Publications

2023

Journal​​

• Sim M, Lee J, Kwon D, Lee D, Park N, Wy S, Ko Y, Kim J, Reference-based read clustering improved the de novo genome assembly of microbial strains, Computational and Structural Biotechnology, 21:444-451, 2023

​Conference

• Kwon D, Park N, Wy S, Kwon K, Moon Y, Kim H, Kim J, SHERLOG: a full homology-based synteny block detection program, ISMB/ECCB , Lyon, France, Jul 23-27, 2023
• Park N, Kim H, Kim J, PAPipe: a pipeline for comprehensive population genetic analysis, ISMB/ECCB , Lyon, France, Jul 23-27, 2023
• Wy S, Kwon D, Park N, Gu M, Ahn J, Sim M, Oh J, Kim J, Kim J, A web-based system for comparative multi-omic analyses, ISMB/ECCB , Lyon, France, Jul 23-27, 2023
• Oh J, Park N, Kim J, Homology-based genome annotation conversion tool, ISMB/ECCB , Lyon, France, Jul 23-27, 2023
• Oh J, Park N, Kim J, Development of a synteny-based genome annotation conversion method, Korea Computer Congress, Jeju, Korea, Jun 17- Jun 20, 2023

2022

Journal​​

• Moon SW, Zhao L, Matloff W, Hobel S, Berger R, Kwon D, Kim J, et al., Brain structure and allelic associations in Alzheimer's disease, CNS Neuroscience & Therapeutics, http://doi.org/10.1111/cns.14073, 2022
• Choi B, Lim C, Lee H, Lee J, Kim J et al., Neuroprotective effects of linear ubiquitin E3 ligase against aging-induced DNA damage and amyloid beta neurotoxicity in the brain of Drosophila melanogaster, Biochemical and Biophysical Research Communications, 637:196-202, 2022
• Damas J, Corbo M, Kim J, et al., Evolution of the ancestral mammalian karyotype and syntenic regions, PNAS, 119 (40) e2209139119, 2022
• Kim H, Sim M, Park N, Kwon K, Kim J, Kim J, msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data, BMC Bioinformatics, 23:383, 2022
• Sim M, Lee J, Wy S, Park N, Lee D, Kwon D, Kim J, Generation and application of pseudo-long reads for metagenome assembly, GigaScience, Volume 11, 2022
• Wy S, Kwon D, Kwon K, Kim J, DLEB: a web application for building deep learning models in biological research, Nucleic Acids Research, 50(W1):W254-W260, 2022

Conference

• Gu M, Wy S, Kim H, Kim J, Identification of lncRNAs and candidate target genes for constructing a database for animals and plants, Korea Software Congress, Jeju, Korea, Dec 20-23, 2022
• ​Sim M, Lee J, Wy S, Park N, Lee D, Kwon D, Kim J, PLR-GEN: a method for generating pseudo-long reads from metagenome short reads, ISMB (Intelligent Systems for Molecular Biology), Madison, USA, Jul 10-14, 2022 
• Wy S, Kwon D, Kwon K, Kim J, DLEB: a web-based application for building deep learning models to solve biological problems, ISMB (Intelligent Systems for Molecular Biology), Madison, USA, Jul 10-14, 2022
• Kim J, Sim M, Park N, Kim J, Construction of a web-based browser for differentially methylated genomic regions in human tissues, Korea Computer Congress, Jeju, Korea, Jun 29- Jul 01, 2022
• Ahn J, Wy S, Kim J, Development of a method for identifying orthologous exons based on multiple sequence alignments and construction of a database for mammals, Korea Computer Congress, Jeju, Korea, Jun 29- Jul 01, 2022

2021

Journal​

• Arora D, Park J, Lim D, Choi B, Cho I, Srikanth K, Kim J, Park W, Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig, BMC Genomics, 22:801, 2021
• Saud H, O'Neil P, Ono Y, Verbruggen B, Aerie R, Kim J, Lee J, Ring B, Kudoh T, Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish, Kryptolebias marmoratus, Development, 148(24):dev199675, 2021
• Kim H, Sim M, Kwon K, Wy S, Kim J, Reference genome-based improvement of Y chromosome assembly, KIISE Transactions on Computing Practices, 27(7):345-351, 2021
• Arora D, Krishnamoorthy S, Lee J, Lee D, Park N, Wy S, Kim H, Park J, Chai H, Lim D, Cho I, Kim J, Park W, Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon, Scientific Reports, 11, 7219, 2021

