Publication

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# Corresponding author

(underlined) Mentored students

Manuscripts under Revision

• Kwon H, Chung D, Kaneko S, Li A, Ma A, Schafer JM, Zhou L, Riesenberg B, Song NJ, Chang Y, Xiao T, Sundi D, Oh DY, Fong L, Ma Q, Li X, and Li Z (2020), "Sex differences in CD8+ T cell programming in the tumor microenvironment." [bioRxiv]

• Huang Z, Zhang Z, Heck R, Hu P, Nanda H, Ren K, Sun Z, Bartolomucci A, Gao Y, Chung D, Zhu W, Shen S, and Ruan HB (2020), "Loss of FSTL1-expressing adipocyte progenitors drives the age-related involution of brown adipose tissue." [bioRxov]

• Richard ML, Wirth JR, Khatiwada A, Chung D, Eudaly J, Gilkeson GS, and Cunningham MA (2021), "Conditional knockout of ERα in CD11c+ cells, impact on survival and inflammatory cytokines in murine lupus."

• Cahill T, da Silveira WA, Renaud L, Williamson T, Chung D, Overton I, Chan S, and Hardiman G (2021), "Induced torpor as a countermeasure for low dose radiation exposure in a zebrafish model."

• Bountress KE, Vladimirov V, McMichael G, Taylor N, Hardiman G, Chung D, Adams ZW, Danielson CK, Amstadter AB (2020), "Gene expression differences between young adults based on trauma history and post-traumatic stress disorder."

Publications

2021

• Chang Z, Allen C, Wan C, Chung D, Zhang C, Li Z, and Ma Q (2020), "IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis," Bioinformatics, OnlineFirst. [bioRxiv] [PubMed]

• Curran T, Sun Z, Gerry B, Findlay VJ, Wallace K, Li Z, Paulos C, Ford M, Rubinstein MP, Chung D#, and Camp ER# (2021), "Differential immune signatures in the tumor microenvironment are associated with colorectal cancer racial disparities," Cancer Medicine, Early View. [PubMed]

2020

• The ENCODE Project Consortium (…, Chung D, … ), Moore J, … , Weng Z (2020), "Expanded encyclopedias of DNA elements in the human and mouse genomes," Nature, 583: 699–710. [PubMed]

  • ENCODE 3 Nature Collection.

• Nam JH, Couch D, da Silveira WA, Yu Z, and Chung D# (2020), "PALMER: Improving pathway annotation based on the biomedical literature mining with a constrained latent block model," BMC Bioinformatics, 21: 432. [PubMed]

• Nam JH, Yun JH, Jin IH#, and Chung D# (2020), "hubViz: A novel tool for hub-centric visualization," Chemometrics and Intelligent Laboratory Systems, 203: 104071. [PubMed]

• Nam JH, Kim D#, and Chung D# (2020), "Sparse linear discriminant analysis using the prior-knowledge-guided block covariance matrix," Chemometrics and Intelligent Laboratory Systems, 206: 104142. [PubMed]

• Nam JH*, Khatiwada A*, Matthews LJ, Schulte BA, Dubno JR, and Chung D# (2020), "Improving age-related hearing loss phenotyping based on paired compositional data using supervised learning approaches," Communications for Statistical Applications and Methods, 27(2): 225-239. (*: Joint first authors) [PubMed]

• Miller C, Lawson A, Chung D, Gebregziabher M, Yeh E, Drake R, and Hill E (2020), "Automating a process convolution approach to account for spatial information in imaging data," Spatial Statistics, 36: 100422. [PubMed]

• Yang Y, Li X, Luan H, Zhang B, Zhang K, Nam JH, Fu M, Munk A, Zhang D, Wang S, Liu Y, Albuquerque JP, Ong Q, Li R, Wang Q, Robert ME, Perry RJ, Chung D, Shulman GI, and Yang X (2020), "OGT suppresses S6K1-mediated macrophage inflammation and metabolic disturbance," Proceedings of the National Academy of Sciences of the United States of America (PNAS), 117(28): 16616-16625. [PubMed]

