Publication

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# Corresponding author

(underlined) Mentored students

Manuscripts under Revision

• Jeon H*, Allen C*, Ovando-Ricardez JA, Chang Y, Rosas L, Vanegas NDP, Cheng H, Xie J, Wang C, Mora AL#, Rojas M#, Ma Q#, and Chung D# (2024), "MAPLE: A hybrid framework for multi-sample spatial transcriptomics data." (*: Joint first authors) [bioRxiv]

• Xie J*, Jung KJ*, Allen C*, Chang Y, Paul S, Li Z, Ma Q, and Chung D# (2024), "Analysis of community connectivity in spatial transcriptomics data." (*: Joint first authors) [bioRxiv]

• Jeon Y, Park J, Jin IH, and Chung D# (2023), "Network-based topic structure visualization" [ArXiv]

• Song NJ, Xie J, Jung KJ, Wang Y, Risenberg B, Jeon H, Ma A, Cox N, Wethington D, Reynolds K, Xiao T, Li A, Kronen P, Denko N, Carbone D, Ma Q, Carson W, Mundy-Bosse B, Burd C, Das J, Chung D, and Li Z (2024), "Natural killer cells regulate distinct CD8+ T cell differentiation program in cancer and contribute to resistance against immune checkpoint blockers."

• Deffenbaugh JL, Jung KJ, Murphy SP, Liu Y, Rau CN, Petersen-Cherubini CL, Collins PL, Chung D, and Lovett-Racke AE (2024), "A novel mouse model of multiple sclerosis induced by EBV-like virus generates a distinct B cell population."

• Gao Z, Erstad D, Sun Z, Janakiraman H, Chung D, Buren GV, Fisher W, Lewin D, Rubinstein M, and Camp ER (2023), "Tumor immune microenvironment differences associated with racial disparities in pancreatic adenocarcinoma."

• Guglietta S, Fanning L, Armeson K, Sun Z, Cousart A, Lewin D, Bookhout C, Kourtidis A, Thaxton J, Crawford T, Baron JA, Chung D, Alekseyenko AV, and Wallace K (2023), "Racial differences in immune gene expression in colorectal adenomas and cancers."

• Kim D, Ouyang Y, Allen C, Chung D, Zhang X, Li Z, and Hong F (2023), "Protein canopy homolog 2 promotes hepatocarcinogenesis through regulation of tumor-associated macrophages."

Publications

2024

• Ara Z, Ganguly A, Peppard D, Chung D, Vucetic S, Motti VG, and Hong S (2024), "Collaborative job seeking for people with autism: Challenges and design opportunities," Accepted to the ACM Conference on Human Factors in Computing Systems (CHI). [ArXiv]

• Hong S, Zampieri M, Hand BN, Motti V, Chung D, and Uzuner O (2024), "Collaborative design for job-seekers with autism: A conceptual framework for future research." Accepted to Neurodiversity at Work Research Conference 2024.

• Yang Y, Denlinger N, Song NJ, Zhang X, Jeon H, Peterson C, Wang Y, Reynolds K, Bolz R, Song C, Wu D, Chan WK, Bezerra E, Epperla N, Voorhees T, Kittai A, Bond D, Sawalha Y, Sigmund A, Reneau J, Rubinstein M, Hanel W, Christian B, Baiocchi R, Maddocks K, Alinari L, Vasu S, de Lima M, Chung D, Jaglowski S, Li Z, Huang X, and Miao J (2024), "Post-infusion PD-1+CD8+CAR-T cells identify patients responsive to CD19-CAR-T therapy in non-Hodgkin's lymphoma," Blood Advances, OnlineFirst. [PubMed]

• Kuhn BN, Cannella N, Crow AD, Lunerti V, Gupta A, Walterhouse SJ, Allen C, Chalhoub RM, Dereschewitz E, Roberts AT, Cockerham M, Beeson A, Nall RW, Palmer AA, Hardiman G, Solberg Woods LC, Chung D, Ciccocioppo R, and Kalivas PW (2024), "A multi-symptomatic model of heroin use disorder in rats reveals distinct behavioral profiles and neuronal correlates of heroin vulnerability versus resiliency," To appear in The American Journal of Psychiatry.

