Publications
▶ Preprints
Oh G, Choi B*, Jung I#, Ye JC (2023) SCHYENA: FOUNDATION MODEL FOR FULL-LENGTH SINGLE-CELL RNA-SEQ ANALYSIS IN BRAIN, arXiv [Preprint]
▶ 2024
Koh J*, Kim S*, Son S, Park H, Kim K, Min S, Lee H, Jhun B, Kang E, Jung I, Kang J, Kim Y, Shin E# (2024) Ruxolitinib Improves Immune‑Dysregulation Features but not Epigenetic Abnormality in a Patient with STAT1 GOF, Journal of Clinical Immunology .
▶ 2023
Kim K*, Kim M*, Lee A*, Song SH*, Kang JK, Eom J, Kang GH, Bae JM, Min S, Kim Y, Lim Y, Kim HS, Kim YJ, Kim TY#, Jung I# (2023) Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer, Cell Reports.
Seok J*, Cho S*, Lee J, Choi Y, Kim SY, Lee S, Kim SH, Jeong S, Jeon M, Lee H, Kim A. R, Choi B, Ha S, Jung I, Yoon K, Park J, Kim JH, Kim BJ, Shin E#, Park S# (2023) A virtual memory CD8+ T cell-originated subset causes alopecia areata through innate-like cytotoxicity, Nature Immunology.
Lee A*, Kim C*, Park S, Joo J, Choi B, Yang D, Jun K, Eom J, Lee S, Chung S, Rissman RA, Chung J, Masliah E#, Jung I# (2023) Characterization of altered molecular mechanisms in Parkinson’s disease through cell type-resolved multi-omics analyses, Science Advances.
Joo J*, Cho S*, Hong S, Min S, Kim K, Kumar R, Choi J, Shin Y#, Jung I# (2023) Probabilistic establishment of speckle-associated inter-chromosomal interactions, Nucleic Acids Research.
Cho N*, Joo J*, Choi S, Kang B, Lee A, Youn S, Park S, Kim E, Masliah E, Ko Y, Cha S, Jung I#, Kim K (2023) A novel splicing variant of DJ-1 in Parkinson's disease induces mitochondrial dysfunction, Heliyon.
▶ 2022
Han S*, Kim K*, Park S, Lee A, Chun H, Jung I# (2022) scAVENGERS: A genotype-based deconvolution of individuals in multiplexed single-cell ATAC-seq data without reference genotypes, NAR Genomics and Bioinformatics.
Kang CK*, Choi B*, Kim S, Sun CH, Yoon SH, Kim K, Chang E, Jung J, Choe PG, Park WB, Kim ES, Kim HB, Kim NJ, Oh MD, Im H, Kim J, Lee YH, Lee J, Chun H, Koh Y, Lee JY#, Moon JH#, Song KH#, Jung I# (2022) Clinical impact of clonal hematopoiesis on severe COVID-19 patients without canonical risk factors, Haematologica.
Choi B*, Kang CK*, Park S, Lee D, Lee A, Ko Y, Kang S-J, Kang K, Kim S, Koh Y, Jung I# (2022) Single-cell transcriptome analyses reveal distinct gene expression signatures of severe COVID-19 in the presence of clonal hematopoiesis, Experimental & Molecular Medicine.
▶ 2021
Chae S*, Hong J*, Kang K*, Shin A, Kim D, Lee S, Kim M, Jung I, Daesoo Kim# (2021) Molecular laterality encodes stress susceptibility in the medial prefrontal cortex, Molecular Brain.
H Jo, T Kim, Y Chun, Jung I, D Lee# (2021) A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast, Nature Communications.
S Han, H Lee, AJ Lee, SK Kim, Jung I, GY Koh, TK Kim, D Lee# (2021) CHD4 Conceals Aberrant CTCF-Binding Sites at TAD Interiors by Regulating Chromatin Accessibility in Mouse Embryonic Stem Cells, Molecules and Cells.
Lee YH, Lee HJ, Kim HC, Lee Y, Nam SK, Hupperetz C, Ma JS, Wang X, Singer S, Kim WS, Kim SJ, Koh Y, Jung I, Kim CH (2021) PD-1 and TIGIT downregulation distinctly affect the effector and early memory phenotypes of CD19-targeting CAR T cells, Molecular Therapy.
Kim K and Jung I# (2021) covNorm: An R Package for Coverage Based Normalization of Hi-C and Capture Hi-C Data, Computational and Structural Biotechnology Journal.
Kim K*, Kim M*, Kim Y*, Lee D#, Jung I# (2021) Hi-C as a molecular rangefinder to examine genome rearrangements, Seminars in Cell and Developmental Biology.
