NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data

Dong‑Jun Lee,Taesoo Kwon,Chang‑Kug Kim,Young‑Joo Seol,Dong‑Suk Park,Tae‑Ho Lee,Byung‑Ohg Ahn 한국유전학회 2020 Genes & Genomics Vol.42 No.11

Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genomeproject consortiums provide standard operation procedures for sequence variation detection methods, there may be differencesin the results because of human selection or error. Objective To standardize the procedure for sequence variation detection and help researchers who are not formally trainedin bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline. Methods The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operatingsystem (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) andUbuntu Linux (version 16.04, 17.0.4). Results The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also providesquality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variantvisualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally,the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA. Conclusions Although there are several pipelines and visualization tools available for NGS data analysis, we developedthe NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that theNGS_SNPAnayzer achieves better performance than other open source tools.

電磁調理器용 ZVS 고주파 인버터의 특성해석

김동희,심광열,오승훈,신수국 嶺南大學校 工業技術硏究所 1996 工業技術硏究所論文集 Vol.24 No.1

In this paper, we proposed a form of load resonant inverter made which use of soft switching technology to reduce stress and turn on/off loss at switching and described about its principle operation with coupling coefficient. The general operation characteristic of the inverter is depicted by introducing normalized control variables. The characteristic of the inverter are evaluated by load time constant and a coupling coefficient. When the load changes suddenly from steady state operation, the characteristics are analyzed. Based on the characteristics value, a method of circuit design is proposed. In addition, the results of its characteristics analysis are compared with that of pspice's simulation and experimental waveform are compared with theoretical ones.

무선 통신망에서 보안 인증 프로토콜 절차

김동국,김희철,나기창,배철수,나상동 조선대학교 전자정보통신연구소 2002 電子情報通信硏究所論文誌 Vol.5 No.1

Recently, We are using B-ISDN(Broadband Integrated Services Digital Network) with backbone based on ATM(Asynchronous Transfer Mode), the rapid incresement of user for Mobile Computing application and conversion to radio ATM networks had brought by mobile phone, portable computer spread using and extension of multimedia service brought multimedia mobile communications service to increasing the demands. ATM networks gives communication services based on protocol stack with communized the features of wire ATM-network on the whole' structure and has structure supported migratory in radio section. In this paper, we are going to look at services of authentication, access control, confidentiality, integrity and key exchange which are used with solution for privacy detection from an intrusion of persons privacy by illegal intrusion and every threat to user and service suppling company. And we are studying existing mechanism about security service, authentication protocol and data integrity supply in connection with packetization and depacketization about protocol. We are supposed to look at the features of existing wire ATM network, security service application in three plane in chapter 2, the features and basic structure about wireless ATM network which is extended to radio section based on wire ATM comparison and analysis about authentication protocol applied to security constituent matters which should improve in chapter 3. we are propose about security authentication protocol in control plane, one of wireless ATM protocol reference model in chapter 4, results and study direction about proposed contents in chapter 5.

국적 항공사의 경쟁력 강화를 위한 포지셔닝 전략에 관한 연구

윤병국,이동희 한국관광정보학회 2001 觀光情報硏究 Vol.- No.9

The international airline industry has a phenomenal growth since the Airline Deregulation Act was enacted in 1978. In recent years, Korea's national flag carriers are facing steep challenges to survive in the ever-growing competition. Under the situation, positioning can be used as a competitive strategy tool. The purpose of the study was to analyze the image of seven airlines that fly to Korea and to develop positioning strategies for Korea's national flag carriers. For the empirical research, the survey data were collected from 700 passengers: 600 passengers who were on board Korean Air and Asiana Airlines and 100 from people who have flown seven major airlines: Korean Air, Asiana Airlines, Japan Airline, United Airline, Cathay Pacific Airways, Thai Airways, Singapore Airlines. Out of 700 samples, 377 were used for statistical analysis. Results of this study are summarized as follows: First, safety was the most significant attribute which influences on airlines image and airlines decision-making. On-time operation was the second most important attribute, but passengers were very unsatisfied with the actual performance. passengers who had the membership with airlines considered importantly the 'system-related service' factores such as frequent flyer program, mileage service, efficient reservation system and quick check-in procedure. Second, according to the results of comparative analysis of airlines, passengers assessed that the Korean Air has a strong image in convenient schedule and frequent flyer program. For the Asiana Airlines, passengers evaluated that the airline's image was found on quality of cabin service, safety, quality in-flight meal, low fares, and on-time operation. For the foreign airlines, passengers expressed that each airline has distinctive image. Future research on airline positioning strategies need to enlarge to more famous airlines. Thus, it is expected to help to set up competitive strategies for Korea's national flag carrier.