• Cannella N, Tambalo S, Lunerti V, Scuppa G, de Vivo L, Kuhn B, Hardiman G, Solberg Woods LC, Chung D, Kalivas P, Soverchia L, Ubaldi M, Bifone A, and Ciccocioppo R (2024), "Long-access heroin self-administration induces region specific grey matter volume reduction and microglial reaction in the rat," Brain Behavior and Immunity, 118: 210-220. [PubMed]

2023

• Allen C, Chang Y, Neelon B, Chang W, Kim HJ, Li Z, Ma Q, and Chung D# (2023), "A Bayesian multivariate mixture model for high throughput spatial transcriptomics," Biometrics, 79: 1775–1787. [bioRxiv] [PubMed]

• Xie J, Jeon H, Xin G, Ma Q, and Chung D# (2023), "LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity," PLOS Computational Biology, 19(7): e1011300. [bioRxiv] [PubMed]

• Khatiwada A, Yilmaz AS, Wolf BJ, Pietrzak M, and Chung D# (2023), "multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results," PLOS Computational Biology, Online ahead of print. [ArXiv] [PubMed]

• Deng Q*, Gupta A*, Jeon H*, Nam JH, Yilmaz AS, Chang W, Pietrzak M, Li L, Kim HJ#, and Chung D# (2023), "graph-GPA 2.0: A graphical model for multi-disease analysis of GWAS results with integration of functional annotation data," Frontiers in Genetics, 14: 1079198. (*: Joint first authors) [ArXiv] [PubMed]

• Jeon H*, Xie J*, Jeon Y*, Jung KJ, Gupta A, Chang W, and Chung D# (2023), "Statistical power analysis for designing bulk, single-cell, and spatial transcriptomics experiments: Review, tutorial, and perspectives," Biomolecules, 13(2), 221. (*: Joint first authors) [ArXiv] [PubMed]

• Sun Z, Chung D, Neelon B, Millar-Wilson A, Ethier SP, Xiao F, Zheng Y, Wallace K, and Hardiman G (2023), "A Bayesian framework for pathway-guided identification of cancer subgroups by integrating multiple types of genomic data," Statistics in Medicine, 42(28): 5266-5284. [PubMed]

• Nagy G, Diabate M, Banerjee T, Adamovich AI, Smith N, Jeon H, Dhar S, Liu W, Burgess K, Chung D, Starita LM, and Parvin JD (2023), "Multiplexed assay of variant effect reveals residues of functional importance in the BRCA1 coiled-coil and serine cluster domains," PLOS One, 18(11): e0293422. [PubMed]

• Liu Z, Wang Q, Ma A, Feng S, Chung D, Zhao J, Ma Q, and Liu B (2023), "Infer disease-associated microbial biomarkers based on metagenomic and metatranscriptomic data," Computers in Biology and Medicine, 165: 107458. [bioRxiv] [PubMed]

• Savardekar H, Allen C, Jeon H, Li J, Quiroga D, Schwarz E, Wu RC, Zelinskas S, Lapurga G, Abero A, Stiff A, Shaffer J, Blaser B, Old M, Wesolowski R, Xin G, Kendra K, Chung D, and Carson W (2022), "Single-cell RNA-seq analysis of patient myeloid-derived suppressor cells and the response to inhibition of Bruton’s tyrosine kinase," Molecular Cancer Research, Online ahead of print. [PubMed]

• Song NJ, Chakravarthy K, Jeon H, Bolyard C, Reynolds K, Weller KP, Reisinger S, Wang Y, Li A, Jiang S, Ma Q, Barouch DH, Rubinstein MP, Shields PG, Oltz EM, Chung D, and Li Z (2023), "mRNA vaccines against SARS-CoV2 induce divergent antigen-specific T cell responses in lung cancer patients," Journal for ImmunoTherapy of Cancer, 12(1): e007922. [PubMed]