Lee A and Jung I# (2021) Functional annotation of lung cancer-associated genetic variants by cell-type specific epigenome and long-range chromatin interactome, Genomics & Informatics.
Kim K*, Jang I*, Kim M*, Choi J, Kim M, Lee B#, Jung I# (2021) 3DIV Update for 2021: a comprehensive resource of 3D genome and 3D cancer genome, Nucleic Acids Research.
▶ 2020
Leem G*, Park J*, Jeon M*, Kim ES, Kim SW, Lee YJ, Choi SJ, Choi B, Park S, Ju YS, Jung I, Kim S, Shin EC, Lee JY#, Park SH#. (2020) 4-1BB co-stimulation further enhances anti-PD-1-mediated reinvigoration of exhausted CD39+ CD8 T cells from primary and metastatic sites of epithelial ovarian cancers, The Journal for ImmunoTherapy of Cancer.
Choi W*, Hwang J*, Cho A, Lee A, Jung I, Cho S, Kim L, Kim Y (2020) NEUROD1 Intrinsically Initiates Differentiation of Induced Pluripotent Stem Cells into Neural Progenitor Cells, Molecules and Cells.
Choi W*, Hwang J*, Cho A*, Lee A, Lee J, Jung I, Cho S, Kim L#, Kim Y# (2020) DNA Methylation of Intragenic CpG Islands are Required for Differentiation from iPSC to NPC, Stem Cell Reviews and Reports.
Kong N and Jung I# (2020) Long-range chromatin interactions in pathogenic expression control, Transcription.
Choi W*, Hwang J*, Lee J*, Cho A, Lee A, Jung I, Cho S, Kim L#, Kim Y# (2020) Chromatin interaction changes during iPSC-NPC model to facilitate study of biologically significant genes involved in differentiation, Genes.
Kim C*, Noda T*, Kim H*, Kim G, Park S, Na Y, Oura S, Shimada K, Bang I, Ahn J, Kim Y, Oh S, Choi H, Kim J, Jung I, Lee H, Okada Y, Ikawa M#, and Baek S# (2020) PHF7 Modulates BRDT stability and Histone-to-Protamine Exchange during Spermiogenesis, Cell Reports.
Yoo M, Park S, Jung I, and Han J# (2020) Persistence of fear memory depends on a delayed elevation of BAF53b and FGF1 expression in the lateral amygdala, Journal of Neuroscience.
Lee J*, Park S*, Jeong H*, Ahn J*, Choi S, Lee H, Choi B, Nam S, Sa M, Kwon J, Jeong S, Lee H, Park S, Park S, Choi J#, Kim S#, Jung I#, and Shin E# (2020) Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19, Science Immunology.
▶ 2019
Kim C*, Jang M*, Kim Y, Leem G, Kim K, Lee H, Kim T, Choi S, Kim H, Han J, Kwon M, Kim J, Lee A, Nam S, Bae S, Lee S, Shin S, Park S, Ahn J, Jung I, Lee K, Park S, Kim H#, Min B#, and Shin ## (2019) VEGF-A drives TOX-dependent T cell exhaustion in anti–PD-1–resistant microsatellite stable colorectal cancers, Science Immunology.
Jung I*#, Schmitt A*, Diao Y*, Lee A, Liu T, Yang D, Catherine Tan, Eom J, Chan M, Chee S, Chiang Z, Kim C, Masliah E, Barr C, Li B, Kuan S, Kim D, Ren B# (2019) A Compendium of Promoter-Centered Long-Range Chromatin Interactions in the Human Genome, Nature Genetics.
Kim K*, Eom J*, and Jung I# (2019) Characterization of structural variations in the context of 3D chromatin structure, Molecules and Cells.
Ryu J*, Kim H*, Yang D, Lee A, Jung I# (2019) A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin, BMC Bioinformatics.
▶ 2018
Park J, Kim C, Shim J, Kim J, Lee H, Lee J, Kim M, Haam K, Jung I, Park S, Chang J, Shin E & Kang S (2018) Effect of combined anti-PD-1 and temozolomide therapy in glioblastoma, OncoImmunology.
Di Iulio J, Bartha I, Wong EHM, Yu HC, Lavrenko V, Yang D, Jung I, Hicks MA, Shah N, Kirkness EF, Fabani MM, Biggs WH, Ren B, Venter JC, Telenti A (2018) The human noncoding genome defined by genetic diversity, Nat Genet.
Yang D*, Jang I*, Choi J, Kim MS, Lee AJ, Kim H, Eom J, Kim D#, Jung I#, Lee B# (2018) 3DIV: A 3D-genome Interaction Viewer and database, Nucleic Acids Research.
▶ ~2017
Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B (2017) A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells, Nat Methods.
