Machine learning applications for biomedical data
Computational methods in cancer genomics
Tumor heterogeneity analysis of cancers
Single-cell sequencing analysis
Analysis of tumor immune microenvironment (TIME)
H.W. Lee, C. Park, *J.-G. Joung, M. Kang, Y.S. Chung, W.J. Oh, S.-Y. Yeom, W.-Y. Park, T.J. Kim, S.I. Seo, Renal Cell Carcinoma-Infiltrating CD3 low Vγ9Vδ1 T Cells Represent Potentially Novel Anti-Tumor Immune Players, Current Issues in Molecular Biology, 43(1):226-239, 2021.
J.Y. Sung, H.-W. Lim, J.-G. Joung†, W.-Y. Park, Pan-cancer Analysis of Alternative Lengthening of Telomere Activity, Cancers,23(8):101386, 2020.
H.K. Kim, *J.-G. Joung, Y.-L Choi, S.-H Lee, B.J. Park, Y.S. Choi, D. Ryu, J.-Y. Nam, M.-S. Lee, Park, W.Y. Park, S.Hwang, H. Cha, H.S. Kim, S. Lee, Y. Jung, J.E. Lee, J. Doh, S. Paik, J.H. Kang, J. Lee, J. Kim, Earlier-phased cancer immunity cycle strongly influences cancer immunity in operable never-smoker lung adenocarcinoma, iScience, 2020.
J.S. Bae, J.W.Lee, J.-G. Joung, K.H. Yoo, H.H. Song, Y.M. Sung, K.W. Sung, Genome-wide association study for the identification of novel genetic variants associated with the risk of neuroblastoma in Korean children, Translational Oncology, 2020.
G. Seong, N. Kim, *J.-G. Joung, E.R. Kim, D.K. Chang, J. Chung, S.N. Hong, Y.-H. Kim, Changes in the Intestinal Microbiota of Patients with Inflammatory Bowel Disease with Clinical Remission during an 8-Week Infliximab Infusion Cycle, Microorganisms, 2020.
N.Y. Kim, H.Y. Kim, K. Lee, Y. Hong, J.H. Cho, J.W. Choi, J.-I. Lee, Y.-L. Suh, B.M. Ku, H.Y. Eum, S. Choi, Y.-L. Choi, J.-G. Joung, W.-Y. Park, H.A. Jung, J.-M. Sun, S.-H. Lee, J.S. Ahn, K. Park, M.-J. Ahn, H.-O. Lee, Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma, Nature Communications, 11(1):2285, 2020.
H.W. Lee, H.H. Cho, *J.-G. Joung, H.G. Jeon, B.C. Jeong, S.S. Jeon, H.M. Lee, D.H., Nam, W.Y. Park, S.I. Seo, H. Park, Integrative Radiogenomics Approach for Risk Assessment of Post-Operative Metastasis in Pathological T1 Renal Cell Carcinoma: A Pilot Retrospective Cohort Study, Cancers , 12(4)E866, 2020.
H.-O. Lee, Y. Hong, Y. B. Cho, V. Pomella, B. Van den Bosch, J. Vanhecke, S. Verbandt, H. Hong, J.-W.Min, N. Kim, H.H. Eum, J. Qian, B. Boeckx, D. Lambrechts, P. Tsantoulis, G. De Hertogh, W. Chung, T. Lee, M. An, H.T. Shin, J.-G. Joung, M.H. Jung, G. Ko, P. Wirapati, S.H. Kim, H.C. Kim, S.H. Yun, I.B.H. Tan, B. Ranjan, W.Y. Lee, T.Y. Kim, J.K. Choi, Y.J. Kim, S. Prabhakar, S. Tejpar, W.-Y. Park, Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer, Nature Genetics, 52(6):594-603, 2020.
