• KOGO NEWS
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• v.3 no.2
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• pp.7.2-7.2
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• 2003

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.305-307
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• 2018

The whole genome sequencing using PacBio RS II platform was performed for a marine bacterium Pseudoalteromonas donghaensis $HJ51^T$ isolated from East Sea of Korea. As a result, three assembled contigs consisting of a chromosome (size of 3,646,857 bp, and G + C content of 41.8%) and two plasmids (size of 842,855 bp and 244,204 bp, and G + C content of 41.3% and 40.4%, respectively) were obtained. The genome included 4,083 protein coding genes and 127 RNA genes. This result could be used for gene sources of biopolymers degradation and the development as a new host with secretion system similar to Escherichia coli.

• Journal of Genetic Medicine
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• v.7 no.2
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• pp.119-124
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• 2010

More than 7,000 rare Mendelian diseases have been reported, but less than half of all rare monogenic disorders has been discovered. In addition, the majority of mutations that are known to cause Mendelian disorders are located in protein-coding regions. Therefore, exome sequencing is an efficient strategy to selectively sequence the coding regions of the human genome to identify novel genes associated with rare genetic disorders. The "exome" represents all of the exons in the human genome, constituting about 1.5% of the human genome. Exome sequencing is carried out by targeted capture and intense parallel sequencing. After the first report of successful exome sequencing for the identification of causal genes and mutations in Freeman Sheldon syndrome, exome sequencing has become a standard approach to identify genes in rare Mendelian disorders. Exome sequencing is also used to search the causal genes and variants in complex diseases. The successful use of exome sequencing in Mendelian disorders and complex diseases will facilitate the development of personalized genomic medicine.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.12-20
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• 2016

Advances in DNA sequencing technologies have contributed to revolutionary understanding of many fundamental biological processes. With unprecedented cost-effective and high-throughput sequencing, a single laboratory can afford to de novo sequence the whole genome for species of interest. In addition, population genetic studies have been remarkably accelerated by numerous molecular markers identified from unbiased genome-wide sequences of population samples. As sequencing technologies have evolved very rapidly, acquiring appropriate individual plants or populations is a major bottleneck in plant research considering the complex nature of plant genome, such as heterozygosity, repetitiveness, and polyploidy. This challenge could be overcome by the old but effective method known as haploid induction. Haploid plants containing half of their sporophytic chromosomes can be rapidly generated mainly by culturing gametophytic cells such as ovules or pollens. Subsequent chromosome doubling in haploid plants can generate stable doubled haploid (DH) with perfect homozygosity. Here, classical methodology to generate and identify haploid plants or DH are summarized. In addition, haploid induction by epigenetic regulation of centromeric histone is explained. Furthermore, the utilization of haploid plant in the genomics era is discussed in the aspect of genome sequencing project and population genetic studies.

• Korean Journal of Microbiology
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• v.54 no.2
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• pp.167-168
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• 2018

Here we report the complete genome sequence of Staphylococcus xylosus S170, strong biofilm-producing strain, which comprised a single circular 2,910,005 bp chromosome and 32.97% G + C content. The genome included 2,674 protein-coding sequences, 22 rRNA genes, and 57 tRNA genes. Gene analysis of S. xylosus S170 could contribute to better understanding of biofilm-forming mechanisms.

• Microbiology and Biotechnology Letters
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• v.49 no.4
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• pp.534-542
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• 2021

Single-molecular guide RNA (sgRNA) plays a role in recognizing the DNA target sequence in CRISPR technology for genome editing and gene expression control. In this study, we systematically compared the length of the target recognition sequence in sgRNAs required for genome editing using Cas9-NG (an engineered Cas9 recognizing 5'-NG as PAM sequence) and gene expression control using deactivated Cas9-NG (dCas9-NG) by targeting the gal promoter in E. coli. In the case of genome editing, the truncation of three nucleotides in the target recognition sequence (TRS) of sgRNA was allowed. In gene expression regulation, we observed that target recognition and binding were possible even if eleven nucleotides were deleted from twenty nucleotides of the TRS. When 4 or more nucleotides are truncated in the TRS of the sgRNA, it is thought that the sgRNA/Cas9-NG complex can specifically bind to the target DNA sequence, but lacks endonuclease activity to perform genome editing. Our study will be helpful in the development of artificial transcription factors and various CRISPR technologies in the field of synthetic biology.

