miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data

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>

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

Lee, Soohyun,Seo, Chae Hwa,Lim, Byungho,Yang, Jin Ok,Oh, Jeongsu,Kim, Minjin,Lee, Sooncheol,Lee, Byungwook,Kang, Changwon,Lee, Sanghyuk Oxford University Press 2011 Nucleic acids research Vol.39 No.2

<P>We propose a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. Our method, NEUMA (Normalization by Expected Uniquely Mappable Area), is based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. Quantitative RT–PCR based on 27 randomly selected genes in two human cell lines and computer simulation experiments demonstrated superior accuracy of NEUMA over other recently developed methods. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (‘consistency coefficient’) for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. We propose that NEUMA could make a standard method in quantifying gene transcript levels from RNA-Seq data.</P>

Genetic Landscape of Open Chromatin in Yeast

Lee, Kibaick,Kim, Sang Cheol,Jung, Inkyung,Kim, Kwoneel,Seo, Jungmin,Lee, Heun-Sik,Bogu, Gireesh K.,Kim, Dongsup,Lee, Sanghyuk,Lee, Byungwook,Choi, Jung Kyoon Public Library of Science 2013 PLoS genetics Vol.9 No.2

<▼1><P>Chromatin regulation underlies a variety of DNA metabolism processes, including transcription, recombination, repair, and replication. To perform a quantitative genetic analysis of chromatin accessibility, we obtained open chromatin profiles across 96 genetically different yeast strains by FAIRE (formaldehyde-assisted isolation of regulatory elements) assay followed by sequencing. While 5∼10% of open chromatin region (OCRs) were significantly affected by variations in their underlying DNA sequences, subtelomeric areas as well as gene-rich and gene-poor regions displayed high levels of sequence-independent variation. We performed quantitative trait loci (QTL) mapping using the FAIRE signal for each OCR as a quantitative trait. While individual OCRs were associated with a handful of specific genetic markers, gene expression levels were associated with many regulatory loci. We found multi-target <I>trans</I>-loci responsible for a very large number of OCRs, which seemed to reflect the widespread influence of certain chromatin regulators. Such regulatory hotspots were enriched for known regulatory functions, such as recombinational DNA repair, telomere replication, and general transcription control. The OCRs associated with these multi-target <I>trans</I>-loci coincided with recombination hotspots, telomeres, and gene-rich regions according to the function of the associated regulators. Our findings provide a global quantitative picture of the genetic architecture of chromatin regulation.</P></▼1><▼2><P><B>Author Summary</B></P><P>Quantitative trait loci (QTL) mapping is a genetic approach that allows the identification of genetic factors underlying a phenotype of interest. Genomic technologies such as DNA microarray and next-generation sequencing provide data that can be used for the analysis of multiple molecular phenotypes. For example, the expression levels of thousands of genes can be associated with subject-specific genome-wide genetic information in expression QTL mapping. Similarly, the genetic regulation of transcription factor binding or epigenetic mechanisms such as DNA methylation or chromatin structure has begun to be investigated. In particular, the mechanisms controlling chromatin accessibility have attracted special interest due to their importance in a variety of DNA regulation processes including recombination, repair, replication, and transcription. In this work, we sought to dissect the genetic architecture of chromatin accessibility regulation by harnessing the power of genetic and genomic techniques. By analyzing open (accessible) chromatin maps of multiple yeast individuals in association with their genetic backgrounds, we were able to characterize the regulatory structure of chromatin traits versus that of gene expression. Importantly, we observed that the genetic loci responsible for multiple open chromatin regions were enriched for known regulatory factors.</P></▼2>

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining

Lee, Myunggyo,Lee, Kyubum,Yu, Namhee,Jang, Insu,Choi, Ikjung,Kim, Pora,Jang, Ye Eun,Kim, Byounggun,Kim, Sunkyu,Lee, Byungwook,Kang, Jaewoo,Lee, Sanghyuk Oxford University Press 2017 Nucleic acids research Vol.45 No.d1

<P>Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/.</P>

A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population

Lee JeongEun,Lee Jean,Jeon Sungwon,Lee Jeongha,Jang Insu,Yang Jin Ok,Park Soojin,이병욱,Choi Jinwook,Choi Byung-Ok,Gee Heon Yung,Oh Jaeseong,Jang In-Jin,Lee Sanghyuk,Baek Daehyun,Koh Youngil,Yoon Sung-So 생화학분자생물학회 2022 Experimental and molecular medicine Vol.54 No.-

Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website (https://www.kobic.re.kr/kova/). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.

