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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 
    Collapse overview
    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. Curran T, Sun Z, Gerry B, Findlay VJ, Wallace K, Li Z, Paulos C, Ford M, Rubinstein MP, Chung D, Camp ER. Differential immune signatures in the tumor microenvironment are associated with colon cancer racial disparities. Cancer Med. 2021 03; 10(5):1805-1814. PMID: 33560598.
      View in: PubMed
    2. Meissner EG, Chung D, Tsao B, Haas DW, Utay NS. IFNL4 Genotype Does Not Associate with CD4 T-Cell Recovery in People Living with Human Immunodeficiency Virus. AIDS Res Hum Retroviruses. 2021 03; 37(3):184-188. PMID: 33066718.
      View in: PubMed
    3. Nam JH, Couch D, da Silveira WA, Yu Z, Chung D. PALMER: improving pathway annotation based on the biomedical literature mining with a constrained latent block model. BMC Bioinformatics. 2020 Oct 02; 21(1):432. PMID: 33008309.
      View in: PubMed
    4. Nam JH, Kim D, Chung D. Sparse Linear Discriminant Analysis using the Prior-Knowledge-Guided Block Covariance Matrix. Chemometr Intell Lab Syst. 2020 Nov 15; 206. PMID: 32968333.
      View in: PubMed
    5. Nam JH, Yun J, Jin IH, Chung D. hubViz: A Novel Tool for Hub-centric Visualization. Chemometr Intell Lab Syst. 2020 Aug 15; 203. PMID: 32753773.
      View in: PubMed
    6. 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 PH, Li Z. RNA binding protein PCBP1 is an intracellular immune checkpoint for shaping T cell responses in cancer immunity. Sci Adv. 2020 May; 6(22):eaaz3865. PMID: 32523987.
      View in: PubMed
    7. Nam JH, Khatiwada A, Matthews LJ, Schulte BA, Dubno JR, Chung D. Ranking subjects based on paired compositional data with application to age-related hearing loss subtyping. Commun Stat Appl Methods. 2020 Mar; 27(2):225-239. PMID: 32566544.
      View in: PubMed
    8. Miller C, Lawson A, Chung D, Gebregziabher M, Yeh E, Drake R, Hill E. Automating a Process Convolution Approach to Account for Spatial Information in Imaging Mass Spectrometry Data. Spat Stat. 2020 Apr; 36. PMID: 32318329.
      View in: PubMed
    9. Hurst KE, Lawrence KA, Robino RA, Ball LE, Chung D, Thaxton JE. Remodeling Translation Primes CD8+ T-cell Antitumor Immunity. Cancer Immunol Res. 2020 05; 8(5):587-595. PMID: 32075802.
      View in: PubMed
    10. Fulmer D, Toomer K, Guo L, Moore K, Glover J, Moore R, Stairley R, Lobo G, Zuo X, Dang Y, Su Y, Fogelgren B, Gerard P, Chung D, Heydarpour M, Mukherjee R, Body SC, Norris RA, Lipschutz JH. Defects in the Exocyst-Cilia Machinery Cause Bicuspid Aortic Valve Disease and Aortic Stenosis. Circulation. 2019 10 15; 140(16):1331-1341. PMID: 31387361.
      View in: PubMed
    11. Couch D, Yu Z, Nam JH, Allen C, Ramos PS, da Silveira WA, Hunt KJ, Hazard ES, Hardiman G, Lawson A, Chung D. GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature. PLoS One. 2019; 14(7):e0219195. PMID: 31260503.
      View in: PubMed
    12. Park HM, Park SY, Chung JO, Cho DH, Park CH, Kim HS, Chung DJ, Choi SK, Rew JS, Chung MY. Association Between Gastric Emptying Time and Incidence of Cardiovascular Diseases in Subjects With Diabetes. J Neurogastroenterol Motil. 2019 Jul 01; 25(3):387-393. PMID: 31177651.
      View in: PubMed
    13. da Silveira WA, Hazard ES, Chung D, Hardiman G. Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses. Methods Mol Biol. 2019; 1908:185-204. PMID: 30649729.
