# Corresponding author
(bold underlined) Mentored students
Manuscripts under Revision
- Wei W, Sun Z, da Silveira WA, Yu Z, Lawson A, Hardiman G, Kelemen LE, Chung D# (2017), "PICS: Pathway-guided identification of cancer subgroups."
- Chung D, Lawson A, and Zheng WJ (2016), "A statistical framework for biomedical literature mining."
- Welch R*, Chung D*, Grass J, Landick R, and Keles S (2016), "Data exploration, quality control, and statistical analysis of ChIP-exo/nexus experiments." (* Joint first authors)
- 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."
- da Silveira WA, Hazard ES, Chung D, and Hardiman G (2016),
"Molecular profiling of RNA tumors using high throughput RNA
sequencing: From raw data to systems level analyses."
- Chung D#, Kim H, and Zhao H (2017), "graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture," PLOS Computational Biology, 13(2): e1005388. [PubMed]
- 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]
- 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)
- Neelon B and Chung D (2016), "The LZIP: A Bayesian latent factor model for correlated zero-inflated counts," Biometrics, 73, 185-196.
- 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]
- 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]
- 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]
- 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]
- 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.
- 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]