• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.390-390
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• 2005

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.672-673
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• 2005

• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.231-231
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• 2022

The GASA protein (Gibberellic acid-stimulated Arabidopsis) are family of small cysteine-rich peptides found in plants. These GASA gene family mainly involved in biotic/abiotic stress responses and plant development. Despite being present in a wide plant species, their action and functions still remain unclear. In this study, using the in-silico analysis method we identified 41 GASA genes in peanuts (Arachis hypogaea L.). Based on the phylogenetic analysis 41 GASA genes are classified in the four major clusters and subclades. Mainly, clusters IV and III comprise the majority of GASA genes 15 and 11 genes respectively, followed by cluster I and cluster II with 9 and 6 genes respectively. Additionally, based on in-silico analysis we predicted the post-transcriptional and post-translational changes of GASA proteins under abiotic stresses such as drought and salt stress would aid our understanding of the regulatory mechanisms. Hence, a further study is planned to evaluate the expression of these GASA genes under stress in different plant tissues to elucidate the possible functional role of GASA genes in peanut plants. These findings might offer insightful data for peanut advancement.

• Genomics & Informatics
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• v.2 no.3
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• pp.134-141
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• 2004

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and a typical hypervascular tumor. Therefore, it is important to find factors related to angiogenesis in the process of HCC malignancy. In order to find angiogenesis-related factors in HCC, we used combined methods of in silico prediction and an experimental assay. We analyzed 1457 genes extracted from cDNA microarray of HCC patients by text-mining, sequence similarity search and domain analysis. As a result, we predicted that 16 genes were likely to be involved in angiogenesis and then the effects of these genes were confirmed by hypoxia response element(HRE)-luciferase assay. For instant, we classified osteopontin into a potent angiogenic factor and coagulation factor XII into a significant anti­angiogenic factor. Collectively, we suggest that using a combination of in silico prediction and experimental approaches, we can identify HCC-specific angiogenesis­related factors effectively and rapidly.

• BMB Reports
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• v.44 no.8
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• pp.523-528
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• 2011

To identify novel genes that are regulated by promoter methylation, a combinational approach involving in silico mining followed by molecular assay was performed. From the expression microarray data registered in the European bioinformatics institute (EBI), genes showing downregulation in breast cancer cells were initially screened and then selected by e-Northern analysis using the Unigene database. A series of these in silico methods identified CAMK2B and ARFGEF1 as candidates, and the two genes were revealed to be hypermethylated in breast cancer cell lines and hypomethylated in normal breast cell lines. Additionally, cancer cell lines showed downregulated expression of these genes. Furthermore, treatment of the cancer cell lines with a demethylation agent, 5-Aza-2'-deoxycytidine, recovered expression of CAMK2B and ARFGEF1, implying that hypermethyaltion silenced gene activity in cancer cells. Taken together, promoter methylations of CAMK2B and ARFGEF1 are novel epigenetic markers identified in breast cancer cell lines and can be utilized for the application to clinical cancer tissues.

• Genomics & Informatics
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• v.14 no.4
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• pp.241-254
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• 2016

Environmental microbes like Bordetella petrii has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in B. petrii challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value. In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No. PRJNA28135) from genome database of National Centre for Biotechnology information. In this regards, the inhibitory effect of nine natural compounds like ajoene (Allium sativum), allicin (A. sativum), cinnamaldehyde (Cinnamomum cassia), curcumin (Curcuma longa), gallotannin (active component of green tea and red wine), isoorientin (Anthopterus wardii), isovitexin (A. wardii), neral (Melissa officinalis), and vitexin (A. wardii) have been acknowledged with anti-bacterial properties and hence tested against identified drug target of B. petrii by implicating computational approach. The in silico studies revealed the hypothesis that lpxD could be a potential drug target and with recommendation of a strong inhibitory effect of selected natural compounds against infection caused due to B. petrii, would be further validated through in vitro experiments.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2161-2166
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• 2015

Estrogen receptors (ERs) are steroid receptors located in the cytoplasm and on the nuclear membrane. The sequence similarities of human $ER{\alpha}$, mouse $ER{\alpha}$, rat $ER{\alpha}$, dog $ER{\alpha}$, and cat $ER{\alpha}$ are above 90%, but structures of $ER{\alpha}$ may different among species. Estrogen can be agonist and antagonist depending on its target organs. This hormone play roles in several diseases including breast cancer. There are variety of the relative binding affinity (RBA) of ER and estrogen species in comparison to $17{\beta}-estradiol$ (E2), which is a natural ligand of both $ER{\alpha}$ and $ER{\beta}$. The RBA of the estrogen species are as following: diethyl stilbestrol (DES) > hexestrol > dienestrol > $17{\beta}-estradiol$ (E2) > 17- estradiol > moxestrol > estriol (E3) >4-OH estradiol > estrone-3-sulfate. Estrogen mimetic drugs, selective estrogen receptor modulators (SERMs), have been used as hormonal therapy for ER positive breast cancer and postmenopausal osteoporosis. In the postgenomic era, in silico models have become effective tools for modern drug discovery. These provide three dimensional structures of many transmembrane receptors and enzymes, which are important targets of de novo drug development. The estimated inhibition constants (Ki) from computational model have been used as a screening procedure before in vitro and in vivo studies.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.221-228
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• 2003

This paper presents a novel method that can identify the individual's haplotype from the given genotypes. Because of the limitation of the conventional single-locus analysis, haplotypes have gained increasing attention in the mapping of complex-disease genes. Conventionally there are two approaches which resolve the individual's haplotypes. One is the molecular haplotypings which have many potential limitations in cost and convenience. The other is the in-silico haplotypings which phase the haplotypes from the diploid genotyped populations, and are cost effective and high-throughput method. In-silico haplotyping is divided into two sub-categories - statistical and computational method. The former computes the frequencies of the common haplotypes, and then resolves the individual's haplotypes. The latter directly resolves the individual's haplotypes using the perfect phylogeny model first proposed by Dan Gusfield [7]. Our method combines two approaches in order to increase the accuracy and the running time. The individuals' haplotypes are resolved by considering the MLE (Maximum Likelihood Estimation) in the process of computing the frequencies of the common haplotypes.

• Biomolecules & Therapeutics
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• v.29 no.5
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• pp.519-526
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• 2021

In a search for effective PPAR-γ agonists, 110 clinical drugs were screened via molecular docking, and 9 drugs, including parecoxib, were selected for subsequent biological evaluation. Molecular docking of parecoxib to the ligand-binding domain of PPAR-γ showed high binding affinity and relevant binding conformation compared with the PPAR-γ ligand/antidiabetic drug rosiglitazone. Per the docking result, parecoxib showed the best PPAR-γ transactivation in Ac2F rat liver cells. Further docking simulation and a luciferase assay suggested parecoxib would be a selective (and partial) PPAR-γ agonist. PPAR-γ activation by parecoxib induced adipocyte differentiation in 3T3-L1 murine preadipocytes. Parecoxib promoted adipogenesis in a dose-dependent manner and enhanced the expression of adipogenesis transcription factors PPAR-γ, C/EBPα, and C/EBPβ. These data indicated that parecoxib might be utilized as a partial PPAR-γ agonist for drug repositioning study.