• Molecules and Cells
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• 제44권7호
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• pp.433-443
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• 2021

Multi-omics approaches are novel frameworks that integrate multiple omics datasets generated from the same patients to better understand the molecular and clinical features of cancers. A wide range of emerging omics and multi-view clustering algorithms now provide unprecedented opportunities to further classify cancers into subtypes, improve the survival prediction and therapeutic outcome of these subtypes, and understand key pathophysiological processes through different molecular layers. In this review, we overview the concept and rationale of multi-omics approaches in cancer research. We also introduce recent advances in the development of multi-omics algorithms and integration methods for multiple-layered datasets from cancer patients. Finally, we summarize the latest findings from large-scale multi-omics studies of various cancers and their implications for patient subtyping and drug development.

• 한국멀티미디어학회논문지
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• 제25권2호
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• pp.363-373
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• 2022

Multi-omics data is difficult to interpret due to the heterogeneity of information by the volume of data, the complexity of characteristics of each data, and the diversity of omics platforms. There is not yet a system for interpreting to visualize research data on environmental diseases concerning environmental harmful substances. We provide MEE, a web-based visualization tool, to comprehensively explore the complexity of data due to the interconnected characteristics of high-dimensional data sets according to exposure to various environmental harmful substances. MEE visualizes omics data of correlation between omics data, subjects and samples by keyword searches of meta data, multi-omics data, and harmful substances. MEE has been demonstrated the versatility by two examples. We confirmed the correlation between smoking and asthma with RNA-seq and Methylation-Chip data, it was visualized that genes (P HACTR3, PXDN, QZMB, SOCS3 etc.) significantly related to autoimmune or inflammatory diseases. To visualize the correlation between atopic dermatitis and heavy metals, we selected 32 genes related immune response by integrated analysis of multi-omics data. However, it did not show a significant correlation between mercury in blood and atopic dermatitis. In the future, should continuously collect an appropriate level of multi-omics data in MEE system, will obtain data to analyze environmental substances and diseases.

• Molecular & Cellular Toxicology
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• 제3권3호
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• pp.208-213
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• 2007

With the help of a development and popularization of microarray technology that enable to us to simultaneously investigate the expression pattern of thousands of genes, the toxicogenomics experimenters can interpret the genome-scale interaction between genes exposed in toxicant or toxicant-related environment. The ultimate and primary goal of toxicogenomics identifies functional context among the group of genes that are differentially or similarly coexpressed under the specific toxic substance. On the other side, public reference databases with transcriptom, proteom, and biological pathway information are needed for the analysis of these complex omics data. However, due to the heterogeneous and independent nature of these databases, it is hard to individually analyze a large omics annotations and their pathway information. Fortunately, several web sites of the public database provide information linked to other. Nevertheless it involves not only approriate information but also unnecessary information to users. Therefore, the systematically integrated database that is suitable to a demand of experimenters is needed. For these reasons, we propose SOP (Search of Omics Pathway) database system which is constructed as the integrated biological database converting heterogeneous feature of public databases into combined feature. In addition, SOP offers user-friendly web interfaces which enable users to submit gene queries for biological interpretation of gene lists derived from omics experiments. Outputs of SOP web interface are supported as the omics annotation table and the visualized pathway maps of KEGG PATHWAY database. We believe that SOP will appear as a helpful tool to perform biological interpretation of genes or proteins traced to omics experiments, lead to new discoveries from their pathway analysis, and design new hypothesis for a next toxicogenomics experiments.

• Journal of Microbiology and Biotechnology
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• 제18권5호
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• pp.859-865
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• 2008

Bacterial glycosyltransferases have drawn growing attention as economical enzymes for oligosaccharide synthesis, with their easy expression and relatively broad substrate specificity. Here, we characterized a glycosyltransferase homolog (Fnu_GT) from a human oral pathogen, Fusobacterium nucleatum. Bioinformatic analysis showed that Fnu_GT belongs to the glycosyltransferases family II. The recombinant Fnu_GT (rFnu_GT) expressed in Escherichia coli displayed the highest glycosylation activity when UDP-galactose (Gal) was used as a donor nucleotide-sugar with heptose or N-acetylglucosamine (GlcNAc) as an acceptor sugar. Interestingly, rFnu_GT transferred the galactose moiety of UDP-Gal to a nonreducing terminal GlcNAc attached to the trimannosyl core glycan, indicating its potential as an enzyme for human-type N-glycan synthesis.