자궁경부 종양에서 Nested PCR을 이용한 인유두종 바이러스 16형 및 18형의 검출과 임상적 의의

최규연,이종국,최승도,배동한,김휘준,김민관 순천향의학연구소 1999 Journal of Soonchunhyang Medical Science Vol.5 No.2

The aim of this study is to estimate the prevalence of HPV types(16, 18) in cervix of gynecologic patients and to elucidate the relationship of HPV types(16, 18) and clinical characteristics. Human papilloma virus(HPV) has attracted attention as one of the viruses linked to human cancers. Numerous clinical, epidemiological, and molecular studies indicate that certain genital HPV types are associated with cervical carcinoma. Of 100 types of HPV identified today, at least 40 have been found in the anogenital mucosa. A classification of these types into three groups with differing pathogenicity has been proposed: HPV type 6, 11, 42, 43, and 44 are detected more frequently in benign lesions such as condylomata; HPV type 31, 33, 35, 51, 52, and 58 are found more often in low grade squamous intraepithelial lesions than invasive lesions; and HPV 16, 18, 45, and 56 are predominant in high grade squamous intraepithelial lesions and invasive carcinoma. To detect HPV types prevalent in carcinoma of the uterine cervix, a type-specific, sensitive polymerase chain reaction(PCR)-based assay for HPV types 16, 18 was applied to 18 cervical carcinomas(15 squamous cell carcinomas and 3 adenocarcinomas), 21 cases of cervical intraepithelial neoplasia(CIN), and 42 samples of cervicitis and histologically normal. DNA extraction from cervical swab was done using DNAzol™(MBI, USA) and Nested PCR was done using HPV detection kit(Bioneer, Korea). The amplified product was analyzed directly on the basis of the site of ethidium bromide-stained band visible after agarose gel electrophoresis. The results were as follows 1. The positivity rates of HPV type 16 and HPV type 18 were 12.5%(90/718), 2,5%(18/718). so, HPV 16 positive cases(12.5%) was five folds as HPV 18 positive cases(2.5%) 2. Forty eight percents(39/81) of HPV 16 or HPV 18 positive cases were CIN, microinvasive cancer. 3. Age, Gestation number, Clinical stage, Histologic cell type in relation to HPV types were not statistically significant.

가토 외고정 모델을 이용한 치밀체형 세라믹스의 골결합능 평가

이재협,이동호,이재학,공현식,안영준,류현승,서준혁,홍국선,김환,장봉순,이춘기 대한정형외과연구학회 2003 대한정형외과연구학회지 Vol.6 No.2

非晶質 silicon 太陽電池 製造 技術 開發

金起柱,金東弼,金元燮,房極生 全北大學校 1985 論文集 Vol.27 No.-

An amorphous semiconductor, which has not long distant orders of atomic arrangement, is dissimilar to crystalline semiconductor in optical and electrical characteristics. For applications as industrial materials. its manufacturing and matters of concern. Glow discharge method was used in this research and improvement of transformation efficiency, technical development of modulation, and reformation of the structure and characteristics of noncrystalline are surveyes.

약골 골절후 발생된 골수염의 처치의 치험례

이철희,서정식,고말식,손동석,김성국 大韓顎顔面成形再建外科學會 1995 Maxillofacial Plastic Reconstructive Surgery Vol.17 No.3

With the use of antibiotics and improved dental care, osteomyelitis of the jaw is less common these days. But sometimes the management of osteomyelitis is more difficult because of appearance of resistant organisms to antibiotics. Treatment of the steomyelitis are incision and drainage, closed catheter irrigations, sequestrectomy, saucerization, hyperbaric ocygen therapy, and resection with or without bone graft. We experienced advanced osteomyelitis due to delayed treatment of left mandibular angle fracture. He have medical history of pschysoprenia. We decided to treat the patient with open reduction and closed cather irrigation. We achived reconsolidation of mandibular fracture accompanied by osteomyelitis by complete removal of inflammatory tissues, rigid fixation with miniplate and closed catheter irrigation.

Session J : Plant Gene Structure and Expression : IDENTIFICATION OF LRE IN Arabidopsis cab PROMOTER AND LRE - BINDING PROTEIN FACTORS

Dong Kug Choi,Hee Jin Park,Hwa Hyung Lee,In Soo Kim 생화학분자생물학회(구 한국생화학분자생물학회) 1993 추계학술대회집 Vol.- No.-

Signaling Pathway Analysis of $MPP^+$-treated Human Neuroblastoma SH-SY5Y Cells

Choi, Dong-Kug,Kim, In Su,Do, Jin Hwan 한국생물공학회 2014 Biotechnology and Bioprocess Engineering Vol.19 No.2

Parkinson's disease (PD) is a common chronic neurodegenerative disorder primarily caused by death of dopaminergic neurons in the substantia nigra pars compacta (SN). Human neuroblastoma SH-SY5Y cells have been broadly utilized in studies of mechanisms of the pathogenesis underlying $MPP^+$-induced PD mimics. However, the pathways impacted in $MPP^+$-treated SH-SY5Y cells have not been examined at genome-wide level. Here, we examined genome-wide response of $MPP^+$-treated SH-SY5Y cells with whole genome expression array including 47,231 probes and identified 169 genes that were significantly differentially expressed in a significance analysis of microarrays. Gene ontology (GO) terms such as GO:0051900 (regulation of mitochondrial depolarization), GO:0008637 (apoptotic mitochondrial changes), GO:0090090 (negative regulation of canonical Wnt receptor signaling pathway), and GO:0009968 (negative regulation of signal transduction) were significantly overrepresented in a differentially expressed genes (DEGs) analysis. The DEG information and their fold changes in expression were used to identify the pathways impacted. Five pathways, including systemic lupus erythematosus, alcoholism, prion diseases, the Wnt signaling pathway, and axon guidance had a significant impact at a threshold of $P_G=0.05$. Our results suggest that $MPP^+$ toxicity of SH-SY5Y cells might be related to transcriptional dysregulation by a nucleosome structural defect, endoplasmic reticulum stress, and inhibited canonical Wnt signaling.