PUBLICATIONS

*: Equally contributed

+: Corresponding author

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), 2022

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 dataGenome 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 sequencingMolecular 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