Publications
selected publications
Kang, J.*, Lee, J.-H.*, …, Lee, S.-H.#, Choi, J. K.#, Park J.-E# (2024). Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types. Nature Communications, 15:4067
Kim, S.*, Leem, G.*, ..., Kang C. M.#, Bang. S.#, Park J.-E# (2024). Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis. Genome Medicine, 16:20.
Kwon, J.*, Kang, J.*, ..., An H. J.#, Lee H.-O.#, Park J.-E#, Choi, J. K.# (2023). Single-cell mapping of combinatorial target antigens for CAR switches using logic gates. Nature Biotechnology, 1-13.
Kang, J.,* Kim, M.*, Yoon, D. Y.*, Kim, W. S., Choi, S. J., Kwon, Y. N., ..., Park, M., Lee, J. S., Park J.-E.#, & Kim, S. M.# (2023). AXL+ SIGLEC6+ dendritic cells in cerebrospinal fluid and brain tissues of patients with autoimmune inflammatory demyelinating disease of CNS. Clinical Immunology, 109686.
Kim, B., Koh, Y., Do, H., Ju, Y., Choi, J. B., Cho, G., ..., Park J.-E.#, Han, Y. M#. (2022). Aberrant Cortical Layer Development of Brain Organoids Derived from Noonan Syndrome-iPSCs. International Journal of Molecular Sciences, 23(22), 13861.
Lee S.*, Kim J.*, Park J.-E#. Single-Cell Toolkits Opening a New Era for Cell Engineering. (2021) Mol Cells. 44(3):127-135.
Park, J.-E.*, Botting, R.A., Domínguez-Conde, C., ... , Taghon, T., Haniffa, M., Teichmann, S.A., (2020) A cell atlas of human thymic development defines T cell repertoire formation. Science 367, eaay3224
Park, J.-E.*, Jardine, L.*, Gottgens, B., Teichmann, S.A., Haniffa, M., (2020) Prenatal development of human immunity. Science 368, 600–603.
Efremova, M.*, Vento-Tormo, R.*, Park, J.-E.*, Teichmann, S. A. & James, K. R. (2020) Immunology in the Era of Single-Cell Technologies. Annu. Rev. Immunol. 38, 727-757
Polański, K.*, Young, M.D.*, Miao, Z., Meyer, K.B., Teichmann, S.A.# and Park, J.-E.#, (2020) BBKNN: Fast Batch Alignment of Single Cell Transcriptomes. Bioinformatics. 36, 964-965
Son, A.*, Park, J.-E.*, Kim, V.N., (2018) PARN and TOE1 Constitute a 3’ End Maturation Module for Nuclear Non-coding RNAs. Cell Reports. 23, 888–898.
Park, J.-E.*, Yi, H.*, Kim, Y.*, Chang, H., Kim, V.N., (2016) Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. Molecular Cell. 62, 462–471.
Park, J.-E.*, Heo, I.*, Tian, Y., Simanshu, D.K., Chang, H., Jee, D., Patel, D.J., Kim, V.N., (2011) Dicer recognizes the 5’ end of RNA for efficient and accurate processing. Nature 475, 201–205.
all publications
[2024]
Kang, J.*, Lee, J.-H.*, …, Lee, S.-H.#, Choi, J. K.#, Park J.-E# (2024). Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types. Nature Communications, 15:4067
Kim, S.*, Leem, G.*, ..., Kang C. M.#, Bang. S.#, Park J.-E# (2024). Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis. Genome Medicine, 16:20.
Kim, H., Chang, W., Chae, S.J., Park, J.-E., Seo, M. and Kim, J.K. (2024). scLENS: data-driven signal detection for unbiased scRNA-seq data analysis. Nature Communications, 15, 3575
[2023]
Kwon, J.*, Kang, J.*, ..., An, H. J.#, Lee, H.-O.#, Park J.-E.#, Choi, J. K.# (2023). Single-cell mapping of combinatorial target antigens for CAR switches using logic gates. Nature Biotechnology, 1-13.