Electroless Nickel Plating of Alumiun Mirrors for Off-Axis Telescope System

Sanghyuk Kim,Soojong Pak,Geon Hee Kim,Gil Jae Lee,Jong-Ho Lee,Su-Min Lee,Seunghyuk Chang,Myungshin Im,Hyuckee Lee 한국천문학회 2013 天文學會報 Vol.38 No.2

대규모 원격 운용환경에서의 전술적 군 센서네트워크 설계

이상혁(Sanghyuk Lee),이수빈(Soobin Lee),송희철(Hee Cheol Song),이황수(Hwang Soo Lee) 한국통신학회 2009 한국통신학회 학술대회논문집 Vol.2009 No.6

선상 이산화탄소 포집시스템 기술에 관한 국제해사기구(IMO) 해양환경보호위원회(MEPC) 논의 동향

이성엽(Seong-yeob Lee),정태환(Tae-hwan Joung),강성길(Seong-gil Kang),이다희(Dahee Lee),김진형(Jinhyung Lee),이상혁(Sanghyuk Lee) 한국해양환경·에너지학회 2021 한국해양환경·에너지학회 학술대회논문집 Vol.2021 No.10

선박은 효율적이며 친환경적인 화물운송 수단이지만, 국제사회는 더 개선된 지구환경을 위해 선박으로부터의 오염물질 방출 저감을 요구하고 있다. 국제해사기구(IMO)는 국제항행을 하는 선박에서 배출되는 온실가스 감축 목표를 2008년 대비 2050년까지 최소 50%로 설정하였다. 현 시점에서 해운사들은 운항속도를 조절함으로써 탄소 배출량 규제에 대응하고 있으며, 조선업계에서는 에너지 효율 개선 장치, 저탄소(LNG, 메탄올 등) 추진 기술, 무탄소(암모니아, 수소 등) 추진 기술 등을 개발하고 있다. 최근 제4차 IMO GHG 연구 결과에서는 IMO 온실가스 감축 목표에 대응하기 위해서 무탄소 및 탄소중립연료 도입이 반드시 필요하다는 결론을 도출하였다. 하지만, 무탄소 대체연료(암모니아, 수소)를 선박에 상용화시키기 위해서는 극복해야할 난제가 상당히 많다. 현재 IMO 해양환경보호위원회(MEPC)에서 논의되고 있는 온실가스 감축 계획이 일정 변경없이 진행되고, 무탄소 선박연료 상용화에 상당한 시간이 소요될 것이라면, 징검다리 기술로서 선상 이산화탄소 포집시스템(Onboard Carbon Capture & Storage System, OCCS)을 고려할 필요가 있다. 본 연구에서는 현재 선박에 고려되고 있는 OCCS 기술을 검토하고, EEDI/EEXI 프레임에 OCCS 영향을 반영하는 산정식을 제안한다. Ships are an efficient and eco-friendly means of transporting cargo, but the international community is demanding lower emissions of pollutants from ships for a better global environment. The International Maritime Organization (IMO) has set its target for reducing greenhouse gas emissions from international vessels at least 50% by 2050 compared to 2008. At this point, shipping companies are responding to regulations on carbon emissions by controlling operating speed, and shipbuilding industries are developing energy efficiency improvement devices, low-carbon (LNG, methanol, etc.) propulsion technologies, and carbon-free (ammonia, hydrogen, etc.) propulsion technologies. Recent results from the fourth IMO GHG study concluded that the introduction of carbon-free and carbon-neutral fuels is essential to respond to IMO greenhouse gas reduction goals. However, there are considerable challenges to overcome in order to commercialize carbon-free alternative fuels (ammonia, hydrogen) on ships. If the greenhouse gas reduction plan, currently being discussed at the IMO Marine Environmental Protection Commission (MEPC), will take considerable time to commercialize carbon-free ship fuels, it is necessary to consider onboard Carbon Capture & Storage System (OCCS) as a stepping stone technology. In this study, we review the OCCS technology currently being considered for ships and propose a formula that reflects the OCCS impact on EEDI/EEXI frames.

Prediction of extreme PM_2.5 concentrations via extreme quantile regression

Lee, SangHyuk,Park, Seoncheol,Lim, Yaeji The Korean Statistical Society 2022 Communications for statistical applications and me Vol.29 No.3

In this paper, we develop a new statistical model to forecast the PM_2.5 level in Seoul, South Korea. The proposed model is based on the extreme quantile regression model with lasso penalty. Various meteorological variables and air pollution variables are considered as predictors in the regression model, and the lasso quantile regression performs variable selection and solves the multicollinearity problem. The final prediction model is obtained by combining various extreme lasso quantile regression estimators and we construct a binary classifier based on the model. Prediction performance is evaluated through the statistical measures of the performance of a binary classification test. We observe that the proposed method works better compared to the other classification methods, and predicts 'very bad' cases of the PM_2.5 level well.