• Ansa-Addo EA, Huang HC, Riesenberg B, Iamsawat S, Borucki D, Nelson MH, Nam JH, Chung D, Paulos CM, Liu B, Yu XZ, Philpott C, Howe OH, and Li Z (2020), "RNA-binding protein PCBP1/hnRNP E1 is an intracellular checkpoint for balancing effector versus regulatory T cells," Science Advances, 6(22): eaaz3865. [PubMed]

• Hurst KE, Lawrence KA, Ball LE, Chung D, and Thaxton JE (2020), "Remodeling translation primes CD8+ T Cell anti-tumor immunity," Cancer Immunology Research, 8(5): 587-595. [PubMed]

• Meissner E, Chung D, Tsao B, Haas D, and Utay N (2020), "IFNL4 genotype does not associate with CD4 T-cell recovery in persons living with HIV," AIDS Research and Human Retroviruses, OnlineFirst. [PubMed]

2019

• Couch D, Yu Z, Nam JH, Allen C, Ramos PS, da Silveira WA, Hunt KJ, Hazard ES, Hardiman G, Lawson A, and Chung D# (2019), "GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature," PLOS One, 14(7): e0219195. [PubMed]

• Speiser JL, Wolf BJ, Chung D, Karvellas CJ, Koch DG, and Durkalski VL (2019), "BiMM forest: A random forest method for modeling clustered and longitudinal binary outcomes," Chemometrics and Intelligent Laboratory Systems, 185: 122-134. [PubMed]

• Speiser JL, Karvellas CJ, Wolf BJ, Chung D, Koch DG, and Durkalski VL (2019), "Predicting daily outcomes in acetaminophen-induced acute liver failure patients with decision tree and random forest analysis," Computer Methods and Programs in Biomedicine, 175: 111-120. [PubMed]

• da Silveira WA, Hazard ES, Chung D, and Hardiman G (2019), "Molecular profiling of RNA tumors using high-throughput RNA sequencing: From raw data to systems level analyses," Methods in Molecular Biology, 1908: 185-204. [PubMed]

• Zhang B, Li MD, Liu Y, Yin R, Yang Y, Mitchell–Richards KA, Nam JH, Li R, Iwakiri Y, Chung D, Robert M, Ehrlich B, Bennett A, Yu J, Nathanson MH, and Yang X (2019), "O-GlcNAc transferase suppresses necroptosis and liver fibrosis," JCI Insight, 4(21): e127709. [PubMed]

• Fulmer DB, Toomer KA, Guo L, Moore K, Glover J, Stairley R, Lobo GP, Zuo X, Dang Y, Su Y, Fogelgren B, Gerard P, Chung D, Heydarpour M, Mukherjee RD, Body SC*, Norris RA*, and Lipschutz JH* (2019), "Defects in the exocyst-cilia machinery cause bicuspid aortic valve disease and aortic stenosis," Circulation, 140(16):1331-1341. (*: Supervised equally) [PubMed]

• Sun B*, Jensen NR*, Chung D, Yang M, LaRue AC, Cheung HW, and Wang Q (2019), "Synergistic effects of SHP2 and PI3K pathway inhibitors in GAB2-overexpressing ovarian cancer," American Journal of Cancer Research, 9(1): 145-159. (*: Joint first authors) [PubMed]

• Commodore A, Mukherjee N, Chung D, Svendsen E, Vena J, Pearce J, Roberts J, Arshad SH, and Karmaus W (2019), "Frequency of heavy vehicle traffic and association with DNA methylation at age 18 years in a subset of the Isle of Wight Birth Cohort," Environmental Epigenetics, 4(4): dvy028. [PubMed]

2018

• Kim HJ, Yu Z, Lawson A, Zhao H, and Chung D# (2018), "Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA," Bioinformatics, 34(12): 2139–2141. [PubMed]

• Wei W, Sun Z, da Silveira WA, Yu Z, Lawson A, Hardiman G, Kelemen LE, and Chung D# (2018), "Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information," Statistical Methods in Medical Research, 28(7): 2137-2149. [PubMed]