Kang, J.,* Kim, M.*, Yoon, D. Y.*, Kim, W. S., Choi, S. J., Kwon, Y. N., ..., Park, M., Lee, J. S., Park J.-E.#, & Kim, S. M.# (2023). AXL+ SIGLEC6+ dendritic cells in cerebrospinal fluid and brain tissues of patients with autoimmune inflammatory demyelinating disease of CNS. Clinical Immunology, 109686.
Kim, H. J., Park, J.-E., Shin, W., Seo, D., Kim, S., Kim, H., ... & Lee, E. J. (2023). Distinct features of B cell receptors in neuromyelitis optica spectrum disorder among CNS inflammatory demyelinating diseases. Journal of Neuroinflammation, 20(1), 225.
Goh, I., Botting, R. A., Rose, A., Webb, S., ..., Park J.-E., ... & Haniffa, M. (2023). Yolk sac cell atlas reveals multiorgan functions during human early development. Science, 381(6659), eadd7564.
Park, D., Lee, D., ..., Park J.-E., Koh, Y., ..., Chung, C. Cryobiopsy: A Breakthrough Strategy for Clinical Utilization of Lung Cancer Organoids. Cells. 2023; 12(14):1854.
Seok, J., Cho, S. D., Lee, J., Choi, Y., Kim, S. Y., Lee, S. M., ..., Park J.-E., ... & Park, S. H. (2023). A virtual memory CD8+ T cell-originated subset causes alopecia areata through innate-like cytotoxicity. Nature Immunology, 1-10.
[2022]
Kim, B., Koh, Y., Do, H., Ju, Y., Choi, J. B., Cho, G., ..., Park J.-E.#, Han, Y. M#. (2022). Aberrant Cortical Layer Development of Brain Organoids Derived from Noonan Syndrome-iPSCs. International Journal of Molecular Sciences, 23(22), 13861.
Yoon, Y. J., Kim, D., Tak, K. Y., ... Park J.-E, Lim, J. Y. (2022). Salivary gland organoid culture maintains distinct glandular properties of murine and human major salivary glands. Nature communications, 13(1), 3291.
Yin, G. N., Kim, D. K., Kang, J. I., Koh Y., Park J.-E., ... & Kim, H. M. (2022). Latrophilin-2 is a novel receptor of LRG1 that rescues vascular and neurological abnormalities and restores diabetic erectile function. Experimental & Molecular Medicine, 54(5), 626-638.
Alsinet, C., Primo, M. N., Lorenzi, V., Bello, E., Kelava, I., Jones, C. P., ..., Park J.-E, ..., & Vento-Tormo, R. (2022). Robust temporal map of human in vitro myelopoiesis using single-cell genomics. Nature Communications, 13(1), 2885.
Domínguez Conde, C., Xu, C., Jarvis, L. B., ..., Park J.-E. , ... & Teichmann, S. A. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376(6594), eabl5197.
Suo, C., Dann, E., Goh, I., Jardine, L., Kleshchevnikov, V., Park, J.-E., ... & Teichmann, S. A. (2022). Mapping the developing human immune system across organs. Science, 376(6597), eabo0510.
[2021]
Lee S.*, Kim J.*, Park J.-E#. Single-Cell Toolkits Opening a New Era for Cell Engineering. Mol Cells. (2021);44(3):127-135.
Reynolds G, Vegh P, Fletcher J, ..., Park J.-E, ... , Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science. 2021 Jan 22;371(6527).
Jain, M. S., Polanski, K., Conde, C. D., Chen, X., Park, J., Mamanova, L., ..., Park J.-E, …, Teichmann SA (2021). MultiMAP: dimensionality reduction and integration of multimodal data. Genome biology, 22(1), 1-26.
Garcia-Alonso, L., Handfield, L. F., Roberts, K.,…, Park J.-E, … & Vento-Tormo, R. (2021). Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nature genetics, 53(12), 1698-1711
[2020]
Park, J.-E.*, Botting, R.A., Domínguez-Conde, C., ... , Taghon, T., Haniffa, M., Teichmann, S.A., 2020, A cell atlas of human thymic development defines T cell repertoire formation. Science 367, eaay3224
Park, J.-E.*, Jardine, L.*, Gottgens, B., Teichmann, S.A., Haniffa, M., 2020. Prenatal development of human immunity. Science 368, 600–603.
