• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.225-235
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• 2011

The change of microbial communities during cyanobacterial bloom was comparatively analyzed by 16S rDNA PCR-DGGE in Daechung Reservoir during 2003~2005. Morphological analysis showed that Cyanophyceae dominated algal community in the bloom. Dominant cyanobacteria were Microcystis, Planktothrix (Oscillatoria), Phormidium and Anabaena. We used 16S rDNA-denaturing gradient gel electrophoresis (DGGE) profiles and phylogenetic affiliations of the DGGE bands to analyze the community structure and diversity of the predominant microbial community. The DGGE band patterns demonstrated that the most frequent bands were identified as Microcystis during the monitoring periods, Planktothrix also dominated on September 2003 and 2004, whereas Anabaena was showed a peak on September 2005 and Aphanizomenon on August 2003. DGGE and phylogenetic analysis provided us new information that could not be obtained by traditional, morphological analysis. The relationship between cyanobacteria and other aquatic bacteria can be traced and their genetic diversity also identified in detail.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2005.11a
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• pp.381-384
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• 2005

현존하는 정보처리 시스템 중에서 가장 뛰어난 성능을 지니고 있는 것은 인간의 두뇌라고 할 수 있다. 두뇌의 정보처리 메커니즘을 보다 정확하게 구현할 수 있는 시스템은 입력에 대한 정확한 인지 능력, 상황 판단 능력, 학습 및 추론 능력, 출력의 결정 능력 등의 성능 구현은 물론이며, 감정과 비교될 수 있는 시스템의 상태를 평가하여 판단 및 결정에 적용함으로써 매우 뛰어난 지능형 시스템이 쥘 수 있다. 이러한 뇌 정보처리 시스템의 구현에 앞서 본 논문에서는 생물학적인 대뇌 피질의 구조를 살피고 정보의 처리 영역을 고찰하고 정보의 흐름을 소개하였으며 이를 바탕으로 뇌 정보처리 메커니즘을 공학적인 측면에서 해석해 보았다. 특히, 뇌 영역의 기능 및 구조적인 특징, 정보의 처리과정 등을 공학적으로 해석하였으며 이는 뇌의 기능을 모방한 공학적인 모델을 구현하는데 있어서 기초가 될 것이다.

• Korean Journal of Environmental Biology
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• v.32 no.4
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• pp.397-402
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• 2014

In June 1992, Convention on Biological Diversity (CBD) was concluded by 158 countries in Rio de Janeiro. And now, 194 member nations are participating in discussions for their own profit. Recently, Nagoya Protocol regarding Access to genetic resources and Benefit-Sharing (ABS) was approved and took effect from October $12^{th}$, 2014. Thus, it is important to understand the impact of CBD and ABS functioning on researchers studying marine biodiversity. Until now, in the previous Conference of the parties to the Convention on Biological Diversity, the interest towards researching marine and marine living resources was relatively low, and accordingly, the discussions regarding marine and marine living resources were delayed. However, in the $12^{th}$ Pyeongchang Conference of the Parties to the Convention on Biological Diversity, the arguments concerning Ecologically or Biologically Significant marine Areas (EBSA) and the other marine related issues were discussed. Although, South Korea has not yet officially joined Nagoya Protocol, however the consultations in regard to Prior and Informed Consent (PIC), Mutually Agreed Terms (MAT) and Global Multilateral Benefit-Sharing Mechanism (GMBSM) were discussed. We belive that as a possessing nation of biological resources, South Korean government authorities should revise their management systems protocol and regulations concerning domestic biological resources, in order to strengthen the information system and help academia and industry to utilize the biological resources abroad easily and effectively.