• Azar J, Evans JP, Sikorski M, Chakravarthy K, McKenney S, Carmody I, Zeng C, Teodorescu R, Song NJ, Harmon J, Bucci D, Velegraki M, Bolyard C, Weller K, Reisinger S, Bhat S, Maddocks K, Gumina R, Vlasova A, Oltz E, Saif L, Chung D, Woyach J, Shields P, Liu SL, Li Z, and Rubinstein M (2023), "Selective suppression of de novo SARS-CoV2 vaccine antibody responses in cancer patients receiving B cell-targeted therapy," JCI Insight, 8(6): e163434. [PubMed]

• Song MA, Wold LE, Aslaner DM, Archer KJ, Patel D, Jeon H, Chung D, Shields PG, Christman JW, and Chung S (2023), "Long-term impact of daily E-cigarette exposure on the lungs of asthmatic mice," Nicotine and Tobacco Research, 25(12): 1904-1908. [PubMed]

• Cahill T, da Silveira WA, Renaud L, Wang H, Williamson T, Chung D, Chan S, Overton I, and Hardiman G (2023), "Investigating the effects of chronic low-dose radiation exposure in the liver of a hypothermic zebrafish model," Scientific Reports, 13: 918. [PubMed]

2022

• Yoo J, Sun Z, Greenacre M, Ma Q, Chung D#, and Kim YM# (2022), "A guideline for the statistical analysis of compositional data in immunology," Communications for Statistical Applications and Methods, 29(4):453-69. [ArXiv]

• Chang Y, He F, Wang J, Chen S, Li J, Liu J, Yu Y, Su L, Ma A, Allen C, Lin Y, Sun S, Liu B, Otero J, Chung D, Fu H, Li Z, Xu D, and Ma Q (2022), “Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning," Computational and Structural Biotechnology Journal, 20: 4600-4617. [PubMed] [bioRxiv]

• Park Y, Su Z, and Chung D (2022), "Envelope-based partial partial least squares with application to cytokine-based biomarker analysis for COVID-19," Statistics in Medicine, 41(23): 4578-4592. [PubMed]

• SenNet Consortium (…, Chung D, … ) (2022), "NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health," Nature Aging, 2: 1090–1100. [PubMed]

• Kwon H, Schafer JM, Song NJ, Kaneko S, Li A, Xiao T, Ma A, Allen C, Das K, Zhou L, Riesenberg B, Chang Y, Weltge P, Velegraki M, Oh DY, Fong L, Ma Q, Sundi D, Chung D#, Li X#, and Li Z# (2022), "Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer," Science Immunology, 7(73): eabq2630. [bioRxiv] [PubMed]

  • This paper was selected as the online cover of Science Immunology, Volume 7, Issue 73 (https://www.science.org/toc/sciimmunol/7/73). 

• Song NJ*,  Allen C*, Vilgelm AE*, Riesenberg BP*, Weller K, Reynolds K, Chakravarthy KB, Kumar A, Khatiwada A, Sun Z, Ma A, Chang Y, Yusuf M, Li A, Zeng C, Evans JP, Bucci D, Gunasena M, Xu M, Liyanage NPM, Bolyard C, Velegraki M, Liu SL, Ma Q, Devenport M, Liu Y, Zheng P, Malvestutto CD#, Chung D#, and Li Z# (2022), "Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology," Journal of Hematology and Oncology, 15: 5. (*: Joint first authors) [medRxiv] [PubMed]

• Li A, Chang Y, Song NJ, Wu X, Chung D, Riesenberg B, Velegraki M, Giuliani G, Das K, Okimoto T, Kwon H, Chakravarthy K, Bolyard C, Zhou L, He K, Gatti-Mays M, Das J, Yang Y, Ma Q, Carbone D, and Li Z (2022), "Selective targeting of GARP-LTGFβ axis in tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell anti-tumor immunity," Journal for ImmunoTherapy of Cancer, 10(9): e005433. [PubMed]