• Journal of the Institute of Convergence Signal Processing
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• v.6 no.1
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• pp.27-32
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• 2005

As a large quantity of Genome sequencing has happened to be done a very much a surprising speed in short period, an automatic genome annotation process has become prerequisite. The most difficult process among with this kind of genome annotation works is to finding out the protein-coding genes within a genome. The main 2 subjects of gene prediction are Eukaryotes and Prokaryotes ; their genes have different structures, therefore, their gene prediction methods will also obviously varies. Until now, it is found that among of the 231 genome sequenced species, 200 have been found to be prokaryotes, therefore, for study of biotechnology studies, through comparative genomics, prokaryotes, rather than eukaryotes could may be more appropriate than eukaryotes. Even more, prokaryotes does not have the gene structure called an intron, so it makes the gene prediction easier. Former prokaryotes gene predictions have been shown to be 80%～ to 90% of accuracy. A recent study is aiming at 100% of gene prediction accuracy. In this paper, especially in the case of the E. coli K-12 and S. typhi genomes, gene prediction accuracy which showed 98.5% and 98.7% was more efficient than previous GLIMMER.

• Annual Conference of KIPS
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• 2012.11a
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• pp.1330-1332
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• 2012

생물정보학 데이터를 분석하는 과정에서 서열 데이터의 시각화는 연구자에게 방대한 서열 데이터의 특성을 눈으로 쉽게 이해하기 위한 필수 과정이다. 대조 실험 데이터나 다중 서열 데이터를 시각화해 주는 많은 도구들이 있지만 방대한 유전체 서열에서 사용자가 원하는 다중 데이터간의 비교 영역을 찾아서 시각화해주는 기능이 부족한 것이 현 상황이다. 본 논문은 불리언 질의를 통해서 다중 전사체 서열을 효율적으로 비교하고 그 결과를 시각화해주는 방법을 제안한다.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.19 no.10
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• pp.2491-2499
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• 2015

Recently, the most popular technique to determine the Genotype, genetic features of individual organisms, is the GBS based on SNP from sequences determined by NGS. As analyzing the sequences by the GBS, TASSEL is the most used program to identify the genotypes. But, TASSEL has limitation that it uses only the partial sequences that is obtained by NGS. We tried to improve the efficiency in use of the sequences in order to solve the limitation. So, we constructed new data sets by quality checking, filtering the unused sequences with error rate below 0.1% and clipping the sequences considering the location of barcode and enzyme. As a result, approximately over 17% of the SNP detection efficiency was increased. In this paper, we suggest the method and the applied programs in order to detect more SNPs by using the disused sequences.

• Proceedings of the Korea Contents Association Conference
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• 2019.05a
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• pp.469-470
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• 2019

차세대염기서열분석법(NGS, Next Generation Sequencing) 기술은 하나의 유전체를 무수히 많은 조각으로 분해하여 각 조각을 동시에 읽어낸 뒤, 전산기술을 이용하여 조합함으로써 방대한 유전체 정보를 빠르게 해독하는 방법이다. 한편, 액체 생검(LB, liquid biopsy)이란 암세포가 깨지면서 생기는 미량의 DNA 조각을 말초혈액 속에서 찾아내 암을 진단하는 기술로 조직 생검(tissue biopsy)에 비해 비침습적이다. 본 논문은 NGS와 LB 기술을 접목했을 때 확진이 가능하고 예후 및 치료경과의 예측이 가능함을 제언하였다.