• Journal of Preventive Medicine and Public Health
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• 제40권2호
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• pp.102-107
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• 2007

Human Genome Project (HGP) could unveil the secrets of human being by a long script of genetic codes, which enabled us to get access to mine the cause of diseases more efficiently. Two wheels for HGP, bioinformatics and high throughput technology are essential techniques for the genomic medicine. While microarray platforms are still evolving, we can screen more than 500,000 genotypes at once. Even we can sequence the whole genome of an organism within a day. Because the future medicne will focus on the genetic susceptibility of individuals, we need to find genetic variations of each person by efficient genotyping methods.

• Genomics & Informatics
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• 제10권1호
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• pp.33-39
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• 2012

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.

• Clinical and Experimental Reproductive Medicine
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• 제51권2호
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• pp.91-101
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• 2024

Infertility is a complex disease characterized by extreme genetic heterogeneity, compounded by various environmental factors. While there are exceptions, individual genetic and genomic variations related to infertility are typically rare, often family-specific, and may serve as susceptibility factors rather than direct causes of the disease. Consequently, identifying the cause of infertility and developing prevention and treatment strategies based on these factors remain challenging tasks, even in the modern genomic era. In this review, we first examine the genetic and genomic variations associated with infertility, and subsequently summarize the concepts and methods of preimplantation genetic testing in light of advances in genome analysis technology.

• 미생물학회지
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• 제54권3호
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• pp.188-199
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• 2018

다양한 미생물학 연구 분야의 발전에 힘입어 유전체역학은 발전되어 왔다. 예를 들어, 대용량서열화 기술의 발전으로 미생물 유전체의 수는 급속도로 증가해 오고 있다. 이러한 풍부한 유전체 데이터는 전에는 보지 못한 보다 더 정확한 미생물종의 동정에 도움을 주는 균주종 타이핑에 새로운 기회를 제공한다. 유전체역학은 유전체에 일반적인 유전자를 찾고 표기하는 것 뿐만 아니라 항균 저항성 유전자를 찾을 수 있다. 균주종 타이핑과 항균 저항성 유전자 찾기는 각각 종을 구분하고 유전체내의 유전자 위치를 결정하는 유전체 역학의 방법들로 시간에 따른 변화가 없는 측면이다. 이에 반하여, 하나의 숙주가 어떤 숙주를 감염시켰는지 알아내기 위해서는 감염된 숙주들 사이의 시간에 따른 동적인 전염 경로를 추론해야 한다. 이렇게, 균주종 타이핑, 항균 저항성 유전자 찾기, 전염 계통수 추론을 통하여 유전체역학의 궁극적인 목표 중 하나인 미생물성 전염병을 보다 효율적으로 감시할 수 있을 것으로 기대된다. 그리고, 대용량서열화 기술 중, 3세대 서열화기술 중 하나인 옥스포드 나노포어 MinION의 보다 나은 휴대성과 빠른 서열화의 성능 덕분에 유전체역학은 더 많은 발전을 거듭할 것으로 보인다. 이에, 본 연구는 항균 저항성 유전자를 찾고 전염병 경로를 추론하는 계산적인 방법에 대하여 살펴보고, 미생물 유전체역학에서 MinION이 응용된 예들에 대하여 논하였다.

• 농업과학연구
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• 제45권3호
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• pp.317-323
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• 2018

The demand for crop production is increasingly becoming steeper due to the rapid population growth. As a result, breeding cycles should be faster than ever before. However, the current breeding methods cannot meet this requirement because traditional phenotyping methods lag far behind even though genotyping methods have been drastically developed with the advent of next-generation sequencing technology over a short period of time. Consequently, phenotyping has become a bottleneck in large-scale genomics-based plant breeding studies. Recently, however, phenomics, a new discipline involving the characterization of a full set of phenotypes in a given species, has emerged as an alternative technology to come up with exponentially increasing genomic data in plant breeding programs. There are many advantages for using new technologies in phenomics. Yet, the necessity of diverse man power and huge funding for cutting-edge equipment prevent many researchers who are interested in this area from adopting this new technique in their research programs. Currently, only a limited number of groups mostly in developed countries have initiated phenomic studies using high throughput methods. In this short article, we describe the strategies to compete with those advanced groups using limited resources in developing countries, followed by a brief introduction of high throughput phenotyping.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.45-52
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• 2000

Genomic approach produces massive amount of data within a short time period, New high-throughput automatic sequencers can generate over a million nucleotide sequence information overnight. A typical DNA chip experiment produces tens of thousands expression information, not to mention the tens of megabyte image files, These data must be handled automatically by computer and stored in electronic database, Thus there is a need for systematic approach of data collection, processing, and analysis. DNA sequence information is translated into amino acid sequence and is analyzed for key motif related to its biological and/or biochemical function. Functional genomics will play a significant role in identifying novel drug targets and diagnostic markers for serious diseases. As an enabling technology for functional genomics, bioinformatics is in great need worldwide, In Korea, a new functional genomics project has been recently launched and it focuses on identi☞ing genes associated with cancers prevalent in Korea, namely gastric and hepatic cancers, This involves gene discovery by high throughput sequencing of cancer cDNA libraries, gene expression profiling by DNA microarray and proteomics, and SNP profiling in Korea patient population, Our bioinformatics team will support all these activities by collecting, processing and analyzing these data.

• 원예과학기술지
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• 제35권2호
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• pp.149-164
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• 2017

Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genome-wide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and marker-trait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.

• Journal of Microbiology and Biotechnology
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• 제32권12호
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• pp.1515-1526
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• 2022

Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.

• International Journal of Oral Biology
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• 제45권3호
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• pp.77-83
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• 2020

In the oral cavity, complex microbial community is shaped by various host and environmental factors. Extensive literature describing the oral microbiome in the context of oral health and disease is available. Advances in DNA sequencing technologies and data analysis have drastically improved the analysis of the oral microbiome. For microbiome study, bacterial 16S ribosomal RNA gene amplification and sequencing is often employed owing to the cost-effective and fast nature of the method. In this review, practical considerations for performing a microbiome study, including experimental design, molecular analysis technology, and general data analysis, will be discussed.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.1-9
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• 2001

scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational sciences and information technology. The informatics revolutions both in clinical informatics and bioinformatics will change the current paradigm of biomedical sciences and practice of clinical medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever much the same way that biochemistry did a generation ago. In this talk, 1 will describe how these technologies will in pact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine teaming algorithms will be presented. Issues of integrated biochip informatics technologies including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and integrated management of biomolecular databases will be discussed. Each step will be given with real examples from ongoing research activities in the context of clinical relevance. Issues of linking molecular genotype and clinical phenotype information will be discussed.