*: Equally contributed
+: Corresponding author
2024
D. S. Kyung*, E. Lee*, S. Chae*, Y. Son*, Y. Moon, D. Hwang+, J. K. Kim+, Y. Lee+, J. K. Seong+. Single-cell transcriptomic analysis reveals dynamic activation of cellular signaling pathways regulating beige adipogenesis. Experimental & Molecular Medicine, 2024
S. Han, B. Kim, D. Y. Hyeon, D. Jeong, J. Ryu, J. Nam, Y. H. Choi, B. Kim, S. C. Park, Y. W. Chung, S. J. Shin, J. Lee, J. K. Kim, J. Park, S. W. Lee, T. Kim, J. H. Cheon, H. Cho, C. Kim, J. Yoon, D. Hwang, J. Ryu, Distinctive CD39+CD9+ lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis. Nature Communications 15:8628, 2024
J. Ahn*, S. Kim*, C. R. Kim, J. Lee, J. M. Kim, T. M. Klompstra, Y. H. Choi, Y. Jeon, Y. Na, J. Kim, Y. Okada, H. Lee, I. S. Kim+, J. K. Kim+, B. Koo+, S. H. Baek+, Dual function of PHF16 in reinstating homeostasis of murine intestinal epithelium after crypt regeneration. Developmental Cell, 2024
S. Byun*, J. Lee*, Y. H. Choi, H. Ko, C. Lee, J. C. Park, S. W. Kim, H. Lee, A. Sharma, K. S. Kim, D. Rudra, J. K. Kim+, S. Im+, Gut microbiota defines functional direction of colonic regulatory T cells with unique TCR repertories. The Journal of Immunology 213(6):886-897, 2024
U. Ojha, S. Kim, C. Y. Rhee, J. You, Y. H. Choi, S. Yoon, S. Y. Park, Y. R. Lee, J. K. Kim, S. Bae, Y. M. Lee, Endothelial RUNX3 controls LSEC dysfunction and angiocrine LRG1 signaling to prevent liver fibrosis. Hepatology, 2024
S. S. Wu, S. Kim, H. Lee, J. Lee, S. Park, R. Bakonyi, I. Teriyapirom, N. Hallay, S. P. Carotta, H. Theussl, J. Kim, J. Lee, B. D. Simons, J. K. Kim, G. Golozza, B. Koo, Red2Flpe-SCON: a versatile, multicolor strategy for generating mosaic conditional knockout mice. Nature Communications 15:4963, 2024
G. Sharma, A. Sharma, I. Kim, D. G. Cha, S. Kim, E. S. Park, J. G. Noh, J. Lee, J. H. Ku, Y. H. Choi, J. Kong, H. Lee, H. Ko, J. Lee, A. Notaro, S. H. Hong, J. H. Rhee, S. G. Kim, C. D. Castro, A. Molinaro, K. Shin, S. Kim, J. K. Kim, D. Rudra, S. Im, A dietary commensal microbe enhances antitumor immunity by activating tumor macrophages to sequester iron. Nature Immunology 25:790-801, 2024
– Highlighted in Nature Immunology
H. K. Lee, S. Y. Kim, S. Chung, B. Choi, J. Kim, D. Yoon, S. I. Jang, A. Yeo, H. G. Kang, J. Lee, Y. H. Choi, J. S. Park, Y. Sung, J. K. Kim+, E. Chang+, D. K. Lee+, Tumor-associated myeloid cells expressing IL-10R2/IL-22R1 as a potential biomarker for diagnosis and recurrence of pancreatic ductal adenocarcinoma. British Journal of Cancer 130:1979-1989, 2024
C. Choi*, Y. L. Jeong*, K. Park, M. Kim*, S. Kim, H. Jo, S. Lee, H. Kim, G. Choi, Y. H. Choi, J. K. Seong, S. Namgoong, Y. Chung, Y. Jung+, J. G. Granneman+, Y. Hyun+, J. K. Kim+, Y. Lee+, TM4SF19-mediated control of lysosomal activity in macrophages contributes to obesity-induced inflammation and metabolic dysfunction. Nature Communications 15:2779, 2024