2020

Journal​

• Shin H, Choi H, Kim N, Park N, Kim H, Kim J, Kim Y, Unraveling the genome-wide impact of recombinant Baculovirus infection in mammalian cells for gene delivery, Genes, 11(11):1306, 2020
• Lee J, Park N, Lee D, Kim J, Evolutionary and functional analysis of Korean native pig using single nucleotide polymorphisms, Molecules and Cells, 43(8), 2020
• Lee D, Lee J, Heo KN, Kwon K, Moon Y, Lim D, Lee KT, Kim J, Population analysis of the Korean native duck using whole-genome sequencing data, BMC Genomics 21, 554, 2020
• Sim M, Lee J, Lee D, Kwon D, Kim J, TAMA: Improved metagenomic sequence classification through meta-analysis, BMC Bioinformatics, 21:185, 2020

Conference​​

• Kim H, Sim M, Kwon K, Kim J, Reference genome-based improvement of Y chromosome assembly, Korea Software Congress, Virtual Conference, Dec 21-23, 2020 (Best Paper Presentation Award)
• Sim M, Lee J, Lee D, Kwon D, Kim J, ​Meta-analysis improves the accuracy of metagenomic sequence classification, ASHG (American Society  of Human Genetics) Annual Meeting, Virtual Conference, Oct 27-30, 2020
• Sim M, Lee J, Kwon D, Lee D, Kim J, Reference genome sequence-based read clustering, ISMB (Intelligent Systems for Molecular Biology), Virtual Conference, Jul 13-16, 2020

2019

Journal​

• Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J, Using INTERSPIA to explore the dynamics of protein-protein interactions among multiple species, Current Protocols in Bioinformatics, 68, e88. doi: 10.1002/cpbi.88, 2019
• Park N, Kwon D, Lee J, Kim J, The present and future of various bioinformatics databases, Communications of KIISE, 37(8):36-45, 2019
• Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang G, Cherry M, Kim J, Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies, PLoS ONE, 14(8): e0221858, 2019
• Farré M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J et al., An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffe camelopardalis tippelskirchi), GigaScience, giz090, doi:10.1093/gigascience/giz090, 2019
• Ko Y, Kim J, and Rodriguez-Zas S, Markov chain Monte Carlo simulation of a Bayesian mixture model for gene network inference, Genes & Genomics, 41(5): 547-555, 2019
• Kwon D, Lee J, Kim J, GMASS: a novel measure for genome assembly structural similarity, BMC Bioinformatics, 20:147, 2019
• Farré M, Kim J, Proskurjakova A, Zhang Y, Kulemzina A, Li Q, Zhou Y, Xiong Y, Johnson J, et al., Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks, Genome Research, doi:10.1101/gr.239863.118, 2019
• Farré M, Li Q, Zhou Y, Damas J, Chemnick L, Kim J et al., A near-chromosome scale genome assembly of the Gemsbok (Oryz gazella): An iconic Antelope of the Kalahari desert, GigaScience, giy162, doi:10.1093/gigascience/giy162, 2019

​Conference​

• Kwon D, Lee J, Kim J, GMASS: a novel measure for genome assembly structural similarity, ASHG (American Society  of Human Genetics) Annual Meeting, Houston, USA, Oct 15-19, 2019
• Wy S, Lee D, Kim J, Transcriptome data simulation and database construction for evaluating analysis programs for differentially expressed genes, KDBC (Korean DataBase Conference), ChunCheon, Korea, Oct 11-12, 2019
• Sim M, Lee J, Lee D, Kwon D, Kim J, Kim J, Meta-analysis for metagenome taxonomy analysis, ISMB/ECCB (Intelligent Systems for Molecular Biology/European Conference on Computational Biology), Basel, Switzerland, Jul 21-25, 2019
• Moon S, Zhao L, Matloff W, Hobel S, Berger R, Kwon D, Kim J et al., Brain structure and allelic association in Alzheimer's disease using neuroimaging and genetics data, AAIC (Alzheimer's Association International Conference), LA, USA, Jul 14-18, 2019

