• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.3-3
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• 2003

With biomedical literature expanding so rapidly, there is an urgent need to discover and organize knowledge extracted from texts. Although factual databases contain crucial information the overwhelming amount of new knowledge remains in textual form (e.g. MEDLINE). In addition, new terms are constantly coined as the relationships linking new genes, drugs, proteins etc. As the size of biomedical literature is expanding, more systems are applying a variety of methods to automate the process of knowledge acquisition and management. In my talk, I focus on the project, GENIA, of our group at the University of Tokyo, the objective of which is to construct an information extraction system of protein - protein interaction from abstracts of MEDLINE. The talk includes (1) Techniques we use fDr named entity recognition (1-a) SOHMM (Self-organized HMM) (1-b) Maximum Entropy Model (1-c) Lexicon-based Recognizer (2) Treatment of term variants and acronym finders (3) Event extraction using a full parser (4) Linguistic resources for text mining (GENIA corpus) (4-a) Semantic Tags (4-b) Structural Annotations (4-c) Co-reference tags (4-d) GENIA ontology I will also talk about possible extension of our work that links the findings of molecular biology with clinical findings, and claim that textual based or conceptual based biology would be a viable alternative to system biology that tends to emphasize the role of simulation models in bioinformatics.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2005년도 추계 학술대회논문집
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• pp.11-19
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• 2005

First, methods of numerical analysis of gas-particle flows is classified into micro, meso and macro scale approaches based on the concept of multi-scale mechanics. Next, the explanation moves on to discrete particle simulation where motion of individual particles is calculated numerically using the Newtonian equations of motion. The author focuses on the cases where particle-to-particle interaction has significant effects on the phenomena. Concerning the particle-to-particle interaction, two cases are considered: the one is collision-dominated flows and the other is the contact-dominated flows. To treat this interaction mathematically, techniques named DEM(Distinct Element Method) or DSMC (Direct Simulation Monte Carlo) have been developed DEM, which has been developed in the field of soil mechanics, is useful for the contact -dominated flows and DSMC method, developed in molecular gas flows, is for the collision-dominated flows. Combining DEM or DSMC with CFD (computer fluid dynamics), the discrete particle simulation becomes a more practical tool for industrial flows because not only the particle-particle interaction but particle-fluid interaction can be handled. As examples of simulations, various results are shown, such as hopper flows, particle segregation phenomena, particle mixing in a rotating drum, dense phase pneumatic conveying, spouted bed, dense phase fluidized bed, fast circulating fluidized bed and so on.

• Journal of Microbiology and Biotechnology
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• 제13권6호
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• pp.949-954
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• 2003

The argG gene of Corynebacterium glutamicum encoding argininosuccinate synthetase (EC6345) was cloned and sequenced. The gene was cloned by heterologous complementation of an Escherichia coli arginine auxotrophic mutant (argG/sup -/). The cloned DNA fragment also complements E. coli argD, argF, and argH mutants, suggesting a clustered organization of the genes in the chromosome. The coding region of the argG gene is 1,206 nucleotides long with a deduced molecular weight of about 44 kDa, comparable with the predicted size of the expressed protein on the SDS-PAGE. Computer analysis revealed that the amino acid sequence of the argG gene product had a high similarity to that of Mycobacterium tuberculosis and Streptomyces clavuligerus. Two conserved sequence motifs within the ArgG appear to be ATP-binding sites which correspond to 2 of the 3 conserved regions found in sequences of all known argininosuccinate synthetases.

• Asian Pacific Journal of Cancer Prevention
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• 제15권6호
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• pp.2433-2438
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• 2014

Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field.

• 한국정보통신학회:학술대회논문집
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• 한국해양정보통신학회 2000년도 추계종합학술대회
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• pp.328-332
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• 2000

최근 지놈(Genome) 프로젝트를 통해 DNA 염기서열에 대한 정보가 밝혀짐에 따라 분자 수준의 유전자 정보를 다루는 기법이 활발히 연구되고 있다. 그리고 밝혀진 서열정보들의 방대함으로 미루어볼 때 이들 정보를 데이터베이스화하고 효과적인 분석을 행하기 위한 새로운 컴퓨터의 알고리즘의 개발 또한 시급한 일이다. 이러한 측면에서 ,본 논문에서는 분자생물학에서 매우 중요한 연구 대상으로 삼고있는 프로모터 서열과 유전자간의 연관성으로 발현되는 특징을 알아내기 위한 연관 규칙 탐사 알고리즘을 연구한다. 기존의 탐사 알고리즘은 트랜잭션 데이터를 대상으로 하지만 본 논문에서는 생물학적 데이터를 대상으로 하였기 때문에 데이터의 형태와 생물학적인 특성을 수용하는 변형된 연관규칙 알고리즘을 설계한다. 본 연구를 통하여 얻어진 결과는 실제 생물학적 실험'대상의 후보조합을 최소화 하므로써 많은 시간과 노력 비용을 절감할 수 있다.