• Kortemeier E, Ramos P, Hunt K, Kim HJ, Hardiman G, and Chung D# (2018), "ShinyGPA: An interactive visualization toolkit for investigating pleiotropic architecture using GWAS datasets," PLOS One, 13(1): e0190949. [PubMed]

• Yu Z, Nam JH, Couch D, Lawson A, and Chung D# (2018), "Identification of pathway-modulating genes using the biomedical literature mining." Zhao Y and Chen DG (eds.), New Frontiers of Biostatistics and Bioinformatics, Springer.

• Speiser JL, Wolf BJ, Chung D, Karvellas CJ, Koch DG, and Durkalski VL (2018), "BiMM tree: A decision tree method for modeling clustered and longitudinal binary outcomes," Communications in Statistics - Simulation and Computation, 49(4): 1004-1023. [PubMed]

• Delongchamp R, Faramawi MF, Feingold E, Chung D, and Abouelenein S (2018), "The association between SNPs and a quantitative trait: Power calculation," European Journal of Environment and Public Health, 2(2): 10. [PubMed]

• da Silveira WA, Renaud L, Simpson J, Glen WB Jr, Hazard ES, Chung D, and Hardiman G (2018), "miRmapper: A tool for interpretation of miRNA-mRNAs interaction networks," Genes, 9(9): 458. [PubMed]

• Lin CY, Kwon H, Rivera GR, Li X, Chung D, and Li Z (2018), "Sex differences in using systemic inflammatory markers to prognosticate patients with head and neck squamous cell carcinoma," Cancer Epidemiology, Biomarkers and Prevention, 27(10):1176-1185. [PubMed]

• Kwon H, Lin CY, Chung D, Li X, and Li Z (2018), "Sex as a predictor of response to cancer immunotherapy" (Correspondence to Conforti et al., 2018, "Cancer immunotherapy efficacy and patients' sex: a systematic review and meta-analysis,"), Lancet Oncology, 19(8): e379. [PubMed]

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, 45(15): e145. (* Joint first authors) [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(1): 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. [PubMed]

2016

• Neelon B and Chung D (2016), "The LZIP: A Bayesian latent factor model for correlated zero-inflated counts," Biometrics, 73(1): 185-196. [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(2): 194–206. (* Joint first authors) [PubMed]

• 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, 2016: 6589843. [PubMed]

• Yang C, Li C, Chung D, Chen M, Gelernter J, and Zhao H (2016), "Introduction to statistical methods in genome-wide association studies," Appasani K (ed.), Genome-Wide Association Studies: From Polymorphism to Personalized Medicine, Cambridge University Press.

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(4): 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(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: 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(11): e1004787. (* Joint first authors) [PubMed]

• Chung D, Zhang Q, and 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]

• 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(3): 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. [PubMed]

  • Highlighted in Nature Reviews Genetics.

• 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(495): 891-903. [PubMed]

• Chung D and Kim H (2011), "Robust classification ensemble method for microarray data," International Journal of Data Mining and Bioinformatics, 5(5): 504-518. [PubMed]

• 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: 17. [PubMed]

• Durtschi RB, Chung D, Gentry LR, Chung MK, and Vorperian HK (2009), “Developmental craniofacial anthropometry: Assessment of race effects,” Clinical Anatomy, 22(7): 800-808. [PubMed]

• Chung D, Chung MK, Durtschi RB, Gentry LR, and Vorperian HK (2008), “Measurement consistency from magnetic resonance images,” Academic Radiology, 15(10): 1322-1330. [PubMed]

• Jung M, Chung D, and Choi M (2008), "Keywords network analysis of articles in the North Korean Journal of preventive medicine 1997-2006," Journal of Preventive Medicine and Public Health, 41(6): 365-72. [PubMed]

• Jung M and Chung D (2008), "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," Journal of Preventive Medicine and Public Health, 41(1): 1-9. [PubMed]