2018

Journal​​

• Damas J, Kim J, Farré M, Griffin D, and Larkin D, Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes, Genome Biology, 19:155, 2018
• Rando H, Farré M, Robson M, Won N, Johnson J, Buch R, Bastounes E, Xiang X, Feng S, Liu S, Xiong Z, Kim J et al., Construction of red fox chromosomal fragments from the short-read genome assembly, Genes, 9(6), 308, 2018
• Lee J, Lee D, Sim M, Kwon D, Kim J, Ko Y, and Kim J, mySyntenyPortal: an application package to construct websites for synteny block analysis, BMC Bioinformatics, 19:216, doi: 10.1186/s12859-018-2219-x, 2018
• Kwon D, Lee D, Kim J, Lee J, Sim M, and Kim J, INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species, Nucleic Acids Research, 46(W1): W89-W94, 2018
• Kim H, Lee B, Han J, Jeong C, Hwang D, Lee M, Kang H, Kim D, Lee D, Kim J, Choi I, and Lee J, The genome of the marine medaka Oryzias melastigma, Molecular Ecology Resources, doi: 10.1111/1755-0998.12769, 2018
• Kim K, Yoon Y, Hong WY, Kim J, Cho Y, and Hwang S, Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea, Applied Biological Chemistry, pp 1–9; doi.org/10.1007/s13765-017-0342-4​, 2018

Conference

• Moon Y, Lee D, Kim J, RWNetSig: protein network-based discovery of cancer driver genes, CSBio, 2018
• Kwon D, Lee D, Kim J, Lee J, Sim M, and Kim J, INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species, American Society of Human Genetics, 2018
• Park N, Lee J, Sim M, Moon Y, Wy S, Kim J, Evolutionary analysis of repeat composition in mammalian genomes, Korea Software Congress, 2018
• Kwon K, Kwon D, Wy S, Kim J, Construction of orthologous SNP database for primates and its visualization, Korea Software Congress, 2018

2017

Journal​

• Lee D, Lim D, Kwon D, Kim J, Lee J, Sim M, Choi BH, Choi SG, and Kim J, Functional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data, Scientific Reports, 7, 17303; doi:10.1038/s41598-017-17817-w, 2017
• Kim J, Farré M, Auvil L, Capitanu B, Larkin DM, Ma J, and Lewin HA, Reconstruction and evolutionary history of eutherian chromosomes, PNAS, 114(27), E5379-E5388, doi:10.1073/pnas.1702012114, 2017
• Kim J, Kern E, Kim T, Sim M, Kim J, Kim Y, Park C, Nadler SA, and Park JK, Phylogenetic analysis of two Plectus mitochondrial genomes (Nematoda: Plectida) supports a sister group relationship between Plectida and Rhabditida within Chromadorea, Molecular Phylogenetics and Evolution, 107:90-102, 2017​
• Rhee J, Choi B, Kim J, Kim B, Lee Y, Kim I, Kanamori A, Choi I, Schartl M, and Lee J, Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus, Scientific Reports, 6, 40121; doi: 10.1038/srep40121, 2017
• Bryan C, Guterman G, Ma K, Lewin H, Larkin D, Kim J, Ma J, and Belmonte M, Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution, IEEE Transactions on Visualization and Computer Graphics, 23(Issue 1), 2017

Conference

• Kim J, Lee D, Sim M, Lee J, and Kim J, The effect of reference species on reference-guided genome assembly, The 6th International Conference on Computational Systems-Biology and Bioinformatics (CSBio), 2017
• Lee J, Lee D, Sim M, Kwon D, Kim J, Ko Y, and Kim J, Web-based applications for large-scale comparative genomics, The 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, ISMB/ECCB, 2017

2016

Journal​ 

• Ko Y, Cho M, Lee J, and Kim J, Identification of disease comorbidity through hidden molecular mechanisms, Scientific Reports, 6, 39433; doi: 10.1038/srep39433, 2016 ​
• Lee D, Cho M, Hong WY, Lim D, Kim HC, Cho YM, Jeong JY, Choi BH, Ko Y, and Kim J, Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population, Molecules and Cells, 39(9):692-698, 2016
• Lee J, Hong WY, Cho M, Sim M, Lee D, Ko Y, and Kim J, Synteny Portal: a web-based application portal for synteny block analysis, Nucleic Acids Research, 44(W1):W35-W40;doi:10.1093/nar/gkw310, 2016
• Oh JW, Choi JH, Lim JB, Wickramanayake D, Wagley Y, Kim J, Lee HC, Seo HG, and Kim TH, Characterization of MUDENG, a novel anti-apoptotic protein, Oncogenesis, 5, e221; doi:10.1038/oncsis.2016.30, 2016 
• Kim BM, Kim J, Choi IY, Raisuddin S, Au Dw, Leung KM, Wu RS, Rhee JS, and Lee JS, Omics of the marine medaka (Oryzias melastigma) and its relevance to marine environmental research, Marine Environmental Research, 113:141-152, 2016