J.S, H. Shin, J.K. Sa , J.S. Bae, H. Koo, S. Jin, H.J. Cho, S.W. Choi, J.M. Kyoung, J.Y. Kim, Y.J. Seo, J.-G. Joung, N.K.D. Kim , D.S. Son, J. Chung, T. Lee, D.S. Kong, J.W. Choi, H.J. Seol, J.I. Lee, Y.L. Suh, W.Y. Park, D.H. Nam, Clinical Targeted Next-Generation sequencing Panels for Detection of Somatic Variants in Gliomas, Cancer Research and Treatment, 52(1): 41-50, 2020.
J. Zhang, G. Eswaran, J. Alonso-Serra, M. Kucukoglu, J. Xiang, W. Yang, A. Elo, K. Nieminen, T. Damen, J.-G. Joung, J.-Y Yun, J.-H Lee, L. Rangni, P.B. Reuille, S. Ahnert, J.Y. Lee, A.P. Mahonen, Y.Helariutta, Transcriptional regulatory framework for cambium development in Arabidopsis roots, Nature Plant, 5(10):1033-1042, 2019.
J. Sung, B. Lee, H.-T. Shin, K.-A. Sohn, W.-Y. Park, J.-G. Joung, Assessment of intratumoral heterogeneity with mutations and gene expression profiles, PLoS One, 14(7):e0219682, 2019.
S. Park, *J.-G. Joung, Y. W. Min, J.-Y. Nam, D. Ryu, D. Oh, W.-Y. Park, S.-H. Lee, Y. L. Choi, M.-J. Ahn, K. Park, J.-M. Sun, Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma, Journal for ImmunoTherapy of Cancer, 7(1):128, 2019.
B.Y. Oh, H.-T. Shin, J.W. Yun, K.-T. Kim, J. Kim, J.S. Bae, Y.B. Cho, W.Y. Lee, S.H. Yun, Y.A. Park, Y.H. Park, Y.-H. Im, J. Lee, J.-G. Joung†, H.C. Kim, W.Y. Park, Intratumor heterogeneity inferred by targeted deep sequencing as prognostic indicator, Scientific Reports, 9(1):4542, 2019.
J.W. Yun, S. Lee, D.Ryu, S. Park, W.-Y. Park, J.-G. Joung†, J. Jeong, Biomarkers associated with tumor heterogeneity in prostate cancer, Translational Oncology, 12(1):43-48, 2019.
S.H. Moon, J.Kim., J.-G. Joung, H. Cha, W.-Y. Park, J.S. Ahn, M.J. Ahn, K.C. Park, J.Y. Cho, K.-H. Lee, B.-T. Kim, S.-H. Lee, Correlations between Metabolic Texture Features, Genetic Heterogeneity, and Mutation Burden in Patients with Lung Cancer, European Journal of Nuclear Medicine and Molecular Imaging, 46(2):446-454, 2019
K.Y. Han, K.-T. Kim, *J.-G. Joung, D.-S Son, Y.J. Kim, A.J, H.-J.Jeon, H.-S. Moon, C.E. Yoo, W.C, H.-O. Lee, D. Park, W.-Y. Park, SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells, Genome Research, 28(1):75-87, 2018.
J.-Y. Nam. B.Y. Oh, H.K. Hon, J.S. Bae, S.Y. Ha, W.Y. Lee, H.C. Kim, S.H. Yun, Y.A. Park, J.-G. Joung†, W.-Y. Park, Y.B. Cho, Molecular characterization of colorectal signet-ring cell carcinoma using whole-exome and RNA sequencing, Translational Oncology, 11(4):836-844, 2018.
H. Lee, J.-G. Joung, H.-T. Shin, D.H. Kim, Y. Kim, H. Kim, O.J. Kwon, Y.M. Shim, H.Y. Lee, K..S. Lee, Y.L. Choi, W.-Y. Park, D.N. Hayes, S.-W. Um, Genomic alterations of ground-glass nodular lung adenocarcinoma, Scientific Report, 8(1):7691, 2018.
