• Experimental and Molecular Medicine
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• v.50 no.11
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• pp.7.1-7.12
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• 2018

Recent findings from The Cancer Genome Atlas project have provided a comprehensive map of genomic alterations that occur in hepatocellular carcinoma (HCC), including unexpected mutations in apolipoprotein B (APOB). We aimed to determine the clinical significance of this non-oncogenetic mutation in HCC. An Apob gene signature was derived from genes that differed between control mice and mice treated with siRNA specific for Apob (1.5-fold difference; P < 0.005). Human gene expression data were collected from four independent HCC cohorts (n = 941). A prediction model was constructed using Bayesian compound covariate prediction, and the robustness of the APOB gene signature was validated in HCC cohorts. The correlation of the APOB signature with previously validated gene signatures was performed, and network analysis was conducted using ingenuity pathway analysis. APOB inactivation was associated with poor prognosis when the APOB gene signature was applied in all human HCC cohorts. Poor prognosis with APOB inactivation was consistently observed through cross-validation with previously reported gene signatures (NCIP A, HS, high-recurrence SNUR, and high RS subtypes). Knowledge-based gene network analysis using genes that differed between low-APOB and high-APOB groups in all four cohorts revealed that low-APOB activity was associated with upregulation of oncogenic and metastatic regulators, such as HGF, MTIF, ERBB2, FOXM1, and CD44, and inhibition of tumor suppressors, such as TP53 and PTEN. In conclusion, APOB inactivation is associated with poor outcome in patients with HCC, and APOB may play a role in regulating multiple genes involved in HCC development.

• Journal of Physiology & Pathology in Korean Medicine
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• v.30 no.6
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• pp.370-375
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• 2016

Recent advances in systems biology are shedding a new light on the traditional medicine research. The systems biology highlights the way each component interacts with each other within a system, and the network behavior that emerges from such interactions. This feature of systems biology can accent the systemic aspects of Korean medicine such as the mechanism of action of herbal formulae, pattern differentiation, and the meridian systems, as both the Korean medicine and the systems biology theorize the human physiological functions and phenomena from a holistic point of view. This paper outlines the meaning of the recent Korean medicine research using the systems biology methodology. We discuss the methodologies of the two fields in a comparative manner, and overview the advantages and limitations of the integrated approaches. Finally, we suggest the future prospects for the systems biology inspired approaches to the Korean medicine research. The systems biology may provide a new modernized research methodology for the Korean medicine that can highlight its unique features.

• Proceedings of the Korea Information Processing Society Conference
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• 2014.11a
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• pp.849-852
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• 2014

Reverse engineering of gene regulatory network is a challenging task in computational biology. To detect a regulatory relationship among genes from time series data is called reverse engineering. Reverse engineering helps to discover the architecture of the underlying gene regulatory network. Besides, it insights into the disease process, biological process and drug discovery. There are many statistical approaches available for reverse engineering of gene regulatory network. In our paper, we propose pairwise mutual information for the reverse engineering of a gene regulatory network from time series data. Firstly, we create random boolean networks by the well-known $Erd{\ddot{o}}s-R{\acute{e}}nyi$ model. Secondly, we generate artificial time series data from that network. Then, we calculate pairwise mutual information for predicting the network. We implement of our system on java platform. To visualize the random boolean network graphically we use cytoscape plugins 2.8.0.

• Proceedings of the Korea Information Processing Society Conference
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• 2005.05a
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• pp.585-588
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• 2005

연구자들이 국외 생명과학관련 문헌정보를 찾으려면 PubMed와 같은 세계적인 문헌정보서비스를 많이 이용하며, 국내 생명과학관련 문헌정보를 찾으려면 KISTI 학회마을, KoreaMed 등 여러 사이트를 방문해야 한다. 이에 생명과학관련 연구를 원활히 수행할 수 있도록 생명정보 데이터베이스와 분석도구를 서비스하고 있는 KISTI 바이오인포매틱스센터(CCBB) 홈페이지에서 인터넷상의 Open Access 문헌정보와 국내 학회정보를 수집하여 메타 데이터베이스를 구축하여 서비스하고자 한다. 또한 생명과학 관련 주제별 Open Archiving 커뮤니티의 구성과 운영을 통한 연구자간의 정보교환을 유도하고, 더불어 논문뿐만 아니라 세미나, 연구노트 등의 최신의 연구정보를 공유할 수 있도록 본 프로토타입 시스템을 설계하였다.

• 한국정보통신설비학회:학술대회논문집
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• 2009.08a
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• pp.131-135
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• 2009

This paper is the introduction of our work on distributed load scheduling in single-level tree network. In this paper, we derive a new calculation model in single-level tree network and show a closed-form formulation of the time for computation system. There are so many examples of the application of this technology such as distributed database, biology computation on genus, grid computing, numerical computing, video and audio signal processing, etc.