K. A. Han, T. Yoon, J. Kim, J. Lee, J. Y. Lee, G. Jang, J. W. Um, J. K. Kim, J. Ko, Specification of neural circuit architecture shaped by context-dependent patterned LAR-RPTP microexons. Nature Communications 15:1624, 2024
B. S. Ko*, M. H. Han*, M. J. Kwon*, D. G. Cha*, Y. Ji, E. S. Park, M. J. Jeon, S. Kim, K. Lee, Y. H. Choi, J. Lee, M. Torras-Llort, K. Yoon, H. Lee, J. K. Kim+, S. B. Lee+, Baf-mediated transcriptional regulation of teashirt is essential for the development of neural progenitor cell lineages. Experimental & Molecular Medicine 56:422-440, 2024
D. Kwon*, S. Park*, Y. L. Jeong*, Y. Kim*, J. Min, C. Lee, J. Choi, Y. H. Choi, H. Kong, Y. Choi, S. Baek, K. Lee, Y. Kang, C. Jeong, G. You, Y. Oh, S. Im, M. Song, J. K. Kim, J. Chang, D. Choi, S. Lee, Fc-fused IL-7 provides broad antiviral effects against respiratory virus infections through IL-17A-producing pulmonary innate-like T cells. Cell Reports Medicine 5(1):101362, 2024
S. Lee*, H. Kim*, B. S. Kim*, S. Chae*, S. Jung*, J. S. Lee, J. Yu, K. Son, M. Chung, J. K. Kim+, D. Hwang+, S. H. Baek+, N. L. Jeon+, Angiogenesis-on-a-chip coupled with single-cell RNA sequencing reveals spatially differential activations of autophagy along angiogenic sprouts. Nature Communications 15:230, 2024
– Featured in a Nature Communications Editors’ Highlights
S. Choi*, J. Lee*, S. Kim*, Y. W. Lee*, G. Kim, S. Hong, S. An, H. Noh, K. E. Kim, D. On, S. G. Lee, H. J. Jang, S. Kim, J. Kim, J. S. Seo, J. J. Kim, I. H. Park, J. Oh, D. Kim, J. Yoon, S. Seok, Y. J. Lee, S. Y. Kim, Y. B. Kim, J. Hwang, H. Lee, H. B. Kim, J. W. Park, J. Yun, J. Shin, J. Seo, K. T. Nam, K. Choi+, H. Kwon+, H. Lee+, J. K. Kim+, J. K. Seong+, A longitudinal molecular and cellular lung atlas of lethal SARS-CoV-2 infection in K18-hACE2 transgenic mice. eBioMedicine 99:104932, 2024
2023
S. M. Han*, E. S. Park*, J. Park*, H. Nahmgoong, Y. H. Choi, J. Oh, K. M. Yim, W. T. Lee, Y. K. Lee, Y. G. Jeon, K. C. Shin, J. Y. Huh, S. H. Choi, J. Park, J. K. Kim+, J. B. Kim+, Unique adipose tissue invariant natural killer T cell subpopulations control adipocyte turnover in mice. Nature Communications 14:8512, 2023
J. Kim*, S. Kim*, S. Lee*, B. Jo, J. Oh, E. Kwon, K. Kim, A. A. Adpaikar, E. Kim, H. Jung, H. Kim, J. Roe, C. P. Hong, J. K. Kim+, B. Koo+, H. Cha+, Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction. Science Advances 9(47):eadi8454, 2023
H. S. Han*, E. Ahn*, E. S. Park*, T. Huh, S. Choi, Y. Kwon, B. H. Choi, J. Lee, Y. H. Choi, Y. L. Jeong, G. B. Lee, M. Kim, J. K. Seong, H. M. Shin, H. R. Kim, M. H. Moon, J. K. Kim+, G. S. Hwang+, S. H. Koo+, Impaired BCAA catabolism in adipose tissues promotes age-associated metabolic derangement. Nature Aging 3:982-1000, 2023
– Highlighted in Nature Aging.