B. Lee, J. Shim, J. Lee, J.-G. Joung†, B. Lee, J.W. Yun, J.S. Bae, H.-T. Shin, K.W. Sung, W.-Y. Park, Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors, Translational Oncology , 11(6): 1390-1397, 2018.
H.T. Shin, Y.L. Choi, J.W. Yun, N.K.D. Kim, S.Y. Kim, H.J. Jeon, J.Y. Nam, C. Lee, D. Ryu, S.C. Kim, K. Park, E. Lee, J.S. Bae, D.S. Son, J.-G. Joung, J. Lee, S.T. Kim, M.J. Ahn, S.H. Lee, J.S. Ahn, W.Y. Lee, B.Y. Oh, Y.H. Park, J.E. Lee, H.K Lee, H.C. Kim, K.M. Kim, Y.H. Im, K. Park, P.J. Park, W.Y. Park, Prevalence and detection of low-allele-fraction variants in clinical cancer samples, Nature Communications, 8(1):1377, 2017.
B.Y. Oh, J. Cho, H.K. Hong, W.-Y. Park, J.-G. Joung†, Y.B. Cho, Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers, Cancer Management and Research, 9:581-589, 2017.
J.-G. Joung, B.Y. Oh, H.K. Hong, H. Al-Khalidi, F. Al-Alem, H.-O. Lee, J.S. Bae, J. Kim, H.-U. Cha, M. Alotaibi, Y.B. Cho, M. Hassanain, W.-Y. Park, W.Y. Lee, Tumor heterogeneity predicts metastatic potential in colorectal cancer, Clinical Cancer Research, 23(23):7209-7216, 2017.
C. Lee, J.S. Bae, G.H. Ryu, N.K.D.Kim, D. Park, J. Chung, S. Kyung, J.-G. Joung, H.T. Shin, S.H. Shin, Y. Kim, B.S. Kim, H. Lee, K.M. Kim, J.S. Kim, W.Y. Park, D.S. Son, A method to evaluate the quality of clinical gene-panel sequencing data for single-nucleotide variant detection, The Journal of Molecular Diagnostics, 19(5):651-658, 2017.
C.H. Shin, H. Lee, H.R. Kim, K.H. Choi, J.-G. Joung, H.H. Kim, Regulation of PLK1 through competition between hnRNPK, and miR-149-3p and miR-193b-5p, Cell Death and Differentiation, 24(11):1861-1871, 2017.
S.N. Hong, *J.-G. Joung, J.S. Bae, J.S Koo, S.J. Park, J.P. Im, Y.S. Kim, J.W. Kim, W.-Y. Park, Y.H. Kim, RNA-seq reveals transcriptomic differences in inflamed and noninflamed intestinal mucosa of Crohn’s disease patients compared with normal mucosa of healthy controls, Inflammantory Bowel Diseases, 23(7):1098-1108, 2017.
H. Jung, H. Y. Yoo, S. H. Lee, S. shin, S. C. Kim, S. Lee, J.-G. Joung, J.-Y. Nam, D. Ryu, J. W. Yun, J. K. Choi, K. K. Kim, S. J. Kim, W. S. Kim, W. Y. Park, and Y. Ko, The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP, Oncotarget, 8(10):17038-17049, 2017.
C.E. Yoo, J.-M. Park, H.S. Moon, J.-G. Joung, D.S. Son, H.-J. J, Y.-J. Kim, K.-Y. Han, J.-M. Sun, K. Park, D. Park, W.-Y. Park, Vertical magnetic sparation of circulating tumor cells and somatic genomic-alteration analysis in lung cancer patients, Scientific Reports, 6:37392, 2016.
S.-W. Um, *J.-G. Joung, H. Lee, H. Kim, K.-T. Kim, J. Park, D. N. Haye, W.-Y. Park, Molecular evolution patterns in metastatic lymph nodes reflect the differential treatment response of advanced primary lung cancer, Cancer Research. 76(22):6568-6576, 2016.
