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- 저자 : TaeWoon Jung (검색결과 3 건)
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SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
Joo, Taewoon,Choi, Ji-Hye,Lee, Ji-Hye,Park, So Eun,Jeon, Youngsic,Jung, Sae Hoon,Woo, Hyun Goo BioMed Central 2019 BMC bioinformatics Vol.20 No.-
<P><B>Backgrounds</B></P><P>Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgently require prompt update of the pipelines. Recent clinical applications of NGS technology such as cell-free DNA, cancer panel, or exosomal RNA sequencing data also require appropriate customization of the processing pipelines. Here, we developed SEQprocess, a highly extendable framework that can provide standard as well as customized pipelines for NGS data processing.</P><P><B>Results</B></P><P>SEQprocess was implemented in an R package with fully modularized steps for data processing that can be easily customized. Currently, six pre-customized pipelines are provided that can be easily executed by non-experts such as biomedical scientists, including the National Cancer Institute’s (NCI) Genomic Data Commons (GDC) pipelines as well as the popularly used pipelines for variant calling (e.g., GATK) and estimation of allele frequency, RNA abundance (e.g., TopHat2/Cufflink), or DNA copy numbers (e.g., Sequenza). In addition, optimized pipelines for the clinical sequencing from cell-free DNA or miR-Seq are also provided. The processed data were transformed into R package-compatible data type ‘ExpressionSet’ or ‘SummarizedExperiment’, which could facilitate subsequent data analysis within R environment. Finally, an automated report summarizing the processing steps are also provided to ensure reproducibility of the NGS data analysis.</P><P><B>Conclusion</B></P><P>SEQprocess provides a highly extendable and R compatible framework that can manage customized and reproducible pipelines for handling multiple legacy NGS processing tools.</P>
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Balance Deficit and Brain Connectivity in Children with Attention-Deficit/Hyperactivity Disorder
SunMi Kim,GiJung Hyun,TaeWoon Jung,YoungDon Son,InHee Cho,BaikSeok Kee,DougHyun Han 대한신경정신의학회 2017 PSYCHIATRY INVESTIGATION Vol.14 No.4
Objective-We aimed to assess disturbances in postural and gait balance and functional connectivity within the brain regions controlling balance in children with attention-deficit/hyperactivity disorder (ADHD). Methods-Thirteen children with ADHD and 13 age- and sex-matched controls were recruited. Gait balance was assessed by the difference in the center of pressure (COP) between the left and right foot, as well as the difference in plantar pressure between the left and right foot during gait. Neuroimaging data were acquired using a 3.0 Tesla MRI scanner. Functional connectivity between the vermis of the cerebellum and all other brain regionswas assessed. Results-The difference in plantar pressure between the left foot and right foot in the ADHD group was greater than that observed in the control group. The average COP jerk score of the right foot in the ADHD group was higher than that observed in the control group. A higher functional connectivity between the cerebellum and the right middle frontal gyrus (premotor cortex) and medial frontal gyrus (cingulate gyrus) was observed in the control group relative to the ADHD group. In the ADHD group, the difference in plantar pressure between the left and right foot was also negatively correlated with the beta-value within the middle frontal gyrus. Conclusion-Children with ADHD had disturbance of balance as assessed by plantar pressure. Decreased brain connectivity from the cerebellum to the premotor cortex and anterior cingulate was associated with disturbances of posture and balance in children with ADHD.
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한방병원에 입원한 흉곽출구증후군을 동반한 Wrist Drop 환자에 대한 한방 치료 1예
민태운,강도현,안재서,이현준,이한솔,김한결,이성민,조소현,지형욱,고일환,김지원,윤정민,정혁진,Min, Taewoon,Kang, Dohyeon,Ahn, Jaeseo,Lee, Hyunjun,Lee, Hansol,Kim, Hankyul,Lee, Seongmin,Cho, Sohyun,Ji, Hyungwook,Ko, Ilhwan,Kim, Jiwon,Yun, Jung 한방재활의학과학회 2022 한방재활의학과학회지 Vol.32 No.4
The purpose of this study is to report the effects of Korean medicine treatment in wrist drop patient with thoracic outlet syndrome. We treated the patient for 8 days using Korean medicine treatment such as herbal medicine, acupuncture, Chuna manual therapy and pharmacopuncture. Changes in the numerical rating scale (NRS), EuroQol five dimension (EQ-5D) index, and symptoms were measured for assessment. After 8 days hospitalization, NRS decreased from 5 to 3, EQ-5D index and the symptoms of the patient also were improved. In conclusion, this case shows that Korean medicine treatment can be an effective treatment for wrist drop with thoracic outlet syndrome.
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