• Kim HJ, Yu Z, Lawson A, Zhao H, and Chung D# (2017), "Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA."
• Wei W, Sun Z, da Silveira WA, Yu Z, Lawson A, Hardiman G, Kelemen LE, and Chung D# (2017), “Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information."
• Yu Z, Nam JH, Couch D, Lawson A, and Chung D# (2017), "Identification of pathway-modulating genes using the biomedical literature mining."
  
• Speiser JL, Wolf BJ, Chung D, Karvellas CJ, Koch DG, and Durkalski VL (2016), "BiMM tree: A decision tree method for modeling clustered and longitudinal binary outcomes."
• Mills JN, Hazard ES, Giordano A, Liu Y, Wilson RC, Chung D, Hardiman G, and Ethier SP (2017), "The 8p11-p12 amplicon oncogene ASH2L regulates expression of genes involved in tumorigenic processes via promoter H3K4me3 in luminal breast cancer."
• Jensen N, Chung D, Wang Q, Ethier SP, Cheung HW (2017), "Synergistic effects of SHP2 and PI3K pathway inhibitors in GAB2-overexpressing ovarian cancer."

Peer-reviewed Publications

2017

• Chung D#, Lawson A, and Zheng WJ (2017), "A statistical framework for biomedical literature mining," Statistics in Medicine, 36(22): 3461-3474. [PubMed]
  
• Chung D#, Kim HJ, and Zhao H (2017), "graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture," PLOS Computational Biology, 13(2): e1005388. [PubMed]
  
• Welch R*, Chung D*, Grass J, Landick R, and Keles S (2017), "Data exploration, quality control, and statistical analysis of ChIP-exo/nexus experiments," Nucleic Acids Research, gkx594. (* Joint first authors)
• Bountress KE, Wei W, Sheerin C, Chung D, Amstadter AB, Mandel H, and Wang Z (2017), "Relationships between GAT1 and PTSD, depression, and substance use disorder," Brain Sciences, 7: 6. [PubMed]
  
• Davis-Turak J, Courtney SM, Hazard ES, Glen WB, Wesselman T, Harbin L, Wolf BJ, Chung D, and Hardiman G (2017), "Genomics pipelines and data integration - Challenges and opportunities in the research setting," Expert Review of Molecular Diagnostics. 17(3):225–237. [PubMed]
• Renaud L, da Silveira WA, Hazard ES, Simpson J, Falcinelli S, Chung D, Carnevali O, and Hardiman G (2017), "The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome," Genes, 8(10):269.
  

2016

• Neelon B and Chung D (2016), "The LZIP: A Bayesian latent factor model for correlated zero-inflated counts," Biometrics, 73, 185-196.
  
• Xie Z*, Zhang D*, Chung D*, Tang Z, Huang H, Dai L, Qi S, Li J, Colak G, Chen Y, Xia C, Peng C, Ruan H, Kirkey M, Wang D, Jensen LM, Kwon OK, Lee S, Pletcher SD, Tan M, Lombard DB, White K, Zhao H, Li J, Roeder RG，Yang X, and Zhao Y (2016), “Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation,” Molecular Cell, 62: 194–206. (* Joint first authors)
• Wei W, Ramos PS, Hunt KJ, Wolf BJ, Hardiman G, and Chung D# (2016), "GPA-MDS: A visualization approach to investigate genetic architecture among phenotypes using GWAS results," International Journal of Genomics, Volume 2016, Article ID 6589843. [PubMed]
  

2015

• Chung D and Kim H (2015), “Accurate ensemble pruning with PL-Bagging,” Computational Statistics and Data Analysis, 83: 1-13.
• Chen X, Chung D, Stefani G, Slack F, and Zhao H (2015), “Statistical issues in binding site identification through CLIP-Seq.” Statistics and its Interface, 8: 419-436.
• Beauchene NA, Myers KS, Chung D, Park DM, Weisnicht AM, Keles S, and Kiley PJ (2015), “The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons.” mBio, 6: e01947-15. [PubMed]
  
• Yang C, Li C, Wang Q, Chung D, and Zhao H (2015), “Implications of pleiotropy: Challenges and opportunities for mining big data in biomedicine.” Frontiers in Genetics, 6: Article 229. [PubMed]
  

2014

• Chung D*, Yang C*, Li C, Gelernter J, and Zhao H (2014), “GPA: A statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data.” PLoS Genetics, 10: e1004787. (* Joint first authors) [PubMed]
  
• Chung D, Zhang Q, Keles S (2014), “MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data,” Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequencing Data, Springer. [Initial version]

2013

• Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, and Keles S (2013), “dPeak: High resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data,” PLoS Computational Biology, 9(10): e1003246. [PubMed]
  
• Myers K, Yan H, Ong I, Chung D, Liang K, Tran F, Keles S, Landick R, and Kiley T (2013), “Genome-scale analysis of E. coli FNR reveals complex features of transcription factor binding,” PLoS Genetics, 9(6): e1003565. [PubMed]
  
• Yang C, Li C, Chung D, Chen M, Gelernter J, and Zhao H (2013), “Introduction to statistical methods in genome-wide association studies,” Appasani K (ed.), Genome-Wide Association Studies: From Polymorphism to Personalized Medicine, Cambridge University Press.
• Sun G, Chung D, Liang K, and Keles S (2013), “Statistical analysis of ChIP-seq data with MOSAiCS,” Methods in Molecular Biology, 1038: 193-212. [PubMed]
  
• Jung M and Chung D (2013), "Evidence of social contextual effects on adolescent smoking in South Korea," Asia-Pacific Journal of Public Health, 25: 260-270. [PubMed]

2011

• Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011), “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,” PLoS Computational Biology, 7(7): e1002111. (Highlighted in Nature Reviews Genetics) [PubMed]
  
• Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, and Keles S (2011), “A statistical framework for the analysis of ChIP-Seq data,” Journal of the American Statistical Association, 106: 891-903. [PubMed]
  
• Chung D and Kim H (2011), "Robust classification ensemble method for microarray data," International Journal of Data Mining and Bioinformatics, 5: 504-518.
• Chung D and Keles S (2011), “eQTL mapping for functional classes of Saccharomyces cerevisiae genes with multivariate sparse partial least squares regression,” Lu HH, Scholkopf B, and Zhao H (Eds.), Handbook of Statistical Bioinformatics, Springer.

Before 2011

• Chung D and Keles S (2010), “Sparse partial least squares classification for high dimensional data,” Statistical Applications in Genetics and Molecular Biology, 9: Article 17.
  
• Durtschi RB, Chung D, Gentry LR, Chung MK, and Vorperian HK (2009), “Developmental craniofacial anthropometry: Assessment of race effects,” Clinical Anatomy, 22: 800-808. [PubMed]
  
• Chung D, Chung MK, Durtschi RB, Gentry LR, and Vorperian HK (2008), “Measurement consistency from magnetic resonance images,” Academic Radiology, 15: 1322-1330. [PubMed]