• Molecules and Cells
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• v.39 no.9
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• pp.692-698
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• 2016

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

• Journal of Korean Society on Water Environment
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• v.32 no.5
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• pp.475-491
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• 2016

The Changwon and Nam streams that run through the Changwon city were evaluated based on longitudinal and horizontal configurations and vegetation state in order to prepare a restoration plan. Riparian vegetation of the Changwon and Nam streams are normally dominated by herbaceous plants. However, the woody plants, Salix pseudolasiogyne, Rubus parvifolius, Salix koreensis, Robinia pseudoacacia, and Amorpha fruticosa have appeared. Planting to introduce various types of plants for landscape architecture has also been observed. Evaluation of naturalness based on the vegetation state of both Changwon and Nam streams showed very low naturalness of degree 1 or 2, with the exception of a few reaches of the upstream sector. In these few reaches of the upstream sector, Salix koreensis and Salix chaenomeloides showed heights at the subtree level, however, they were located at the position of shrubland close to the waterway. These reaches were, therefore, evaluated as degree 3 rather than degree 4 in naturalness. The result of diagnostic evaluation classified by reach indicated the requirement for active restoration, such as transformation of the channelized stream into a meandering one and a step-type cross section into a pool-type one, introduction of vegetation suitable to the region and site, and creation of an ecological network between the stream and the surrounding terrestrial ecosystems.

• KIPS Transactions on Software and Data Engineering
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• v.5 no.6
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• pp.295-306
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• 2016

The purpose of this paper is both to analyze research trends and to predict industrial flows using the meta-data from the previous studies on data quality. There have been many attempts to analyze the research trends in various fields till lately. However, analysis of previous studies on data quality has produced poor results because of its vast scope and data. Therefore, in this paper, we used a text mining, social network analysis for time series network analysis to analyze the vast scope and data of data quality collected from a Web of Science index database of papers published in the international data quality-field journals for 10 years. The analysis results are as follows: Decreases in Mathematical & Computational Biology, Chemistry, Health Care Sciences & Services, Biochemistry & Molecular Biology, Biochemistry & Molecular Biology, and Medical Information Science. Increases, on the contrary, in Environmental Sciences, Water Resources, Geology, and Instruments & Instrumentation. In addition, the social network analysis results show that the subjects which have the high centrality are analysis, algorithm, and network, and also, image, model, sensor, and optimization are increasing subjects in the data quality field. Furthermore, the industrial connection analysis result on data quality shows that there is high correlation between technique, industry, health, infrastructure, and customer service. And it predicted that the Environmental Sciences, Biotechnology, and Health Industry will be continuously developed. This paper will be useful for people, not only who are in the data quality industry field, but also the researchers who analyze research patterns and find out the industry connection on data quality.

• Journal of the Korea Society of Computer and Information
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• v.21 no.3
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• pp.65-71
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• 2016

To reduce the expenses for development a novel drug, systems biology has been studied actively. Target prediction, a part of systems biology, contributes to finding a new purpose for FDA(Food and Drug Administration) approved drugs and development novel drugs. In this paper, we propose a classification model for predicting novel target genes based on relation between target genes and disease related genes. After collecting known target genes from TTD(Therapeutic Target Database) and disease related genes from OMIM(Online Mendelian Inheritance in Man), we analyzed the effect of target genes on disease related genes based on PPI(Protein-Protein Interactions) network. We focused on the distinguishing characteristics between known target genes and random target genes, and used the characteristics as features for building a classifier. Because our model is constructed using information about only a disease and its known targets, the model can be applied to unusual diseases without similar drugs and diseases, while existing models for finding new drug-disease associations are based on drug-drug similarity and disease-disease similarity. We validated accuracy of the model using LOOCV of ten times and the AUCs were 0.74 on Alzheimer's disease and 0.71 on Breast cancer.

• BMB Reports
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• v.40 no.3
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• pp.302-314
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• 2007

N type calcium channels (CaV2.2) play a key role in the gating of transmitter release at presynaptic nerve terminals. These channels are generally regarded as parts of a multimolecular complex that can modulate their open probability and ensure their location near the vesicle docking and fusion sites. However, the proteins that comprise this component remain poorly characterized. We have carried out the first open screen of presynaptic CaV2.2 complex members by an antibody-mediated capture of the channel from purified rat brain synaptosome lysate followed by mass spectroscopy. 589 unique peptides resulted in a high confidence match of 104 total proteins and 40 synaptosome proteome proteins. This screen identified several known CaV2.2 interacting proteins including syntaxin 1, VAMP, protein phosphatase 2A, $G_{o\alpha}$, G$\beta$ and spectrin and also a number of novel proteins, including clathrin, adaptin, dynamin, dynein, NSF and actin. The unexpected proteins were classified within a number of functional classes that include exocytosis, endocytosis, cytoplasmic matrix, modulators, chaperones, and cell-signaling molecules and this list was contrasted to previous reports that catalogue the synaptosome proteome. The failure to detect any postsynaptic density proteins suggests that the channel itself does not exhibit stable trans-synaptic attachments. Our results suggest that the channel is anchored to a cytoplasmic matrix related to the previously described particle web.