S. I. Jang, H. K. Lee, E. J. Chang, S. Kim, S. Y. Kim, I. Y. Hong, J. K. Kim, H. S. Lee, J. Yang, J. H. Cho, D. K. Lee+, Improved predictability of pancreatic ductal adenocarcinoma diagnosis using a blood immune cell biomarker panel developed from bulk mRNA sequencing and single-cell RNA-sequencing. Cancer Immunology, Immunotherapy 72:2757-2768, 2023
J. Kwon, S. Seok, S. Kim, H. An, A. D. Choudhury, S. Woo, J. Oh, J. K. Kim, D. C. Voon+, D. Kim+, J. W. Park+, A synergistic partnership between IL-33/ST2 and Wnt pathway through Bcl-xL drives gastric cancer stemness and metastasis. Oncogene 42:501–515, 2023
2022
J. Ha*, B. S. Kim*, B. Min, J. Nam, J. G. Lee, M. Lee, B. H. Yoon, Y. H. Choi, I. Im, J. S. Park, H. Choi, A. Baek, S. M. Cho, M. O. Lee, K. H. Nam, J. Y. Mun, M. Kim, S. Y. Kim, M. Y. Son, Y. K. Kang, J. S. Lee+, J. K. Kim+, J. Kim+, Intermediate cells of in vitro cellular reprogramming and in vivo tissue regeneration require desmoplakin. Science Advances 8(43):eabk1239, 2022
– Selected as the Top 100 Outstanding National Research and Development Achievements for 2023
K. W. Jo, D. Lee*, D. G. Cha*, E. Oh, Y. H. Choi, S. Kim, E. S. Park, J. K. Kim, K. T. Kim+, Gossypetin ameliorates 5xFAD spatial learning and memory through enhanced phagocytosis against Aβ. Alzheimer’s Research & Therapy 14:158, 2022
J. Lee*, S. Kim*, S. Han*, J. Min, B. Caldwell, A.-Diane Bamford, Andreia S. Rocha, J. Park, S. Lee, S. S. Wu, H. Lee, J. Fink, S. Pilat-Carotta, J. Kim, M. Josserand, R. Szep-Bakonyi, Y. An, Y. S. Ju, A. Philpott, B. D. Simons, D. E. Stange, E. Choi+, B. Koo+, and J. K. Kim+, p57Kip2 imposes the reserve stem cell state of gastric chief cells. Cell Stem Cell 29:826-839, 2022
D. Rengaraj*, D. G. Cha*, H. J. Lee*, K. Y. Lee, Y. H. Choi, K. M. Jung, Y. M. Kim, H. J. Choi, H. J. Choi, E. Yoo, S. J. Woo, J. S. Park, K. J. Park, J. K. Kim+, J. Y. Han+, Dissecting chicken germ cell dynamics by combining a germ cell tracing transgenic chicken model with single-cell RNA sequencing. Computational and Structural Biotechnology Journal 20:1654-1669, 2022
D. Kwon, E. S. Park, M. Kim, Y. H. Choi, M. Lee, S. Joo, Y. Kang, M. Lee, S. Jo, S-W. Lee, J. K. Kim+ & Y. J. Lee+, Homeostatic serum IgE is secreted by plasma cells in the thymus and enhances mast cell survival. Nature Communications 13:1418, 2022
H. Nahmgoong*, Y. G. Jeon*, E. S. Park*, Y. H. Choi, S. M. Han, J. Park, Y. Ji, J. H. Sohn, J. S. Han, Y. Y. Kim, I. J. Hwang, Y. K. Lee, J. Y. Huh, S. S. Choe, T. J. Oh, S. H. Choi, J. K. Kim+, J. B. Kim+, Distinct properties of adipose stem cell subpopulations determine fat depot-specific characteristics. Cell Metabolism 34:458-472, 2022
– Featured as Cover Story
– Highlighted in Nature Reviews Endocrinology
S. I. Jang, J. H. Cho, S. Y. Kim, I. Y. Hong, J. S. Park, H. S. Kee, G. Park, J. K. Kim, H. K. Lee, D. K. Lee, Validation of IL-7R as an Immunological Biomarker for Human Pancreatic Ductal Adenocarcinoma. Cancers 14(3):853, 2022
2021
M. K. Yum, S. Han, J. Fink, S-H. S. Wu, C. Dabrowska, T. Trendafilova, R. Mustata, L. Chatzeli, R. Azzarelli, I. Pshenichnaya, E. Lee, F. England, J. K. Kim, D. E. Stange, A. Philpott, J-H. Lee, B-K. Koo, B. D. Simons, Tracing oncogene-driven remodelling of the intestinal stem cell niche, Nature 594:442–447, 2021
2020
M. Lee*, E. Lee*, S. K. Han*, Y. H. Choi, D. Kwon, H. Choi, K. Lee, E. S. Park, M. Rha, D. J. Joo, E. Shin, S. Kim+, J. K. Kim+, Y. J. Lee+, Single-cell RNA sequencing identifies shared differentiation paths of mouse thymic innate T cells, Nature Communications 11:4367, 2020