Schmitt, AD., Hu, M., Jung, I., Xu, Z., Qiu, Y., Tan, CL., Li, Y., Lin, S., Lin, Y., Barr, CL., Ren, B. (2016) A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome, Cell Rep.
Dahl, JA.*, Jung, I.*, Aanes, H., Greggains, GD., Manf, A., Lerdrup, M., Li, G., Kuan, S., Li, B., Lee, AY., Preissl, S., Jermstad, I., Haugn, MD., Suganthan, R., Bjoras, M., Hansen, K., Dalen, KT., Fedorsak, P., Ren, B., Klungland (2016) Broad histone H3K4me3 domains in mouse oocytes modulate maternal to zygotic transition, Nature.
Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. (2016) A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening, Genome Research.
Jung I, Seo J, Lee HS, Stanton LW, Kim D, Choi JK. (2015) Global mapping of the regulatory interactions of histone residues, FEBS Lett.
Leung, D.*, Jung, I.*, Rajagopal, N.*, Schmitt, A., Selvaraj, S., Lee, AY., Yen, CA., Lin, S., Lin, Y., Qiu, Y., Xie, W., Yue, F., Hariharan, M., Ray, P., Kuan, S., Edsall, L., Yang, H., Chi, NC., Zhang, MQ., Ecker, JR., & Ren, B. (2015) Integrative analysis of haplotype-resolved epigenomes across human tissues, Nature.
Dixon, J.*, Jung, I.*, Selvaraj, S.*, Shen, Y., Antosiewicz-Bourget, J., Lee, AY., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanekov, V., Ecker, J., Thomson, J., & Ren, B. (2015) Chromatin architecture reorganization during stem cell differentiation, Nature.
Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, DU., Jung, I., Wu, H., Zhai, Y., Tang, Y., Lu, Y., Wu, Y., Jia, Z., Li, W., Zhang, MQ., Ren, B., Krainer, AR., Maniatis, T., We, Q. (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell.
Schultz, M., He, Y., Whitaker, JW., Hariharan, M., Mukamel, EA., Leung, D., Rajagopal, N., Nery, JR., Urich, MA., Chen, H., Lin, L., Lin, Y., Jung, I., Schmitt, AD., Selvaraj, S., Ren, B., Sejnowski, TJ., Wang, W., Ecker, JR. (2015) Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation, Nature.
Jung I*, Park J*, Choi C, Kim D (2015) Identification of novel trans-crosstalk between histone modifications via genome-wide analysis of maximal deletion effect. Genes & Genomics.
Lee, K.*, Kim, S.C*, Jung, I.*, Kim, K., Seo, J., Lee, HS., Bogu, G.K., Kim, D., Lee, S., Lee, B. & Choi, J.K. (2013) Genetic landscape of open chromatin in yeast, PLoS Genet.
Jung I*, & Kim, D. (2013) LinkNMF: Identification of histone modification modules in the human genome using nonnegative matrix factorization, Gene.
Kim SK*, Jung I*, Kim M, Lee H, Kang K, Han YH, Kim YS, Kim D & Lee D. (2012) Human histone H3K79 methyltransferase DOT1L methyltransferase Binds Actively Transcribing RNA Polymerase II to Regulate Gene Expression, J. Biol. Chem.
Jung, I.*, Kim, S.K.*, Kim, M.*, Han, Y.M.,, Kim, Y.S., Kim, D. & Lee, D. (2012) H2B monoubiquitylation is a 5’-enriched active transcription mark and correlates with exon-intron structure in human cells, Genome Research.
Jung, I. & Kim, D. (2012) Histone modification profiles characterize function-specific gene regulation, Journal of Theoretical Biology.
Kim, N., Kim, H., Jung, I., Kim, Y., Kim, D. & Han, Y.M. (2011) Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation.
Jung, I., Lee, J., Choi, C. & Kim, D. (2011) Inferring relative activity between pathway and downstream genes to classify melanoma cancer progression, IBC.
Jung, I., Matsuyama, A., Yoshida, M. & Kim, D. (2010) PostMod: Sequence-based prediction of phosphorylation sites by considering indirect relationships, BMC Bioinformatics.
Jung, I. & Kim, D. (2009) Regulatory patterns of histone modifications to control the DNA methylation status at CpG islands, IBC.
Jung, I. & Kim, D. (2009) SIMPRO: simple protein homology detection method by using indirect signals, Bioinformatics. 25:729-735
Jung, I., Lee, J., Lee, S.Y. & Kim, D. (2008) Application of Nonnegative Matrix Factorization to Improve Profile-Profile Alignment Features for Fold Recognition, BMC Bioinformatics.
* - Equally contributed
# - Corresponding author