• Genomics & Informatics
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• v.3 no.2
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• pp.52-54
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• 2005

Visualization of the homology information is an important method to analyze the evolutionary and functional meanings of genes. With a database containing model genomes of Homo sapiens, Mus muculus, and Rattus norvegicus, we constructed a web­based comparative analysis tool, BioCovi, to visualize the homology information of mammalian sequences on a very large scale. The user interface has several features: it marks regions whose identity is greater than that specified, it shows or hides gaps from the result of global sequence alignment, and it inverts the graph when total identity is higher than the threshold specified.

• Genomics & Informatics
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• v.3 no.2
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• pp.47-51
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• 2005

Molecular mechanisms of biological processes are typically represented as 'pathways' that have a graph­analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and the semantics is embedded implicitly. The kinds of interactions that connect biological entities are likewise diverse. Consequently, how to model or process pathway data is not a trivial issue. In this review article, we give an overview of the challenges in pathway database development by taking the INOH project as an example.

• Journal of the Institute of Electronics Engineers of Korea SC
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• v.45 no.4
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• pp.42-50
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• 2008

The real-time bio-signal monitoring system based on the ZigBee and SIP/RTP has proposed and implemented for telemedicine but that has some problems at the stabilities to transmit bio-signal from the sensors to the other sides. In this paper, we designed and implemented a real-time bio-signal monitoring system that is focused on the reliability and efficiency for transmitting bio-signal at real-time. We designed the system to have enhanced architecture and performance in the ubiquitous sensor network, SIP/RTP real-time transmission and management of the database. The Bluetooth network is combined with ZigBee network to distribute traffic of the ECG and the other bio-signal. The modified and multiplied RTP session is used to ensure real-time transmission of ECG, other bio-signals and speech information on the internet. The modified ECG compression method based on DWLT and MSVQ is used to reduce data rate for storing ECG to the database. Finally we implemented a system that has improved performance for transmitting bio-signal from the sensors to the monitoring console and database. This implemented system makes possible to make various applications to serve U-health care services.

• Genomics & Informatics
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• v.6 no.3
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• pp.142-146
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• 2008

In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

• Proceedings of the PSK Conference
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• 2001.04a
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• pp.78-79
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• 2001

• Proceedings of the Korean Society of Computer Information Conference
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• 2012.07a
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• pp.409-410
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• 2012

본 논문에서는 스마트케어 서비스를 위해, Android 운영체제를 기반으로 하는 Device에서 ADK를 이용해 혈압계를 제어하는 방법을 제안한다. 이 방법은 소프트웨어와 하드웨어를 결합한 kit인 ADK를 사용하여 Hardware를 잘 모르는 사람들도 Android에서 Hardware의 GPIO에 좀 더 쉽게 접근하고 제어할 수 있어 보다 다양한 기능을 구현할 수 있다. 또한 이 방법으로 얻은 혈압계 데이터를 Database에 저장하여 데이터통신망을 통해 전문의에게 Feedback을 받음으로써 굳이 병원을 방문하지 않더라도 개인의 건강을 보다 편리하게 관리할 수 있어 한 단계 수준 높은 진단을 받을 수 있다.

• Genomics & Informatics
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• v.7 no.1
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• pp.49-51
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• 2009

Although abundant biology data have been accumulated in public biology databases, such as GenBank and PIR, few easy-interface services are provided for users to access or update them. We have developed a system, named BioStore, that is composed of several programs to aid users to not only access public data but also share their own data easily. The service can be used for maintaining a local database as a repository of raw data files of several public databases and distributing the data files to other users. Currently, BioStore manipulates major bio-databases and will expand to include more databases and more useful interfaces.

• Genomics & Informatics
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• v.16 no.4
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• pp.24.1-24.4
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• 2018

Taxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases-Greengenes, Silva, and EzBioCloud-and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We show that EzBioCloud performs well compared with other existing databases.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.245-250
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• 2003

There are currently about 6000 bacterial species with validly published names, but scientists assume that these may be less than 1% of bacterial species present on the earth. Microbial resource is one of the most important bioresources in bioinderstry and provides us with high economic values. To find missing ones, the studies of metagenome, metabolome, and proteome about microbes have started recently in developed countries. We construct the information system that integrates information on microbial genome resources and manages the information to support efficient research of microbial genome application, and name this system 'Bio-Meta Information System (Bio-MIS)'. Bio-MIS consists of integrated microbial genome resources database, microbial genome resources input system, integrated microbial genome resources search engine, microbial resources on-line distribution system, portal service and management via internet. In the future, we will include public database connection and implement useful bioinformatics software for analyzing microbial genome resources. The web-site is accessible at http://biomis.probionic.com

• Journal of the Korea Institute of Information and Communication Engineering
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• v.9 no.8
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• pp.1828-1833
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• 2005

The Integration of biological databases is critically important because of the interconnectedness of biological research. But it's not easy to integrate these databases for the different formats and designers in heterogeneous environments. So initial design is indispensable to integrate heterogeneous databases. In this paper, after we performed conceptual modeling on a popular nucleotide database, GenBank and a protein database, Swiss-Prot and integrated them by considering cross-reference. we also propose the integration system architecture called Bio-Gateway System, which can help users query closely linked information between two biological databases within one system differently from existing systems as well as query easily on condition that user knows fine condition for less effort.