• 대한전기학회논문지:전기물성ㆍ응용부문C
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• 제49권1호
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• pp.13-18
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• 2000

We have fabricated LB ultra-thin films of maleate system by LB technique and evaluated the deposited status of LB ultra-thin films by I-V characteristics such as capacitance. It was found that the thickness of LB ultra-thin per layer is $27~30[{\AA}]$ by XRD. And, we have known that the conductivity along the horizontal direction of LB ultra-thin films was about $10^{-8}[S/cm]$, it corresponds to the semiconducting materials. Also, the I-V characteristics along the vertical direction of LB ultra-thin films was dominated by Schottky type current, the activation energy obtained by current-temperature characteristics was about 0.84[eV] and the conductivity was about $10^{-14}[S/cm]$, it corresponds to the insulator. And, the anisotropic conduction mechanism of the LB ultra-thin films in vertical direction and horizontal direction is determined by the hydrophilic group and the hydrophobic group in LB ultra-thin films. The above results are applicable to the semiconductor devices such as switching device, which function at the molecular level.

• 정보처리학회논문지:컴퓨터 및 통신 시스템
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• 제3권1호
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• pp.1-6
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• 2014

현재까지 컨벡스헐 (convex hull) 의 계산 알고리즘들은 주로 점 집합 (point set) 에 대해 연구가 수행되어 왔다. 본 논문에서는 이산 공간에서 다양한 반경을 갖는 구 집합에 대한 컨벡스헐을 근사하는 방법을 제시한다. 구 집합에 대한 컨벡스헐 계산은, 특히 단백질 분자의 구조적인 특성을 연구하는 여러 응용분야에서 계산 효율성을 증대시키기 위한 기반 기술이라 할 수 있다. 분자에 대응하는 구의 집합에 대해 복셀 맵 (voxel map) 자료구조를 적용하고 이를 이용하여 컨벡스헐을 계산하는 알고리즘을 제시한다. 제안된 방법은 GPU를 활용한 병렬처리를 수행하여 평균적으로 6,400개 이하의 구가 포함된 집합에 대해 40ms 이내에 컨벡스헐을 계산하는 성능을 보인다.

• 미생물학회지
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• 제24권4호
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• pp.400-405
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• 1986

이미 발표된 각 시료들의 tRNAAn 염기 서열을 이용하여 세통학적 연구플 하였나. archaebacterium안 H. volcano가 진핵생물과 연계된 결과는 진핵생물이 eubacteria와의 공통척 조상에셔 분화되지 않았음을 세시하며 Phage $T_{4}$와 $T_{s}$,의 연계 순서는 그들이 각각 독럽적으로 숙주로부터 분화되였음을 내타낸다. tRNA의 염기 순서의 상관관계를 이용한 연구 결과가 기존의 다른 연구 결고 및 고생물학적 기록들과도 일치함을 알 수 있었다.

• 천문학회보
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• 제41권2호
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• pp.38.1-38.1
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• 2016

TRAO has been newly equipped with a multi-beam receiver system, 16 pixel MMIC preamplifiers in a $4{\times}4$ array, a FFT spectrometer, and new control computer systems. In our new receiver systems one can make simultaneous observations with two molecular lines maximum 15 GHz apart with a spectral band width of 60 MHz. Typical system temperatures are about 160 - 200 K at 86 ~ 100 KHz and 400 - 500 K at 115 GHz in the dry weather. The new systems using On-The-Fly mode were found to be very efficient in making quick and sensitive maps of large clouds with a high velocity resolution (~0.04 km/s at 100 GHz). TRAO now calls for proposals for 2016 and 2017 observing season for everybody. In the talk we will introduce the current status of TRAO upgrade and its scientific preliminary results.

• Genomics & Informatics
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• 제5권2호
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• pp.83-87
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• 2007

The analysis of DNA microarray data is a rapidly evolving area of bioinformatics, and various types of microarray are emerging as some of the most exciting technologies for use in biological and clinical research. In recent years, microarray technology has been utilized in various applications such as the profiling of mRNAs, assessment of DNA copy number, genotyping, and detection of methylated sequences. However, the analysis of these heterogeneous microarray platform experiments does not need to be performed separately. Rather, these platforms can be co-analyzed in combination, for cross-validation. There are a number of separate laboratory information management systems (LIMS) that individually address some of the needs for each platform. However, to our knowledge there are no unified LIMS systems capable of organizing all of the information regarding multi-platform microarray experiments, while additionally integrating this information with tools to perform the analysis. In order to address these requirements, we developed a web-based LIMS system that provides an integrated framework for storing and analyzing microarray information generated by the various platforms. This system enables an easy integration of modules that transform, analyze and/or visualize multi-platform microarray data.