I. Noorani, J. de la Rosa, Y. H. Choi, A. Strong, H. Ponstingl, M. S. Vijayabaskar, J. Lee, E. Lee, A. Richard-Londt, M. Friedrich, F. Furlanetto, R. Fuente, R. Banerjee, F. Yang, F. Law, C. Watts, R. Rad, G. Vassiliou, J. K. Kim, T. Santarius, S. Brandner, A. Bradley, PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas, Genome Biology 21:181, 2020
J. H. Lee, E. A. Ribeiro, J. Kim, B. Ko, H. Kronman, Y. H. Jeong, J. K. Kim, P. H. Janak, E. J. Nestler, J. W. Koo, J.-H. Kim, Dopaminergic Regulation of Nucleus Accumbens Cholinergic Interneurons Demarcates Susceptibility to Cocaine Addiction, Biological Psychiatry 88:746-757, 2020
D. Lee*, Y. H. Choi*, J. Seo, J. K. Kim+, S. B. Lee+, Discovery of new epigenomicsbased biomarkers and the early diagnosis of neurodegenerative diseases, Ageing Research Reviews 61:101069, 2020
H. Haselimashhadi H, J. C. Mason, V. Munoz-Fuentes, F. López-Gómez, K. Babalola, E. F. Acar, V. Kumar, J. White, A. M. Flenniken, R. King, E. Straiton, J. R. Seavitt, A. Gaspero, A. Garza, A. E. Christianson, C. W. Hsu, C. L. Reynolds, D. G. Lanza, I. Lorenzo, J. R. Green, J. J. Gallegos, R. Bohat, R. C. Samaco, S. Veeraragavan, J. K. Kim, G. Miller, H. Fuchs, L. Garrett, L. Becker, Y. K. Kang, D. Clary, S. Y. Cho, M. Tamura, N. Tanaka, K. D. Soo, A. Bezginov, G. B. About, M. F. Champy, L. Vasseur, S. Leblanc, H. Meziane, M. Selloum, P. T. Reilly, N. Spielmann, H. Maier, V. Gailus-Durner, T. Sorg, M. Hiroshi, O. Yuichi, J. D. Heaney, M. E. Dickinson, W. Wolfgang, G. P. Tocchini-Valentini, K. C. K. Lloyd, C. McKerlie, J. K. Seong, H. Yann, M. H. de Angelis, S. D. M. Brown, D. Smedley, P. Flicek, A. M. Mallon, H. Parkinson, T. F. Meehan, Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data, Bioinformatics 36:1492-1500, 2020
2019
A. T. Y. Yeung*, Y. H. Choi*, A. H. Y. Lee, C. Hale, H. Ponstingl, D. Pickard, D. Goulding, M. Thomas, E. Gill, J. K. Kim, A. Bradley, R. E. W. Hancock, G. Dougan, A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Salmonella Infection, mBio 10:e02169-19, 2019
S. Han*, J. Fink*, D. J. Jörg , E. Lee , M. K. Yum, L. Chatzeli, S. R. Merker, M. Josserand, T. Trendafilova, A. Andersson-Rolf, C. Dabrowska, H. Kim, R. Naumann, J. H. Lee, N. Sasaki, R. L. Mort, O. Basak, H. Clevers, D. E. Stange, A. Philpott, J. K. Kim+, B. D. Simons+, B-K. Koo+, Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells, Cell Stem Cell 25:342-356, 2019
Y. H Choi, J. K. Kim, Dissecting Cellular Heterogeneity Using Single-Cell RNA Sequencing, Molecules and Cells 42:189-199, 2019
B. Kim*, E. Lee*, J. K. Kim, Analysis of Technical and Biological Variability in Single-Cell RNA Sequencing, Methods in Molecular Biology 1935:25-43, 2019
B. Park, S. Chang, G. J. Lee, B. Kang, J. K. Kim, H. Park, Wnt3a disrupts GR-TEAD4-PPARγ2 positive circuits and cytoskeletal rearrangement in a β-catenin-dependent manner during early adipogenesis, Cell Death & Disease 10:16, 2019
2018
V. Muñoz-Fuentes, P. Cacheiro, T. F. Meehan, J. A. Aguilar-Pimentel, S. D. M. Brown, A. M. Flenniken, P. Flicek, A. Galli, H. H. Mashhadi, M. H. Angelis, J. K. Kim, K. C. K. Lloyd, C. McKerlie, H. Morgan, S. A. Murray, L. M. J. Nutter, P. T. Reilly, J. R. Seavitt, J. K. Seong, M. Simon, H. Wardle-Jones, A. Mallon, D. Smedley, H. E. Parkinson, The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation, Conservation Genetics 19:995-1005, 2018
2017
K. Godze, J. K. Kim, A. A. Kolodziejczyk, K. N. Natarajan, E. T. Triglia, B. mifsud, S. Elderkin, J. C. Marioni, S. A. Teichmann, Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression, Nature Communications 8:36, 2017