      View in: PubMed
    14. Byun DW, Moon SH, Kim T, Lee HH, Park HM, Kang MI, Ha YC, Chung HY, Yoon BK, Kim TY, Chae SU, Shin CS, Yang KH, Lee JH, Chang JS, Kim SH, Kim IJ, Koh JM, Jung JH, Yi KW, Yoo JJ, Chung DJ, Lee YK, Yoon HK, Hong S, Kim DY, Baek KH, Kim HJ, Kim YJ, Kang S, Min YK. Assessment of patient-reported outcomes (PROs): treatment satisfaction, medication adherence, and quality of life (QoL) and the associated factors in postmenopausal osteoporosis (PMO) patients in Korea. J Bone Miner Metab. 2019 May; 37(3):563-572. PMID: 30238428.
      View in: PubMed
    15. da Silveira WA, Renaud L, Simpson J, Glen WB, Hazard ES, Chung D, Hardiman G. miRmapper: A Tool for Interpretation of miRNA?mRNA Interaction Networks. Genes (Basel). 2018 Sep 14; 9(9). PMID: 30223528.
      View in: PubMed
    16. Lin CY, Kwon H, Rangel Rivera GO, Li X, Chung D, Li Z. Sex Differences in Using Systemic Inflammatory Markers to Prognosticate Patients with Head and Neck Squamous Cell Carcinoma. Cancer Epidemiol Biomarkers Prev. 2018 10; 27(10):1176-1185. PMID: 30049843.
      View in: PubMed
    17. 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. 2019 07; 28(7):2137-2149. PMID: 29336210.
      View in: PubMed
    18. 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
    19. 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
    20. Chung D, Lawson A, Zheng WJ. A statistical framework for biomedical literature mining. Stat Med. 2017 Sep 30; 36(22):3461-3474. PMID: 28675924.
      View in: PubMed
    21. Chung D, Kim HJ, Zhao H. graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. PLoS Comput Biol. 2017 02; 13(2):e1005388. PMID: 28212402.
      View in: PubMed
    22. 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
    23. 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
    24. Takeyama N, Vidhyarkorn S, Chung DJ, Siripongsakun S, Kim HJ, Lu DS, Raman SS. Does hepatobiliary phase sequence qualitatively outperform unenhanced T1-weighted imaging in assessment of the ablation margin 24 hours after thermal ablation of hepatocellular carcinomas? Abdom Radiol (NY). 2016 10; 41(10):1942-55. PMID: 27271219.
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    25. 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
    26. Kim HS, Kang WK, Chung DJ. Appendiceal Immunoglobulin G4-Related Disease Mimicking Appendiceal Tumor or Appendicitis: A Case Report. Korean J Radiol. 2016 Jan-Feb; 17(1):56-8. PMID: 26798216.
      View in: PubMed
    27. Chung D, Kim H. Accurate ensemble pruning using PL-bagging. Comput. Stat. Data Anal. 2015; 83:1-13.
    28. 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.
      View in: PubMed
    29. Song SM, Yang HW, Jung MK, Heo J, Cho CM, Goo YK, Hong Y, Chung DI. Two human cases of Diphyllobothrium nihonkaiense infection in Korea. Korean J Parasitol. 2014 Apr; 52(2):197-9. PMID: 24850965.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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
    33. 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.
    34. 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.
    35. 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
    36. Moon EK, Xuan YH, Chung DI, Hong Y, Kong HH. Microarray analysis of differentially expressed genes between cysts and trophozoites of Acanthamoeba castellanii. Korean J Parasitol. 2011 Dec; 49(4):341-7. PMID: 22355200.
      View in: PubMed
    37. 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.
      View in: PubMed
    38. 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.
    39. 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
    40. 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.
    41. Chung D, Keles S. Sparse partial least squares classification for high dimensional data. Stat Appl Genet Mol Biol. 2010; 9:Article17. PMID: 20361856.
      View in: PubMed
    42. Choi SH, Cho MK, Ahn SC, Lee JE, Lee JS, Kim DH, Xuan YH, Hong YC, Kong HH, Chung DI, Yu HS. Endosymbionts of Acanthamoeba isolated from domestic tap water in Korea. Korean J Parasitol. 2009 Dec; 47(4):337-44. PMID: 19967080.
      View in: PubMed
    43. 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.
      View in: PubMed
    44. 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
    45. 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.
      View in: PubMed
    46. 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
    47. Kim JH, Park YS, Chung CG, Park KS, Chung DJ, Kim HJ. Feasibility and utility of transradial cerebral angiography: experience during the learning period. Korean J Radiol. 2006 Jan-Mar; 7(1):7-13. PMID: 16549950.
      View in: PubMed
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