M.-S, Kwon, J.Min, H.-Y. Jeon, K, Hwang, C. Kim, J. Lee, J.-G. Joung, W.-Y. Park, H.S. Lee, Paradoxical delay of senescence upon depletion of BRCA2 in telomerase-deficient worms, FEBS Open Bio, 2016.
H.G. Kang, H. Lee, Y.H. Ahn, J.M. Ko, I.-S. Ha, H.I Cheong, J.-G. Joung, J. Nam, M.H Cho, J.I.Shin, J. Kim, H.W. Park, Y.S. Park, W.Y. Chung, D.-Y. Lee, S.Y. Kim, W.Y. Park, Targeted exome sequencing resolves allelic and genetic heterogeneity in genetic diagnosis of nephronophthisis-related ciliopathy, Experimental & Molecular Medicine. 48(8):e251, 2016.
J.-G. Joung, S.Y. Ha, J.S. Bae, J.-Y. Nam, G.-Y. Gwak, C.-K. Park, W.-Y. Park, S.-Y Song, Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma, Oncotarget, 8(2):2076-2082, 2016.
D.Ryu, H.J. Kim, *J.-G. Joung, H.-O Lee, J.S. Bae, S.J.Kim, H. Kim, W.-Y. Park, K. Kim, Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker, Oncotarget, 7(30):47127-47133, 2016.
D.Ryu, J.-G. Joung, N.K. Kim, K.T. Kim, W.Y. Park, Deciphering intratumor heterogeneity using cancer genome analysis, Human Genetics, 135(6):635-42, 2016.
J.H Kim, S.M. Ki, J.-G Joung, E.Scott, S.Heynen-Genel, P.Aza-Blanc, C.H. Kwon, J.Kim, J.Gleeson, J.E Lee, Genome-wide screen identifies novel machineries required for both ciliogenesis with cell cycle arrest upon serum starvation, BBA – Molecular Cell Research, 1863(6):1307-1318, 2016.
J.-G. Joung, J.S. Bae, S.C. Kim, H.C. Jung, W.-Y. Park, S.-Y Song, Genomic characterization and comparison of multi-regional and pooled tumor biopsy specimens, PLoS ONE, 11(3):e0152574, 2016.
J. Gim, Y.B.Cho, H.K. Hong, H.C. Kim. S.H. Yun, H.-G. Wu, S.-Y Jeong, Je-Gun Joung, T. Park, W.-Y. Park, W.Y. Lee, Predicting multi-class response to preperative chemoradiotherapy in rectal cancer patients, Radiation Oncology, 11(1):50, 2016.
H. Lee, S.J. Hwang, H.R. Kim, C.H. Shin, K.H. Choi, J.-G. Joung, H.H. Kim, Neurofibromatosis 2 (NF2) controls the invasiveness of glioblastoma through YAP-dependent expression of CYR61/CCN1 and miR-296-3p, Biochim Biophys Acta., 859(4):599-611, 2016.
N. Kim, A. Cho, H. Watanabe, Y.-L. Choi, M. Aziz, M. Kassner, J.-G. Joung, A.K.J. Park, J.M. Francis, J.S.Bae, S. Ahn, K.-M. Kim, J. O. Park, W.-Y. Park, M.-J. Ahn, K. Park., H.H. Yin, J. Cho, Integrated genomic approaches identify upregulation of SCRN1 as a novel mechanism associated with acquired resistance to erlotinib in PC9 cells harboring oncogenic EGFR mutation, Oncotarget, 7(12):13797-809 , 2016.
J.-K. Rhee, H. Li, J.-G. Joung, K.-B. Hwang, B.-T. Zhang, S.-Y. Shin, Survey of computational haplotype determination methods for single individual, Genes & Genomics, 32(1): 1-12, 2016.