• SchaferJ, Xiao T, Kwon H, Collier K, Chang Y, Bolyard C, Chung D, Yang Y, Sundi D, Ma Q, Theodorescu D, Li X, and Li Z (2022), "Sex-biased adaptive immune regulation in cancer development and therapy," iScience, 25(8): 104717. [PubMed]

• Ngoi SM, Yang Y, Iwanowycz S, Gutierrez J, Li Y, Williams C, Hill M, Chung D, Allen C, and Liu B (2022), "Migrating type 2 dendritic cells prime mucosal Th17 cells specific to small intestinal commensal bacteria," The Journal of Immunology, 209(6): 1200-1211. [PubMed]

• Kuhn BN, Cannella N, Crow AD, Roberts AT, Lunerti V, Allen C, Nall R, Hardiman G, Solberg-Woods LC, Chung D, Ciccocioppo R, and Kalivas P (2022), "Novelty-induced locomotor behavior predicts heroin addiction vulnerability in male, but not female, rats," Psychopharmacology, 239, 3605–3620. [PubMed]

• 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 (2022), "Brown adipose tissue involution associated with progressive restriction in progenitor 1 competence," Cell Reports, 39: 110575. [bioRxiv] [PubMed]

• Richard ML, Wirth JR, Khatiwada A, Chung D, Eudaly J, Gilkeson GS, and Cunningham MA (2022), "Conditional knockout of ERα in CD11c+ cells impacts female survival and inflammatory cytokine profile in murine lupus," Immunology, 167(3):354-367. [PubMed]

2021

• Khatiwada A, Wolf BJ, Yilmaz AS, Ramos PS, Pietrzak M, Lawson A, Hunt KJ, Kim HJ, and Chung D# (2021), "GPA-Tree: Statistical approach for functional-annotation-tree-guided prioritization of GWAS results," Bioinformatics, 38: 1067-1074. [ArXiv] [PubMed]

• Allen C, Kuhn BN, Cannella N, Crow AD, Roberts AT, Lunerti V, Ubaldi M, Hardiman G, Solberg-Woods LC, Ciccocioppo R, Kalivas PW, and Chung D# (2021), "Network-based discovery of opioid use vulnerability in rats using the Bayesian stochastic block model," Frontiers in Psychiatry, 12: 745468. [bioRxiv] [PubMed]

• Chang Y, Allen C, Wan C, Chung D, Zhang C, Li Z, and Ma Q (2021), "IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis," Bioinformatics, 37: 3045-3047. [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, 10: 1805–1814. [PubMed]

• Zhang B, Lapenta K, Wang Q, Nam JH, Chung D, Robert ME, Nathanson MH, and Yang X (2021), "Trefoil factor 2 secreted from damaged hepatocytes activates hepatic stellate cells," Journal of Biological Chemistry, 297(1): 100887. [PubMed]

• Bountress KE, Vladimirov V, McMichael G, Taylor N, Hardiman G, Chung D, Adams ZW, Danielson CK, Amstadter AB (2021), "Gene expression differences between young adults based on trauma history and post-traumatic stress disorder," Frontiers in Psychiatry, 12: 581093. [PubMed] [e-book]

• 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," Cells, 10(4): 906. [PubMed]

• Meissner E, Chung D, Tsao B, Haas D, and Utay N (2021), "IFNL4 genotype does not associate with CD4 T-cell recovery in persons living with HIV," AIDS Research and Human Retroviruses, 37(3): 184-188. [PubMed]

• Burton HJ, Khatiwada A, Chung D, and Meissner EG (2021), "Association of referral source and substance use with hepatitis C virus outcomes at a Southern academic medical center," Southern Medical Journal, 115(6): 352-357. [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), "Ranking subjects based on paired compositional data with application to age-related hearing loss subtyping," 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]

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] [ArXiv]

• 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]

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