• The KIPS Transactions:PartB
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• v.15B no.4
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• pp.375-382
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• 2008

A protein's subcellular localization is considered an essential part of the description of its associated biomolecular phenomena. As the volume of biomolecular reports has increased, there has been a great deal of research on text mining to detect protein subcellular localization information in documents. It has been argued that linguistic information, especially syntactic information, is useful for identifying the subcellular localizations of proteins of interest. However, previous systems for detecting protein subcellular localization information used only shallow syntactic parsers, and showed poor performance. Thus, there remains a need to use a full syntactic parser and to apply deep linguistic knowledge to the analysis of text for protein subcellular localization information. In addition, we have attempted to use semantic information from the WordNet thesaurus. To improve performance in detecting protein subcellular localization information, this paper proposes a three-step method based on a full syntactic dependency parser and WordNet thesaurus. In the first step, we constructed syntactic dependency paths from each protein to its location candidate, and then converted the syntactic dependency paths into dependency trees. In the second step, we retrieved root information of the syntactic dependency trees. In the final step, we extracted syn-semantic patterns of protein subtrees and location subtrees. From the root and subtree nodes, we extracted syntactic category and syntactic direction as syntactic information, and synset offset of the WordNet thesaurus as semantic information. According to the root information and syn-semantic patterns of subtrees from the training data, we extracted (protein, localization) pairs from the test sentences. Even with no biomolecular knowledge, our method showed reasonable performance in experimental results using Medline abstract data. Our proposed method gave an F-measure of 74.53% for training data and 58.90% for test data, significantly outperforming previous methods, by 12-25%.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.87-96
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• 2001

삼성종합기술원에서는 인간의 genomic DNA의 이상을 발견하여 이와 연관된 질병을 진단하는 DNA chip을 개발하고 있다. 이를 위하여 특정한 염기서열의 변화에 따라 민감하게 hybridization strength가 변화하는 oligomer를 선택해야 한다. 따라서, specificity가 가장 큰 probe를 골라내야 한다. 여기에는 열역학적인 고려와 여러가지 물리화학적인 approximation이 사용되며, DNA chip 생산 공정에 의존하는 요소도 포함되어 있다 모든 생산용 data와 결과의 분석은 database를 기반으로 이루어지며, 자동화된 통계적 분석법과 최적화 방법이 함께 사용된다.

• Korean Journal of Environmental Biology
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• v.22 no.3
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• pp.369-375
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• 2004

This experiment was studied to obtain basic environmental effects and biological information on the early growth of larval mitten crab (Eriocheir sinensis). Mitten crabs were maintained for each larval stage with solutions containing 0.1, 0.2, and 0.3 ppm of cadmium (Cd) and mercury (Hg). The relationship between survival rate of mitten crabs and metal content in the growth chamber showed a positive correlations. However, it showed a significant difference in the 96 $hr- LC^{50}$ values of Cd and Hg for the E. sinensis larvae from the first zoea larva to juvenile. Hg was more toxic to E. sinensis larval than Cd. When Cd and Hg are released into the water, they enter E. sinensis larval and are biological magnified. These results of survival rate and bioaccumulation are very important when considering the survival of the mitten crab.

• Korean Journal of Ecology and Environment
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• v.55 no.1
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• pp.60-75
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• 2022

The Bayesian algorithm model is a model algorithm that calculates probabilities based on input data and is mainly used for complex disasters, water quality management, the ecological structure between living things or living-non-living factors. In this study, we analyzed the main factors affected Korean Estuary Trophic Diatom Index (KETDI) change based on the Bayesian network analysis using the diatom community and physicochemical factors in the domestic estuarine aquatic ecosystem. For Bayesian analysis, estuarine diatom habitat data and estuarine aquatic diatom health (2008~2019) data were used. Data were classified into habitat, physical, chemical, and biological factors. Each data was input to the Bayesian network model (GeNIE model) and performed estuary aquatic network analysis along with the nationwide and each coast. From 2008 to 2019, a total of 625 taxa of diatoms were identified, consisting of 2 orders, 5 suborders, 18 families, 141 genera, 595 species, 29 varieties, and 1 species. Nitzschia inconspicua had the highest cumulative cell density, followed by Nitzschia palea, Pseudostaurosira elliptica and Achnanthidium minutissimum. As a result of analyzing the ecological network of diatom health assessment in the estuary ecosystem using the Bayesian network model, the biological factor was the most sensitive factor influencing the health assessment score was. In contrast, the habitat and physicochemical factors had relatively low sensitivity. The most sensitive taxa of diatoms to the assessment of estuarine aquatic health were Nitzschia inconspicua, N. fonticola, Achnanthes convergens, and Pseudostaurosira elliptica. In addition, the ratio of industrial area and cattle shed near the habitat was sensitively linked to the health assessment. The major taxa sensitive to diatom health evaluation differed according to coast. Bayesian network analysis was useful to identify major variables including diatom taxa affecting aquatic health even in complex ecological structures such as estuary ecosystems. In addition, it is possible to identify the restoration target accurately when restoring the consequently damaged estuary aquatic ecosystem.