Conference

• Bryan C, Guterman G, Ma K, Lewin H, Larkin D, Kim J, Ma J, and Belmonte M, Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution, IEEE VIS, 23-28 October 2016, Baltimore, Maryland, USA
• Kwon D, Lee J, Cho M, Lee D, and Kim J, Benchmarking algorithms to improve the accuracy of searching conserved DNA sequence regions, Korea Computer Congress, 2016
• Lee J, Sim M, and Kim J, Efficient pairwise whole-genome alignment by utilizing existing alignments of relevant species, The 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2016

2015

Journal​

• Lee D, Lee J, Hong WY, Jang E, and Kim J, AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes, Journal of KIISE, 42(12):1584-1589, 2015 (Best Paper Award)
• Moon  SW, Dinov ID, Kim J, Zamanyan A, Hobel S, Thompson PM, and Toga AW, Structural Neuroimaging Genetics Interactions in Alzheimer’s Disease, Journal of Alzheimer’s Disease, 48(4):1051-1064, 2015
• Choi M, Lee J, Le MT, Nguyen DT, Park S, Soundrarajan N, Schachtschneider KM, Kim J, et al., Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing, DNA Research, 22(5):343-55, 2015
• Yun S, Furlong M, Sim M, Cho M, Park S, Cho E, Reys-Alcaraz A, Hwang J, Kim J, and Seong J, Prevertebrate Local Gene Duplication Facilitated Expansion of the Neuropeptide GPCR Superfamily, Molecular Biology and Evolution, 32(11):2803-17, 2015
• Lee J, Lee H, Hong WY, Jang E, and Kim J, FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples. Journal of Microbiological Methods, 115:121-128, 2015

• Seok HS, Seok SH, and Kim J, Effects of omics data combinations on in silico tumor-normal tissue classification. Genes & Genomics, 37(6):525-535, 2015

• Sim M, and Kim J, Metagenome assembly through clustering of next-generation sequencing data using protein sequences. Journal of Microbiological Methods, 109:180-187, 2015

Conference

• Cho M, Lee D, Hong WY, Lee J, and Kim J, evoSNPI: a pipeline for the evolutionary analysis of the origin of single nucleotide polymorphisms and the change of protein interactions. The 6th International Conference on Computational Systems-Biology and Bioinformatics, CSBio2015
• Lee D, Lee J, Hong WY, Jang E, and Kim J, AGB (Ancestral Genome Browser): a web interface for browsing reconstructed ancestral genomes, Korean DataBase Conference, 2015 (Best Paper Award)
• Cho M, Ko Y, and Kim J,  Network-guided gene set enrichment analyzer for predicting disease comorbidity, The 11th KOGO Winter Symposium, 2015

2014

Journal

• Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, et al., Alignathon: A competitive assessment of whole genome alignment methods. Genome Research, 24(12):2077-89, 2014

• Seok HS, Hong W, and Kim J, Estimating the composition of species in metagenomes by clustering of next-generation read sequences. Methods, 69(3):213-219, 2014
• Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, Huang Z, Gorbunova V, Zhang L, Zhao W, Wildman DE, Xiong Y, Gudkov A, Zheng Q, Rechavi G, Liu S, Bazak L, Chen J, Knisbacher BA, Lu Y, Shams I, Gajda K, Farré M, Kim J, et al., Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications, 5:3966. doi: 10.1038/ncomms4966, 2014
• Seok H and Sim M, Lee D, and Kim J, A clustering method for next-generation sequences of bacterial genomes through multiomics data mapping. Genes & Genomics, 36(2):191-196, 2014
• Kim J, and Ma J, PSAR-Align: improving multiple sequence alignment using probabilistic sampling. Bioinformatics, 30(7):1010-1012, 2014
• Seok H, and Kim J, Computational prediction of transcription factor binding sites based on an integrative approach incorporating genomic and epigenomic features. Genes & Genomics, 36(1):25-30, 2014
• Lee J, and Kim J, Use of reference genomes for high-quality de novo genome assembly, Communications of The Korea Information Science Society, 10(32):28-32, 2014

