Publications

2022

Journal

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, Accepted, 2022
Wy S, Kwon D, Kwon K, Kim J, DLEB: a web application for building deep learning models in biological research, Nucleic Acids Research, gkac369, 2022

Conference

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

2021

Journal

Saud H, O'Neil P, Ono Y, Verbruggen B, Aerie R, Kim J, Lee J, Ring B, Kudoh T, Molecular mechanisms of embroynic tail development in the self-fertilizing mangrove killfish, 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, gky378, doi:10.1093/nar/gky378, 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

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