• Journal of the Korean Society for information Management
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• v.31 no.1
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• pp.231-250
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• 2014

Due to the recent development of Information and Communication Technologies (ICT), the amount of research publications has increased exponentially. In response to this rapid growth, the demand of automated text processing methods has risen to deal with massive amount of text data. Biomedical text mining discovering hidden biological meanings and treatments from biomedical literatures becomes a pivotal methodology and it helps medical disciplines reduce the time and cost. Many researchers have conducted literature-based discovery studies to generate new hypotheses. However, existing approaches either require intensive manual process of during the procedures or a semi-automatic procedure to find and select biomedical entities. In addition, they had limitations of showing one dimension that is, the cause-and-effect relationship between two concepts. Thus;this study proposed a novel approach to discover various relationships among source and target concepts and their intermediate concepts by expanding intermediate concepts to multi-levels. This study provided distinct perspectives for literature-based discovery by not only discovering the meaningful relationship among concepts in biomedical literature through graph-based path interference but also being able to generate feasible new hypotheses.

• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.253-255
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• 2004

인간(human)에게 나타나는 다양성(variation)은 인체의 유전체(genome) 안에서 발생된 SNP(Single Nucleotide Polymorphism)에 의해 나타난다고 알려져 있다. 유전체내의 SNP과 다양성에 대한 연관 연구(Associate study)를 할 때에 약 30여 억 개로 추정되는 염기서열(DNA sequence)물 모두 분석한다면 많은 비용과 시간을 필요로 할 것이다. 이런 비용과 시간을 줄이기 위친 적은 수의 대표 SNP(=tagSNP)을 찾는 연구가 현재 진행 중이다. 우리는 LD계수｜D;｜을 block 분할에 이용하여 생물학적인 의미를 부여한 후, 전산적인 최적해를 찾는 접근을 이용했다. 또한, 기존 연구에서는 large-scale data에 대한 처리가 불가능해서 chromosome의 일부분의 데이터에 대해서안 분석이 시도되었다. 더욱 광범위한 분석을 위해서 chromosome 단위의 처리가 필요하다. 우리는 chromosome단위의 SNP data를 한 번에 처리가 가능한 시스템인 MarSel를 구현하였다

• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.259-261
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• 2004

최근 이슈가 되고 있는 시스템 생물학(Systems Biology)은 생물학적인 이론과 컴퓨터의 계산적인 모델링 그리고 실험의 상호 의존적인 통합으로써 특징 지워진다. 그 중 컴퓨터의 계산적인 모델링에 대한 연구가 무엇보다 중요한 비중을 차지하고 있다. 하지만 계산적인 모델링에서 여러 자원을 통합하기 위한 공통의 기반 구조나 표준에 대한 연구는 미흡한 실정이다. 이러한 문제점을 해결하기 위해 KML 기반의 형식을 갖춘 SBML(Systems Biology Markup Language)이 시스템 생물학의 표준으로 개발되어 연구 중에 있다. 현재 시스템 생물학 분야에서 개발중인 시뮬레이션과 데이터 분석을 위한 다양한 응용 어플리케이션이 이미 SBML 문서를 지원하고 있다. 본 연구에서는 시스템 생물학 분야에서 SBML 표준에 대한 중요성을 인식하여, 객체지향 바이오 데이터베이스로부터 질의 결과를 SBML 문서로 변환하고, 반대로 외부의 SBML 문서를 객체지향 데이터베이스에 저장하는 변환기를 제안하며, 데이터를 검색하고 저장하는데 발생하는 중복이나 동의어 관계의 모호성을 줄이고 정확성을 높이기 위한 방안으로 온톨로지 기법을 적용한다.