• 한국축산식품학회지
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• 제43권6호
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• pp.1067-1086
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• 2023

With rapid advances in meat science in recent decades, changes in meat quality during the pre-slaughter phase of muscle growth and the post-slaughter process from muscle to meat have been investigated. Commonly used techniques have evolved from early physicochemical indicators such as meat color, tenderness, water holding capacity, flavor, and pH to various omic tools such as genomics, transcriptomics, proteomics, and metabolomics to explore fundamental molecular mechanisms and screen biomarkers related to meat quality and taste characteristics. This review highlights the application of omics and integrated multi-omics in meat quality and taste characteristics studies. It also discusses challenges and future perspectives of multi-omics technology to improve meat quality and taste. Consequently, multi-omics techniques can elucidate the molecular mechanisms responsible for changes of meat quality at transcriptome, proteome, and metabolome levels. In addition, the application of multi-omics technology has great potential for exploring and identifying biomarkers for meat quality and quality control that can make it easier to optimize production processes in the meat industry.

• Mass Spectrometry Letters
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• 제15권1호
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• pp.49-53
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• 2024

Ceramide is a lipid in which sphingoid bases and fatty acids are linked by amide bonds. As a marker of skin disease in the human stratum corneum, its disease-causing and therapeutic effects have been partially confirmed, and it is therefore an important element in commercially available cosmetic formulations. However, structural diversity caused by differences in the chain length, number, and location of hydroxyl groups makes quality control difficult. In this study, a method was established to separate different ceramide species using reversed-phase LC-MS/MS and thus enable qualitative evaluation. Separation of four standards was achieved within a short retention time, and the accuracy and sensitivity of the method were demonstrated by the low limit of detection (LOD) calculated based on the calibration curve showing linearity, with R² > 0.994. After verification of reproducibility and reliability through intra- and inter-day analyses, the efficiency of the method was confirmed through analysis of commercial cosmetic raw materials.

• 한국정보통신학회:학술대회논문집
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• 한국정보통신학회 2015년도 춘계학술대회
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• pp.768-770
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• 2015

유전체 염기서열 분석비용이 크게 감소하면서 유전체 정보 생산이 본격화됨에 따라 시스템 생물학 기반의 통합 및 표준화된 오믹스 데이터베이스 구축이 필요하다. 이에 따라 현재 진행중인 연구 수행의 결과로 얻어진 차세대유전체서열(NGS) 및 전사체(transcriptome) 등의 대용량 정보를 수집하였고 이를 표준화 형식에 맞춰 농업생명공학정보센터(NABIC)에 등록하였다. 또한 농업생명자원 생물정보를 품목별, 개체별로 통합 저장소를 구축하였으며 농업생명자원 생물정보를 품목별, 개체별로 통합 저장소를 구축하였다. 농업생명공학정보센터 오믹스 정보등록시스템 서비스와의 연계 및 확충작업을 하기위해 시스템 기능 개선 및 유지보수 작업을 수행하였다.

• Genomics & Informatics
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• 제19권2호
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• pp.13.1-13.8
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• 2021

Ranked in the topmost position among the deadliest diseases in the world, cardiovascular diseases (CVDs) are a global burden with alterations in heart and blood vessels. Early diagnostics and prognostics could be the best possible solution in CVD management. OMICS (genomics, proteomics, transcriptomics, and metabolomics) approaches could be able to tackle the challenges against CVDs. Genome-wide association studies along with next-generation sequencing with various computational biology tools could lead a new sight in early detection and possible therapeutics of CVDs. Human cardiac proteins are also characterized by mass spectrophotometry which could open the scope of proteomics approaches in CVD. Besides this, regulation of gene expression by transcriptomics approaches exhibits a new insight while metabolomics is the endpoint on the downstream of multi-omics approaches to confront CVDs from the early onset. Although a lot of challenges needed to overcome in CVD management, OMICS approaches are certainly a new prospect.

• Bulletin of the Korean Chemical Society
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• 제33권5호
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• pp.1773-1776
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• 2012

• 한국작물학회:학술대회논문집
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• 한국작물학회 2021년도 춘계학술대회
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• pp.119-119
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• 2021