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Complete genome sequence of a methicillin-resistant Staphylococcus schleiferi strain from canine otitis externa in Korea

Lee GY, Yang SJ

The increase in canine skin and soft tissue infections, such as pyoderma and otitis, caused by Staphylococcus schleiferi strains, is of significant zoonotic concern. In this study, we report the...
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High-quality draft genome and characterization of commercially potent probiotic Lactobacillus strains

Sulthana A, Lakshmi SG, Madempudi

Lactobacillus acidophilus UBLA-34, L. paracasei UBLPC-35, L. plantarum UBLP-40, and L. reuteri UBLRU-87 were isolated from different varieties of fermented foods. To determine the probiotic safety at the strain level,...
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Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data

Lee Y, Park K, Koh I

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate....
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Association of Korean fermented cabbage kimchi consumption with an incidence of metabolic syndrome: 10-year follow-up results of the Korean Genome and Epidemiology Study

Seo SH, Hong J, Son IH, Han YH, Hyun T

PURPOSE: This study examined the associations of Korean fermented cabbage kimchi consumption with the incidence risk of metabolic syndrome and its components in Korean adults. METHODS: We used the community-based cohort...
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Cellulitis Caused by a Novel Cupriavidus Species Strain J1218 Identified by Whole Genome Sequencing

Ko YJ, Yoon SY, Lim CS, Lee CK

We report a case of cellulitis caused by a novel Cupriavidus species identified using whole-genome sequence analysis. Subcutaneous tissue biopsies from the left lower leg of a 67-year-old man who...
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Association between Serum Gamma-Glutamyltransferase and Prevalence of Metabolic Syndrome Using Data from the Korean Genome and Epidemiology Study

Lee MY, Hyon DS, Huh JH, Kim HK, Han SK, Kim JY, Koh SB

BACKGROUND: The aim of this study was to determine whether there is a positive correlation between gamma-glutamyltransferase (GGT) levels and the prevalence of metabolic syndrome and whether GGT can be...
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Genome Engineering for Osteoarthritis: From Designer Cells to Disease-Modifying Drugs

Choi YR, Collins KH, Lee JW, Kang HJ, Guilak F

BACKGROUND: Osteoarthritis (OA) is a highly prevalent degenerative joint disease involving joint cartilage and its surrounding tissues. OA is the leading cause of pain and disability worldwide. At present, there...
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A Relationship between Dietary Patterns and Dyslipidemia in Urban-dwelling Middle-Aged Korean Men: Using Korean Genome and Epidemiology Study (KoGES)

Na W, Chung B, Sohn C

An increase in the prevalence of dyslipidemia has been strongly associated with the mortality rate of cardiovascular disease. We conducted a cross-sectional analysis to determine the relationship between dietary patterns...
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The length of guide RNA and target DNA heteroduplex effects on CRISPR/Cas9 mediated genome editing efficiency in porcine cells

Lv J, Wu S, Wei R, Li Y, Jin J, Mu Y, Zhang Y, Kong Q, Weng X, Liu Z

The clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile genome editing tool with high efficiency. A guide sequence of 20 nucleotides (nt) is commonly...
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Generation of knockout mouse models of cyclin-dependent kinase inhibitors by engineered nuclease-mediated genome editing

Park BM, Roh JI, Lee J, Lee HW

Cell cycle dysfunction can cause severe diseases, including neurodegenerative disease and cancer. Mutations in cyclin-dependent kinase inhibitors controlling the G1 phase of the cell cycle are prevalent in various cancers....
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Genome Sequencing of Human Cytomegalovirus Strain LCW and Identification of Asia-specific Cluster

Kang JH, Yoon JH, Hwang HR, Lee CH

Human cytomegalovirus (HCMV) is a ubiquitous human pathogen and contains double stranded DNA genome with approximately 230 kbp. Molecular genomic studies of HCMV have been attempted in order to understand...
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Principles of Archaeogenetics and the Current Trends of Ancient Genome Studies

Kim T, Woo EJ, Pak S

Archaeogenetics is an academic discipline that aims to establish scientific facts of human history by integrating ancient DNA analyses with archaeological and anthropological evidence. After ancient DNA research was initiated...
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Using low-coverage whole genome sequencing technique to analyze the chromosomal copy number alterations in the exfoliative cells of cervical cancer

Ren T, Suo J, Liu S, Wang S, Shu S, Xiang Y, Lang JH

OBJECTIVES: We analyzed the chromosomal-arm-level copy number alterations (CNAs) in the cervical exfoliative cell and tissue samples by using the low-coverage whole genomic sequencing technique. METHODS: In this study, we retrospectively...
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mRNA Expression of SLC5A5 and SLC2A Family Genes in Papillary Thyroid Cancer: An Analysis of The Cancer Genome Atlas

Suh S, Kim YH, Goh TS, Jeong DC, Lee CS, Jang JY, Cha W, Han ME, Kim SJ, Kim IJ, Pak K

PURPOSE: The present study investigated the dynamics and prognostic role of messenger RNA (mRNA) expression responsible for 18F-fluorodeoxyglucose (FDG) uptake in FDG positron emission tomography (PET) and radioactive iodine (131I)...
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BCL2 Regulation according to Molecular Subtype of Breast Cancer by Analysis of The Cancer Genome Atlas Database

Hwang KT, Kim K, Chang JH, Oh S, Kim YA, Lee JY, Jung SH, Choi IS

PURPOSE: We investigated B-cell lymphoma 2 (BCL2) regulation across DNA, RNA, protein, and methylation status according to molecular subtype of breast cancer using The Cancer Genome Atlas (TCGA) database. MATERIALS AND...
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Glycated Hemoglobin and Cancer Risk in Korean Adults: Results from Korean Genome and Epidemiology Study

Kim JY, Lee YS, Jo G, Shin MJ

The purpose of this study was to test whether elevated glycated hemoglobin A1c (HbA1c) levels are associated with cancer incidence in the Korean population. In cohorts of the Korea Genome...
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Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments

Ryoo S, Lee J, Oh JY, Kim BK, Kim Y, Kim JH, Shin C, Lee SH

BACKGROUND: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been...
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Identification and characterization of atypical porcine pestivirus genomes in newborn piglets with congenital tremor in China

Shen H, Liu X, Zhang P, Wang L, Liu Y, Zhang L, Liang P, Song C

Recently, a novel atypical porcine pestivirus (APPV) in pig was reported. In this study, two APPV strains, APPV-China/GZ01/2016 (GZ01) and APPV-China/GD-SD/2016 (GD-SD), were identified in two newborn piglet herds with...
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Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data

Lee YS, Shin D

Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution...
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Apolipoprotein A5 3'-UTR variants and cardiometabolic traits in Koreans: results from the Korean genome and epidemiology study and the Korea National Health and Nutrition Examination Survey

Kim OY, Moon J, Jo G, Kwak SY, Kim JY, Shin MJ

BACKGROUND/OBJECTIVES: This study aimed to test the association between APOA5 3'-UTR variants (rs662799) and cardiometabolic traits in Koreans. SUBJECTS/METHODS: For this study, epidemiological data, Apolipoprotein A5 (APOA5) genotype information, and lymphoblastoid...
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