Y. Huang*, J. K. Kim*, D. V. Do, C. Lee, C. A. Penfold, J. J. Zylicz, J. C. Marioni, J. A. Hackett, M. A. Surani, STELLA modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition, eLife 6:e22345, 2017
2016
T. Ilicic*, J. K. Kim*, F. O. Bagger, D. McCarthy, A. A. Kolodziejczyk, J. C. Marioni, S. A. Teichmann, Classification of low quality cells from single cell RNA-seq data, Genome Biology 17:29, 2016
2015
J. K. Kim, A. A. Kolodziejczyk, T. Ilicic, S. A. Teichmann, J. C. Marioni, Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression, Nature Communications 6:8687, 2015
A. Kolodziejczyk*, J. K. Kim*, J. C. Tsang, T. Ilicic, J. Henriksson, K. N. Natarajan, A. C. Tuck, X. Gao, M. Buhler, P. Liu, J. C. Marioni, S. A. Teichmann, Single cell RNA-Sequencing of pluripotent states unlocks modular transcriptional variation, Cell Stem Cell 17:471-485, 2015
A. Kolodziejczyk, J. K. Kim, V. Svensson, J. C. Marioni, S. A. Teichmann, The technology and biology of single cell RNA sequencing, Molecular Cell 58:610-620, 2015
2014
J. R. Peat, W. Dean, S. J. Clark, F. Krueger, S. A. Smallwood, G. Ficz, J. K. Kim, J. C. Marioni, T. A. Hore, W. Reik, Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation, Cell Reports 9:1-11, 2014
Y. Choi, J. K. Kim, J. Y. Yoo, NFkB and STAT3 synergistically activate the expression of FAT10, a gene counteracting the tumor suppressor p53, Molecular Oncology 8(3):642-655, 2014
2013
P. Brennecke*, S. Anders*, J. K. Kim*, A. A. Kolodziejczyk, X. Zhang, V. Proserpio, B. Baying, V. Benes, S. A. Teichmann, J. C. Marioni, and M. G. Heisler, Accounting for technical noise in single-cell RNA-seq experiments, Nature Methods 10(11):1093-1095, 2013
J. K. Kim and J. C. Marioni, Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data, Genome Biology 14(1):R7, 2013
2012
Y. M. Oh*, J. K. Kim*, S. Choi, and J-Y, Yoo, Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices, Nucleic Acids Research 40(5):e38, 2012
2011
J. K. Kim and S. Choi, Probabilistic models for semi-supervised discriminative motif discovery in DNA sequences, IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(5):1309-1317, 2011
2009
J. K. Kim and S. Choi, Clustering sequence sets for motif discovery, in Advances in Neural Information Processing Systems (NIPS-2009), Vancouver, Canada, December 7-10, 2009
Y. M. Oh*, J. K. Kim*, Y. Choi, S. Choi, and J-Y, Yoo, Prediction and Experimental Validation of Novel STAT3 Target Genes in Human Cancer Cells, PLoS ONE 4(9):e6911, 2009
J. K. Kim and S. Choi, Clustering with r-regular graphs, Pattern Recognition 42:2020-2028, 2009
2008
D. W. Lee*, J. K. Kim*, S. Lee, S. Choi, S. Kim, and I. Hwang, Arabidopsis nuclear-encoded plastid transit peptides contain multiple sequence subgroups with distinctive chloroplast-targeting sequence motifs, Plant Cell 20(6):1603-1622, 2008
S. Kim, J. K. Kim, and S. Choi, Independent arrays or independent time courses for gene expression time series data analysis, Neurocomputing 71:2377-2387, 2008
2006
J. K. Kim, S. Y. Bang, and S. Choi, Sequence driven features for prediction of subcellular localization of proteins, Pattern Recognition 39(12):2301-2311, 2006
J. K. Kim and S. Choi, Tree-dependent components of gene expression data for clustering, in Proc. of International Conference on Artificial Neural Networks (ICANN2006) (LNCS 4132), Athens, Greece, September 10-14 2006
J. K. Kim, G. P. S. Raghava, S. Y. Bang, and S. Choi, Prediction of subcellular localization of proteins using pairwise sequence alignment and support vector machine, Pattern Recognition Letters 27(9):996-1001, 2006