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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>
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>
Relation between Certainty and Uncertainty with Fuzzy Entropy and Similarity Measure
Sanghyuk Lee,Yujia Zhai 한국융합학회 2014 한국융합학회논문지 Vol.5 No.4
We survey the relation of fuzzy entropy measure and similarity measure. Each measure represents features of data uncertainty and certainty between comparative data group. With the help of one-to-one correspondence characteristics, distance measure and similarity measure have been expressed by the complementary characteristics. We construct similarity measure using distance measure, and verification of usefulness is proved. Furthermore analysis of similarity measure from fuzzy entropy measure is also discussed.
( Sanghyuk Lee ),( Donghyun Kim ),( Kyungsik Son ),( Yongje Choi ),( Wonsub Chung ) 대한금속재료학회(구 대한금속학회) 2016 대한금속·재료학회지 Vol.54 No.5
A typical brightener-propargyl alcohol-was added to enhance the cutting performance during Ni-diamond composite electrodeposition. Electrochemical analysis was performed and mechanical properties such as hardness and wear resistance were examined. In addition, the surface morphology of composite coating layers was observed using an optical microscope, and using image analysis software, the dispersivity of the diamond particles was analyzed to calculate the number of single diamond particles. A galvanostatic test was employed to identify the electrodeposition mechanism as a function of the concentration of propargyl alcohol. When 0.1 mg/ℓ of propargyl alcohol was added, the dispersivity and adhesion performances of the Ni-diamond coating layer were optimized for cutting tools. (Received September 22, 2015)
Sanghyuk Lee,Seung-Hi Lee,Chung Choo Chung 제어로봇시스템학회 2018 제어로봇시스템학회 국제학술대회 논문집 Vol.2018 No.10
This paper presents a new vehicle localization method that improves rear-view camera usage during automatic parking. Measuring the position of a parking stall with cameras is significantly affected by vehicle’s pitch motion during parking. The pitch motion is influenced by the number of passengers and its jerk while moving backward, and leads to inaccurate distance measurement during parking. To cope with the problem, a new vehicle localization using an interacting multiple model (IMM) Kalman filter is proposed. The IMM filter is to improve the accuracy of the camera measurement influenced by pitch changes during backward motion. In this paper, we used two models based on the car’s pitch motion. We obtained improved vehicle localization performance using the IMM Kalman filter and validated its performance experimentally via a real-vehicle experiment with a various number of passengers.