Heejoon Chae


No contact information.

International Papers

  • Kim HJ, Moon JH, Shin JS, Kim B, Kim JS, Yoon IH, Min BH, Kim JM, Kang SJ, Kim YH, Jo K, Choi J, Chae H, Lee WW, Kim S, Park CG. Bioinformatics analyses with peripheral blood RNA-sequencing unveiled the cause of the graft loss after pig-to-nonhuman primate islet xenotransplantation model. Scientific Reports. 2019 Dec 11
  • Ahn H, Jung I, Chae H, Kang D, Jung W, Kim S. HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis. BMC Bioinformatics, 2019 Dec 2.
  • Choi J, Park Y, Kim S, Chae H. CloudBS: A MapReducebased bisulfite sequencing aligner on cloud. Journal of Bioinformatics and Computational Biology. 2018 Dec 19.
  • Seo S, Park Y, Chae H. BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data. BMC Bioinformatics. 2018 Dec 10.
  • Ahn H, Jung I, Chae H, Kang D, Jung W, Kim S. HTRgene: Integrating Multiple Heterogeneous Time-series Data to Investigate Cold and Heat Stress Response Signaling Genes in Arabidopsis. The 2018 International Conference on Bioinformatics and Biomedicine (BIBM). 2018 Dec 4. [Invited to BMC Bioinformatics]
  • Oh M, Rhee S, Moon JH, Chae H, Lee S, Kang J, Kim S, Literature-based condition-specific miRNA-mRNA target prediction. PLoS ONE. 2017 Mar 31.
  • Chae H, Lee S, Nephew KP, Kim S, Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC Systems Biology, 2016 Dec 23.
  • Hur B, Lim S, Chae H, Seo S, Lee S, Kang J, Kim S. CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments. Biology Direct, 2016 Nov 1.
  • Chae H, Lee S, Seo S, Jung D, Chang H, Nephew KP, Kim S. BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data. Methods. 2016 Jul 28.
  • Jeong HM, Lee S, Chae H, Kim R, Kwon MJ, Oh E, Choi YL, Kim S, Shin YK. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis. Epigenomics. 2016 Jun 8.
  • Hur B, Chae HJ, Kim S. Combined analysis of gene regulatory network and SNP information enhances identification of potential gene markers in mouse knockout studies with small number of samples. BMC Medical Genomics. 2015 8(Suppl 2): S10.
  • Rhee S, Chae H, Kim S. PlantMirnaT: miRNA and mRNA integrated analysis fully utilizing characteristics of plant sequencing data. Methods. 2015 Jul 15;83:80-7.
  • Chae H, Rhee SM, Nephew KP, Kim S. BioVLAB-MMIA-NGS: MicroRNA-mRNA integrated analysis using high throughput sequencing data. Bioinformatics, 2014.
  • An JH, Kim KS, Chae HJ, Kim S, DegPack: A web package using a non-parametric and information theoretic algorithm to identify differentially expressed genes in multiclass RNA-seq samples, Methods, 2014.
  • Rhee J, Kim K, Chae H, Evans J, Yan P, Zhang B, Gray J, Spellman P, Huang T, Nephew K and Kim S. Integrated Analysis of Genome-wide DNA Methylation and Gene Expression Profiles in Molecular Subtypes of Breast Cancer, Nucleic Acids Res. 2013 July 2;41(18):8464-8474.doi: 10.1093/nar/gkt643
  • Chae HJ, Park, JW, Lee SW, Nephew KP, Kim S. Comparative Analysis Using K-mer and K-flank Patterns Provides Evidence for CpG Island Sequence Evolution in Mammalian Genomes, Nucleic Acids Res. 2013 May 1;41(9):4783-91.
  • An JH, Kim KS, Rhee SM, Chae HJ, Nephew KP, Kim S. Genome-wide analysis and modeling of DNA methylation susceptibility in 30 breast cancer cell lines by using CpG flanking sequences. Journal of Bioinformatics and Computational Biology. 2013 Jun;11(3):1341003. doi: 10.1142/S0219720013410035.
  • Chae H, Jung I, Lee H, Marru S, Lee SW and Kim S. Bio and Health informatics meets Cloud : BioVLab as an example. Health Information Science and Systems 2013, 1:6
  • Rao X, Evans J, Chae H, Pilrose J, Kim S, Yan P, Huang RL, Lai HC, Lin H, Liu Y, Miller D, Rhee JK, Huang YW, Gu F, Gray JW, Huang TM, Nephew KP. CpG island shore methylation regulates caveolin-1 expression in breast cancer. Oncogene, 2012 Nov 5. doi: 10.1038/onc.2012.474.
  • Lee H, Yang Y, Chae H, Nam S, Choi D, Tangchaisin P, Herath C, Marru S, Nephew K, Kim S. BioVLAB-MMIA: A Cloud Environment for microRNA andmRNA Integrated Analysis (MMIA) on Amazon EC2, IEEE Transactions on NanoBioscience, Volume 11, Issue 3, Sept. 2012 ISSN 1536-1241. doi:10.1109/TNB.2012.2212030
  • Hollenhorst PC, Ferris MW, Hull MA, Chae H, Kim S, Graves BJ. Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells. Genes Dev. 2011 Oct 15;25(20):2147-57.

Conference Papers

  • Ahn H, Chae H, Kim S, Integration of heterogeneous time series gene expression data by clustering on time dimension, 2017 IEEE International Conference on Big Data and Smart Computing (BigComp 2017)
  • Hur B, Chae H and Kim S, Combined analysis of gene regulatory network and SNP information enhances identification of potential gene markers in mouse knockout studies with small number of samples. The 8th International Conference on Systems Biology and the 4th Translational Bioinformatics Conference (ISB/TBC 2014), Qingdao, October 2014
  • Marru S, Chae H, Tangchaisin P, Kim S, Pierce M, Nephew K. Transitioning BioVLab cloud workbench to a science gateway. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery. No. 40. 2011.
  • Lee HR, Yang Y, Chae HJ, Nam SY, Choi DH, Tangchaisin P, Herath C, Marru S, Nephew K, and Kim S. BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2011).
  • Chae H, Ashki H, Chio KM, Kim S. EGGSlicer: Predicting biologically meaningful gene sets from gene clusters using gene ontology information, Proc. ACM Conference on Bioinformatics and Computational Biology, 2010

Domestic Papers

  • 서석준, 오민식, 정인욱, 채희준, 김선. BioVLAB-클라우드 기반의 생물정보학 분석 시스템, 정보과학회지, Vol.31, No.3, 2013년 3월, pp.108-114.


  • Lee CJ, Evans J, Kim KS, Chae HJ, and Kim S. Determining the Effect of DNA Methylation on Gene Expression in Cancer Cells. Gene Function Analysis, Methods in Molecular Biology, vol. 1101, Michael F. Ochs edited, Springer, 2013.

Visiting student ~ Feburary 2017