcome these limitations have been hampered by inadequate sensitivity, specificity and flexibility of the microarray systems. The oligonucleotide CGH microarray system overcomes several scientific hurdles that have impeded comparative genomic studies of cancer. This new system can reliably detect single copy deletions in chromosomes. The system includes a whole human genome microarray, reagents for sample preparation, an optimized microarray processing protocol, and software for data analysis and visualization. In this study, we determined the sensitivity, accuracy and reproducibility of the new system. Using this assay, we find that the performance of the complete system was maintained over a range of input genomic DNA from 5 ug down to 0.15 ug.

• 대한전기학회논문지:전기물성ㆍ응용부문C
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• 제53권5호
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• pp.286-292
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• 2004

In this study, an integrated microelectrode array was fabricated on glass slide using microfabrication technology. Probe DNAs consisting of mercaptohexyl moiety at their 5-end were spotted on the gold electrode using micropipette or DNA arrayer utilizing the affinity between gold and sulfur. Cyclic voltammetry in 5mM ferricyanide/ferrocyanide solution at 100 ㎷/s confirmed the immobilization of probe DNA on the gold electrodes. When several DNAs were detected electrochemically, there was a difference between target DNA and control DNA in the anodic peak current values. It was derived from specific binding of Hoechst 33258 to the double stranded DNA due to hybridization of target DNA. It suggested that this DNA chip could recognize the sequence specific genes. It suggested that multichannel electrochemical DNA microarray is useful to develop a portable device for clinical gene diagnostic System.

• 한국통신학회논문지
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• 제30권3C호
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• pp.112-118
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• 2005

본 논문에서는 교잡반응된 스팟을 템플릿 정합법으로 감지하는 온-오프 형태의 DNA 마이크로어레이 영상의 자동분석을 위한 새로운 비선형 정합도를 제안한다. HPV DNA 칩의 목표 스팟은 인유두종 바이러스(HPV)의 종을 알아내기 위해서 설계된다. 제안하는 척도는 전체 템플릿 영역을 이진 문턱값으로 양극화하여 스팟 영역 내의 밝은 화소의 개수를 취해서 얻는다. 이 척도를 추정된 마커 위치의 정확도 관점에서 평가하여 정규화된 상관도보다 우수함을 보인다.

• 대한전기학회논문지:전기물성ㆍ응용부문C
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• 제51권7호
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• pp.328-334
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• 2002

The DNA chips are devices associating the specific recognition properties of two DNA single strands through hybridization process with the performances of the microtechnology. In the literature, the "Gene chip" or "DNA chip" terminology is employed in a wide way and includes macroarrays and microarrays. Standard definitions are not yet clearly exposed. Generally, the difference between macro and microarray concerns the number of active areas and their size, Macroarrays correspond to devices containing some tens spots of 500$\mu$m or larger in diameter. microarrays concern devices containing thousnads spots of size less than 500$\mu$m. The key technical parameters for evaluating microarray-manufacturing technologies include microarray density and design, biochemical composition and versatility, repreducibility, throughput, quality, cost and ease of prototyping. Here we report, a new method in which minute particles are arranged in a random fashion on a chip pattern using random fluidic self-assembly (RFSA) method by hydrophobic interaction. We intend to improve the stability of the particles at the time of arrangement by establishing a wall on the chip pattern, besides distinction of an individual particle is enabled by giving a tag structure. This study demonstrates the fabrication of a chip pattern, immobilization of DNA to the particles and arrangement of the minute particle groups on the chip pattern by hydrophobic interaction.ophobic interaction.

• 응용통계연구
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• 제24권5호
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• pp.847-859
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• 2011

cDNA microarray-based comparative genomic hybridization(CGH) data includes low-intensity spots and thus a statistical strategy is needed to detect subtle differences between different cancer classes. In this study, genes displaying a high frequency of alteration in one of the different classes were selected among the pre-selected genes that show relatively large variations between genes compared to total variations. Utilizing copy-number changes of the selected genes, this study suggests a statistical approach to predict patients' classes with increased performance by pre-classifying patients with similar genetic alteration scores. Two-stage logistic regression model(TLRM) was suggested to pre-classify homogeneous patients and predict patients' classes for cancer prediction; a decision tree(DT) was combined with logistic regression on the set of informative genes. TLRM was constructed in cDNA microarray-based CGH data from the Cancer Metastasis Research Center(CMRC) at Yonsei University; it predicted the patients' clinical diagnoses with perfect matches (except for one patient among the high-risk and low-risk classified patients where the performance of predictions is critical due to the high sensitivity and specificity requirements for clinical treatments. Accuracy validated by leave-one-out cross-validation(LOOCV) was 83.3% while other classification methods of CART and DT performed as comparisons showed worse performances than TLRM.