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Dongjun Chung

Title
InstitutionMedical University of South Carolina
DepartmentPublic Health Sciences
AddressP.O. Box MSC 835
302J
Cannon Place - 135 Cannon St.
Phone843-876-0099
Fax843-792-1126
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    Collapse Overview 
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    My research activities focus on statistical genomics and genetics, including methodological studies and their applications. I am also interested in the machine learning and statistical computing techniques related to these problems. Currently, I am especially working on developing statistical methods and software for (1) the analysis of next generation sequencing data, including ChIP-Seq, CLIP-Seq, and RNA-Seq, and (2) the integrative analysis of high throughput genomic data, with application to genome-wide association studies (GWAS), cancer genomics, and studies of gene regulatory mechanisms.


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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Kortemeier E, Ramos PS, Hunt KJ, Kim HJ, Hardiman G, Chung D. ShinyGPA: An interactive visualization toolkit for investigating pleiotropic architecture using GWAS datasets. PLoS One. 2018; 13(1):e0190949. PMID: 29309429.
      View in: PubMed
    2. Wei W, Sun Z, da Silveira WA, Yu Z, Lawson A, Hardiman G, Kelemen LE, Chung D. Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information. Stat Methods Med Res. 2018 Jan 01; 962280217752980. PMID: 29336210.
      View in: PubMed
    3. Renaud L, Silveira WAD, Hazard ES, Simpson J, Falcinelli S, Chung D, Carnevali O, Hardiman G. The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome. Genes (Basel). 2017 Oct 13; 8(10). PMID: 29027980.
      View in: PubMed
    4. Chung D, Kim HJ, Zhao H. graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. PLoS Comput Biol. 2017 Feb; 13(2):e1005388. PMID: 28212402.
      View in: PubMed
    5. Bountress KE, Wei W, Sheerin C, Chung D, Amstadter AB, Mandel H, Wang Z. Relationships between GAT1 and PTSD, Depression, and Substance Use Disorder. Brain Sci. 2017 Jan 05; 7(1). PMID: 28067785.
      View in: PubMed
    6. Wei W, Ramos PS, Hunt KJ, Wolf BJ, Hardiman G, Chung D. GPA-MDS: A Visualization Approach to Investigate Genetic Architecture among Phenotypes Using GWAS Results. Int J Genomics. 2016; 2016:6589843. PMID: 27868058.
      View in: PubMed
    7. Neelon B, Chung D. The LZIP: A Bayesian latent factor model for correlated zero-inflated counts. Biometrics. 2017 03; 73(1):185-196. PMID: 27378066.
      View in: PubMed
    8. Chung D, Kim H. Accurate ensemble pruning using PL-bagging. Comput. Stat. Data Anal. 2015; 83:1-13.
    9. Chung D, Yang C, Li C, Gelernter J, Zhao H. GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation. PLoS Genet. 2014 Nov; 10(11):e1004787. PMID: 25393678; PMCID: PMC4230845.
    10. Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keles S. dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data. PLoS Comput Biol. 2013; 9(10):e1003246. PMID: 24146601; PMCID: PMC3798280.
    11. Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keles S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet. 2013 Jun; 9(6):e1003565. PMID: 23818864; PMCID: PMC3688515.
    12. Sun G, Chung D, Liang K, Keles S. Statistical analysis of ChIP-seq data with MOSAiCS. Methods Mol Biol. 2013; 1038:193-212. PMID: 23872977.
      View in: PubMed
    13. Yang C, Li C, Chung D, Chen M, Gelernter J, Zhao H. Appasani K (ed.), Genome-Wide Association Studies: From Polymorphism to Personalized Medicine, Cambridge University Press. Introduction to statistical methods in genome-wide association studies. 2013.
    14. Chung D, Zhang Q, Keles S. Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequence Data, Springer. MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data. 2013.
    15. Jung M, Chung D. Evidence of social contextual effects on adolescent smoking in South Korea. Asia Pac J Public Health. 2013 May; 25(3):260-70. PMID: 23070756.
      View in: PubMed
    16. Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keles S. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PLoS Comput Biol. 2011 Jul; 7(7):e1002111. PMID: 21779159; PMCID: PMC3136429.
    17. Chung D, Kim H. Robust classification ensemble method for microarray data. Int J Data Min Bioinform. 2011; 5(5):504-18. PMID: 22145531.
      View in: PubMed
    18. Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, Keles S. A statistical framework for the analysis of ChIP-Seq data. J. Amer. Statist. Assoc. 2011; 106:891-903.
    19. Chung D, Keles S. Lu H, Scholkopf B, and Zhao H (eds.), Handbook of Statistical Bioinformatics, Springer. eQTL mapping for functional classes of Saccharomyces cerevisiae genes with multivariate sparse partial least squares regression. 2011.
    20. Chung D, Keles S. Sparse partial least squares classification for high dimensional data. Stat Appl Genet Mol Biol. 2010; 9:Article17. PMID: 20361856; PMCID: PMC2861314.
    21. Durtschi RB, Chung D, Gentry LR, Chung MK, Vorperian HK. Developmental craniofacial anthropometry: Assessment of race effects. Clin Anat. 2009 Oct; 22(7):800-8. PMID: 19753647; PMCID: PMC2846695.
    22. Jung M, Chung D, Choi M. [Keywords network analysis of articles in the North Korean Journal of preventive medicine 1997-2006]. J Prev Med Public Health. 2008 Nov; 41(6):365-72. PMID: 19037165.
      View in: PubMed
    23. Chung D, Chung MK, Durtschi RB, Gentry LR, Vorperian HK. Measurement consistency from magnetic resonance images. Acad Radiol. 2008 Oct; 15(10):1322-30. PMID: 18790405; PMCID: PMC2849302.
    24. Jung M, Chung D. [Co-author and keyword networks and their clustering appearance in preventive medicine fields in Korea: analysis of papers in the Journal of Preventive Medicine and Public Health, 1991~2006]. J Prev Med Public Health. 2008 Jan; 41(1):1-9. PMID: 18250599.
      View in: PubMed
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