• 제어로봇시스템학회:학술대회논문집
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• 2005.06a
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• pp.838-841
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• 2005

DNA Chip is able to show DNA-Data that includes diseases of sample to User by using complementary characters of DNA. So this paper studied Neural Network algorithm for Image data processing of DNA-chip. DNA chip outputs image data of colors and intensities of lights when some sample DNA is putted on DNA-chip, and we can classify pattern of these image data on user pc environment through artificial neural network and some of image processing algorithms. Ultimate aim is developing of pattern classifying algorithm, simulating this algorithm and so getting information of one's diseases through applying this algorithm. Namely, this paper study artificial neural network algorithm for classifying pattern of image data that is obtained from DNA-chip. And, by using histogram, gradient edge, ANN and learning algorithm, we can analyze and classifying pattern of this DNA-chip image data. so we are able to monitor, and simulating this algorithm.

• Journal of Information Processing Systems
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• v.2 no.3 s.4
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• pp.189-193
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• 2006

In this study we propose an automatic reading system for diagnostic DNA chips. We define a general specification for an automatic reading system and propose a possible implementation method. The proposed system performs the whole reading process automatically without any user intervention, covering image acquisition, image analysis, and report generation. We applied the system for the automatic report generation of a commercialized DNA chip for cervical cancer detection. The fluorescence image of the hybridization result was acquired with a $GenePix^{TM}$ scanner using its library running in HTML pages. The processing of the acquired image and the report generation were executed by a component object module programmed with Microsoft Visual C++ 6.0. To generate the report document, we made an HWP 2002 document template with marker strings that were supposed to be searched and replaced with the corresponding information such as patient information and diagnosis results. The proposed system generates the report document by reading the template and changing the marker strings with the resultant contents. The system is expected to facilitate the usage of a diagnostic DNA chip for mass screening by the automation of a conventional manual reading process, shortening its processing time, and quantifying the reading criteria.

• Journal of the Korean Institute of Intelligent Systems
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• v.16 no.5
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• pp.556-561
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• 2006

It is very important to classify the DNA Chip image pattern in order to acquire useful information about genetic disease of people. In this paper, we developed the novel pattern classification method of DNA Chip image using MLP based back-propagation and Self organizing Map learning algorithm. And then we compared and analyzed these classified pattern results. Also we carried out experiment in the MV2440 board using CPU Cote for S3C2440(ARM 920T) and PC environment, and displayed its results in order to give the genetic information to user mote easily in various environment.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.28 no.8C
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• pp.803-810
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• 2003

This paper addresses an image processing technique for the human papillomavirus (HPV) DNA chip to discriminate whether the probes are hybridized with the target DNA. HPV DNA chip is designed to determine HPV gene-types by using DNA probes for 22 HPV types. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker- dot locations with a small variation attributable to the accuracy of the dotter and the scanner. The probes are quadruplicated to enhance diagnostic fidelity. frier knowledge including the marker relative distance and the replication information of probes is integrated into the template matching technique with normalized covariance measure. It was demonstrated that the employment of both of the prior knowledges can be accomplished by simply averaging the template matching measures over the positions of the markers and probes. The resulting proposed scheme yields stable marker locating and probe classification.

• Journal of KIISE:Computer Systems and Theory
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• v.29 no.7
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• pp.411-421
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• 2002

In this Paper we propose a new Image analysis algorithm for microarray processing and a method to locate the position of the grid cell using the topology of the grid spots. Microarray is a device which enables a parallel experiment of 10 to 100 thousands of test genes in order to measure the gene expression. Because of the huge data obtained by a experiment automated image analysis is needed. The final output of this microarray experiment is a set of 16-bit gray level image files which consist of grid-structured spots. In this paper we propose one algorithm which located the address of spots (spot indices) using graph structure from image data and a method which determines the precise location and shape of each spot by measuring the inclination of grid structure. Several experiments are given from real data sets.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.45-52
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• 2000

Genomic approach produces massive amount of data within a short time period, New high-throughput automatic sequencers can generate over a million nucleotide sequence information overnight. A typical DNA chip experiment produces tens of thousands expression information, not to mention the tens of megabyte image files, These data must be handled automatically by computer and stored in electronic database, Thus there is a need for systematic approach of data collection, processing, and analysis. DNA sequence information is translated into amino acid sequence and is analyzed for key motif related to its biological and/or biochemical function. Functional genomics will play a significant role in identifying novel drug targets and diagnostic markers for serious diseases. As an enabling technology for functional genomics, bioinformatics is in great need worldwide, In Korea, a new functional genomics project has been recently launched and it focuses on identi☞ing genes associated with cancers prevalent in Korea, namely gastric and hepatic cancers, This involves gene discovery by high throughput sequencing of cancer cDNA libraries, gene expression profiling by DNA microarray and proteomics, and SNP profiling in Korea patient population, Our bioinformatics team will support all these activities by collecting, processing and analyzing these data.

• 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.

• Proceedings of the Korean Information Science Society Conference
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• 2000.10b
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• pp.392-394
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• 2000

본 논문에서는 DNA칩 이미지 처리시스템을 위한 완전 그리딩 알고리즘을 제안한다. DNA칩 이미지를 분석하여 처리할 수 있는 많은 DNA칩 분석 시스템이 있다. 하지만 이전의 시스템들은 정확한 이미지 처리를 통한 올바른 유전자 발현정보를 얻기 위해서 많은 사용자의 개입이 필요한 단점이 있었다. 본 논문에서는 사용자의 개입이 없는 정확한 자동 이미지 처리를 위해서, $\varepsilon$-그래프 모델링 기법을 제시하고, MBR, Mass, Geometry 등 세가지 종류의 반점(spot) 중심을 이용한 완전 그리딩 알고리즘을 제안한다. 제시된 이미지 처리 기술은 완전한 자동 DNA칩 분석 시스템으로, 사용자의 개입없이도 정확한 DNA칩 위치 정보를 얻을 수 있다.

• Journal of KIISE:Computer Systems and Theory
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• v.31 no.9
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• pp.514-526
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• 2004

Microarray is a new technique for gene expression experiment, which has gained biologist's attention for recent years. This technology enables us to obtain hundreds and thousands of expression of gene or genotype at once using microarray Since it requires manual work to analyze patterns of gene expression, we want to develop an effective and automated tools to analyze microarray image. However it is difficult to analyze DNA chip images automatically due to several problems such as the variation of spot position, the irregularity of spot shape and size, and sample contamination. Especially, one of the most difficult problems in microarray analysis is the block and spot addressing, which is performed by manual or semi automated work in all the commercial tools. In this paper we propose a new algorithm to address the position of spot and block using a new concept of regular structure grid searching. In our algorithm, first we construct maximal I-regular sequences from the set of input points. Secondly we calculate the rotational angle and unit distance. Finally, we construct I-regularity graph by allowing pseudo points and then we compute the spot/block address using this graph. Experiment results showed that our algorithm is highly robust and reliable. Supplement information is available on http://jade.cs.pusan.ac.kr/~autogrid.