Conference

• Hong WY, and Kim J, Effect of a k-mer size on the performance of metagenome sequence clustering, Korea Computer Congress, 2014
• Lee J, and Kim J, M2ID-Converter: unified web interface for converting microbial multi-omic identifiers, Korea Computer Congress, 2014
• Lee J, Lee D, Jang E, Cho M and Kim J, A computational pipeline for revealing the evolutionary history of sequence variants, The 23rd KOGO Annual Conference, 2014

2013

Journal

• Choi Y, Kang IC, Cho E, Kim J, Jeong K, and Jung S, Molecular Docking and Molecular Dynamics Simulations of the Kinase Domain Inhibitor for an Epidermal Growth Factor Receptor. Bull. Korean Chem. Soc. 34(8):2515, 2013
• Tahir MN, Qamar R, Mischnick P, Kim J, and Jung S, A Rapid Click Chemistry Using Beta-Cyclodextrin Immobilized on Glass Micro-Particles. Letters In Organic Chemistry, 10(4):269-276, 2013
• Rajesh T, Jeon JM, Kim YH, Kim HJ, Yi da H, Park SH, Choi KY, Kim YG, Kim J, Jung S, Park HY, and Yang YH, Functional analysis of the gene SCO1782 encoding Streptomyces hemolysin (S-hemolysin) in Streptomyces coelicolor M145. Toxicon, 71:159-65. doi: 10.1016/j.toxicon.2013.05.023, 2013
• Ge RL, Cai Q, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang L, Huang Y, et al., Draft genome sequence of the Tibetan antelope. Nature Communications, 4:1858. doi: 10.1038/ncomms2860, 2013
• Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge R, Auvil L, Capitanu B, Zhang G, Lewin HA, and Ma J, Reference-Assisted Chromosome Assembly, PNAS, 110(5):1785-90, 2013

Conference

• Sim M, Seok H, and Kim J, A next-generation Sequence Clustering Method for E. Coli through Proteomics-genomics Data Mapping. The 4th International Conference on Computational Systems-Biology and Bioinformatics, CSBio2013
• Sim M, and Kim J, Identifying evolutionary breakpoint regions by using reconstructed ancestral genomes, Korea Computer Congress, 2013

• Lee D, and Kim J, Benchmarks of de novo metagenome assemblers, Korea Computer Congress, 2013

2012

Journal

• Swine Genome Sequencing Consortium, Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 15;491(7424):393-8, 2012
• Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, et al., The yak genome and adaptation to life at high-altitude. Nature Genetics, 1;44(8):946-9, 2012

2011

Journal

• Kim J, and Ma J, PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Research, 39(15):6359-68, 2011 
  Early version appeared in the Proceedings of 15th International Conference on Research in Computational Molecular Biology (RECOMB), 2011

2010

Journal

• Kim J, and Sinha S, Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics, 11(1):54, 2010
• Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, et al., Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances. PLoS Computational Biology, 6(1):e1000652, 2010
• The Nasonia Genome Working Group, Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species. Science, 327: 343-348, 2010

2009

Journal

• Kim J, He X, and Sinha S, Evolution of regulatory sequences in 12 Drosophila species. PLoS Genetics, 5(1):e1000330, Jan. 2009

2008

Conference

• Kim S, Kim J, Ko Y, Hwang S, and Han J, PerRank: Personalized Rank Retrieval with Categorical and Numerical Attributes. The 9th International Conference on Web-Age Information Management (WAIM 2008), Jul. 2008

2007

Journal

• Kim J and Sinha S, Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics, 23(3):289-97, 2007

2002

Conference

• Kim G, Kim D, Park S, Kim J, Oh J, Lee S and Jun C, Supplier-Oriented Electronic Catalog Management System. CALS/EC KOREA 2002 International Conference, Nov. 2002
• Kim D, Kim J, and Lee S, Catalog Integration for Electronic Commerce through Category- Hierarchy Merging Technique. The 12th International Workshop on Research Issues on Data Engineering, Engineering E-Commerce/E-Business Systems (RIDE-2EC 2002), Feb. 2002

2000

Conference

• Kim J, Kim D, and Lee S, Automatic Category Merging Technique in Electronic Commerce. Korea Information Science Society Fall Conference, Oct. 2000

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Bioinformatics Laboratory since 07/02/2012
Dept. of Biomedical Science and Engineering, Konkuk University
Room 406-1 Animal Science Bldg. 120 Neungdong-ro, Gwangjin-gu, Seoul 05029 Korea