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Jang, Insu,Chang, Hyeshik,Jun, Yukyung,Park, Seongjin,Yang, Jin Ok,Lee, Byungwook,Kim, Wankyu,Kim, V. Narry,Lee, Sanghyuk Oxford University Press 2015 Bioinformatics Vol.31 No.4
<P><B>Summary:</B> Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase.</P><P><B>Availability and implementation:</B> miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr.</P><P><B>Contact:</B> sanghyuk@ewha.ac.kr</P>
lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
Park, Charny,Yu, Namhee,Choi, Ikjung,Kim, Wankyu,Lee, Sanghyuk Oxford University Press 2014 Bioinformatics Vol.30 No.17
<P><B>Motivation:</B> A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need.</P><P><B>Results:</B> We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein–lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface.</P><P><B>Availability and implementation:</B> lncRNAtor is available at http://lncrnator.ewha.ac.kr/.</P><P><B>Contact:</B> sanghyuk@ewha.ac.kr</P><P><B>Supplementary information:</B> Supplementary data are available at <I>Bioinformatics</I> online.</P>
Characterization of TNNC1 as a Novel Tumor Suppressor of Lung Adenocarcinoma
Kim, Suyeon,Kim, Jaewon,Jung, Yeonjoo,Jun, Yukyung,Jung, Yeonhwa,Lee, Hee-Young,Keum, Juhee,Park, Byung Jo,Lee, Jinseon,Kim, Jhingook,Lee, Sanghyuk,Kim, Jaesang Korean Society for Molecular and Cellular Biology 2020 Molecules and cells Vol.43 No.7
In this study, we describe a novel function of TNNC1 (Troponin C1, Slow Skeletal and Cardiac Type), a component of actin-bound troponin, as a tumor suppressor of lung adenocarcinoma (LUAD). First, the expression of TNNC1 was strongly down-regulated in cancer tissues compared to matched normal lung tissues, and down-regulation of TNNC1 was shown to be strongly correlated with increased mortality among LUAD patients. Interestingly, TNNC1 expression was enhanced by suppression of KRAS, and ectopic expression of TNNC1 in turn inhibited KRAS<SUP>G12D</SUP>-mediated anchorage independent growth of NIH3T3 cells. Consistently, activation of KRAS pathway in LUAD patients was shown to be strongly correlated with down-regulation of TNNC1. In addition, ectopic expression of TNNC1 inhibited colony formation of multiple LUAD cell lines and induced DNA damage, cell cycle arrest and ultimately apoptosis. We further examined potential correlations between expression levels of TNNC1 and various clinical parameters and found that low-level expression is significantly associated with invasiveness of the tumor. Indeed, RNA interference-mediated down-regulation of TNNC1 led to significant enhancement of invasiveness in vitro. Collectively, our data indicate that TNNC1 has a novel function as a tumor suppressor and is targeted for down-regulation by KRAS pathway during the carcinogenesis of LUAD.
Epidemiological Characteristics of COVID-19 Outbreak at Fitness Centers in Cheonan, Korea
Bae Sanghyuk,Kim Hwami,Jung Tae-Young,Lim Ji-Ae,Jo Da-Hye,Kang Gi-Seok,Jeong Seung-Hee,Choi Dong-Kwon,Kim Hye-Jin,Cheon Young Hee,Chun Min-kyo,Kim Miyoung,Choi Siwon,Chun Chaemin,Shin Seung Hwan,Kim H 대한의학회 2020 Journal of Korean medical science Vol.35 No.31
Background: In February 2020, a coronavirus disease 2019 (COVID-19) outbreak was reported in fitness centers in Cheonan, Korea. Methods: From February 24 to March 13, an epidemiological investigation was conducted on the fitness center outbreak. All those who were screened were tested for severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) using real-time reverse transcriptase polymerase chain reaction. Contacts were traced and self-isolated for 14 days. We determined the epidemiological characteristics of confirmed cases of SARS-CoV-2 infection, and estimated the time-dependent reproduction number to assess the transmission dynamics of the infection. Results: A total of 116 cases were confirmed, and 1,687 contacts were traced. The source cases were 8 Zumba instructors who led aerobics classes in 10 fitness centers, and had the largest average number of contacts. A total of 57 Zumba class participants, 37 of their family members, and 14 other contacts were confirmed as cases. The attack rate was 7.3%. The contacts at Zumba classes and homes had a higher attack rate than other contacts. The mean serial interval (± standard deviation) were estimated to be 5.2 (± 3.8) days. The time- dependent reproduction number was estimated to be 6.1 at the beginning of the outbreak, but it dropped to less than 1, 2 days after the epidemiological investigation was launched. Conclusion: The results suggest that the COVID-19 outbreak was effectively contained with rigorous contact tracing, isolating, and testing in combination with social distancing without a lock-down.
ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs
Kim, Namshin,Lim, Dajeong,Lee, Sanghyuk,Kim, Heebal Oxford University Press 2005 Nucleic acids research Vol.33 No.2
<P>RT–PCR is one of the most powerful and direct methods to detect transcript variants due to alternative splicing (AS) that increase transcript diversity significantly in vertebrates. ASePCR is an efficient web-based application that emulates RT–PCR in various tissues. It estimates the amplicon size for a given primer pair based on the transcript models identified by the reverse e-PCR program of the NCBI. The tissue specificity of each PCR band is deduced from the tissue information of expressed sequence tag (EST) sequences compatible with each transcript structure. The output page shows PCR bands like a gel electrophoresis in various tissues. Each band in the output picture represents a putative isoform that could happen in a tissue-specific manner. It also shows the EST alignment and tissue information in the genome browser. Furthermore, the user can compare the AS patterns of orthologous genes in other species. The ASePCR, available at , supports the transcriptome models of the RefSeq, Ensembl, ECgene and AceView for human, mouse, rat and chicken genomes. It will be a valuable web resource to explore the transcriptome diversity associated with different tissues and organs in multiple species.</P>
Development of SED Camera for Quasars in Early Universe (SQUEAN)
Kim, Sanghyuk,Jeon, Yiseul,Lee, Hye-In,Park, Woojin,Ji, Tae-Geun,Hyun, Minhee,Choi, Changsu,Im, Myungshin,Pak, Soojong Astronomical Society of the Pacific 2016 Publications of the Astronomical Society of the Pa Vol.128 No.969
<P>We describe the characteristics and performance of a camera system, Spectral energy distribution Camera for Quasars in Early Universe (SQUEAN). It was developed to measure SEDs of high-redshift quasar candidates (z greater than or similar to 5) and other targets, e.g., young stellar objects, supernovae, and gamma-ray bursts, and to trace the time variability of SEDs of objects such as active galactic nuclei (AGNs). SQUEAN consists of an on-axis focal plane camera module, an autoguiding system, and mechanical supporting structures. The science camera module is composed of a focal reducer, a customizable filter wheel, and a CCD camera on the focal plane. The filter wheel uses filter cartridges that can house filters with different shapes and sizes, enabling the filter wheel to hold 20 filters of 50 mm x 50 mm size, 10 filters of 86 mm x 86 mm size, or many other combinations. The initial filter mask was applied to calibrate the filter wheel with high accuracy, and we verified that the filter position is repeatable at much less than one pixel accuracy. We installed and tested 50 nm medium bandwidth filters of 600-1050 nm and other filters at the commissioning observation in 2015 February. We found that SQUEAN can reach limiting magnitudes of 23.3-25.3 AB mag at 5 sigma in a one-hour total integration time.</P>