Efremova, M.*, Vento-Tormo, R.*, Park, J.-E.*, Teichmann, S. A. & James, K. R. Immunology in the Era of Single-Cell Technologies. 2020, Annu. Rev. Immunol. 38, 727-757
Lavaert, M., Liang, K.L., Vandamme, N., Park, J.-E., Roels, J., Kowalczyk, M.S., Li, B., Ashenberg, O., Tabaka, M., Dionne, D., Tickle, T.L., Slyper, M., Rozenblatt-Rosen, O., Vandekerckhove, B., Leclercq, G., Regev, A., Van Vlierberghe, P., Guilliams, M., Teichmann, S.A., Saeys, Y., Taghon, T., 2020. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity.
Choi, J., Park, J.-E., Tsagkogeorga, G., Yanagita, M., Koo, B.-K., Han, N., Lee, J.-H., 2020, Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration, Cell Stem Cell 27, 366-382.e7
Fernandes, H. J. R., Patikas, N., Foskolou, S., Field, S. F., Park, J.-E., Byrne, M. L., Bassett, A. R., & Metzakopian, E. (2020). Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses. Cell Reports, 33(2), 108263.
Campinoti, S., Gjinovci, A., Ragazzini, R., Zanieri, L., ..., Park, J.-E., …, Bonfanti, P. (2020). Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds. Nature Communications, 11(1), 6372.
Polański, K.*, Young, M.D.*, Miao, Z., Meyer, K.B., Teichmann, S.A.# and Park, J.-E.#, 2020. BBKNN: Fast Batch Alignment of Single Cell Transcriptomes. Bioinformatics. 36, 964-965
[2019]
Popescu, D.-M.*, Botting, R.A.*, Stephenson, E.*, ..., Park, J.-E., ..., Göttgens, B., Laurenti, E., Behjati, S., Teichmann, S.A., Haniffa, M., 2019. Decoding the development of the blood and immune systems during human fetal liver haematopoiesis. Nature 574, 365–371
[2018]
Son, A.*, Park, J.-E.*, Kim, V.N., 2018. PARN and TOE1 Constitute a 3’ End Maturation Module for Nuclear Non-coding RNAs. Cell Reports. 23, 888–898.
Park, J.-E.*, Polanski, K.*, Meyer, K., Teichmann, S.A., 2018. Fast batch alignment of single cell transcriptomes unifies multiple mouse cell atlases into an integrated landscape. bioRxiv. 397042. (Published in Bioinformatics, 2020, Polanski et. al.)
Vento-Tormo, R.*, Efremova, M.*, ..., Park, J.-E., ... , Haniffa, M., Moffett, A., Teichmann, S.A., 2018. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature 563, 347–353.
Pramanik, J.*, Chen, X., Kar, G., Henriksson, J., Gomes, T., Park, J.-E., Natarajan, K., Meyer, K.B., Miao, Z., McKenzie, A.N.J., Mahata, B., Teichmann, S.A., 2018. Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. Genome Medicine 10, 76.
Hagai, T.*, Chen, X., ..., Park, J.-E., ..., Haniffa, M., Nourmohammad, A., Lässig, M., Teichmann, S.A., 2018. Gene expression variability across cells and species shapes innate immunity. Nature 563, 197–202.
[2016]
Park, J.-E.*, Yi, H.*, Kim, Y.*, Chang, H., Kim, V.N., 2016. Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. Molecular Cell. 62, 462–471.
Sim, S.-E., Lim, C.-S., Kim, J.-I., Seo, D., Chun, H., Yu, N.-K., Lee, J., Kang, S.J., Ko, H.-G., Choi, J.-H., Kim, T., Jang, E.-H., Han, J., Bak, M.S., Park, J.-E., Jang, D.-J., Baek, D., Lee, Y.-S., Kaang, B.-K., 2016. The Brain-Enriched MicroRNA miR-9-3p Regulates Synaptic Plasticity and Memory. J. Neurosci. 36, 8641–8652.
[2015]
Boo, K.*, Bhin, J.*, Jeon, Y., Kim, J., Shin, H.-J.R., Park, J.-E., Kim, K., Kim, C.R., Jang, H., Kim, I.-H., Kim, V.N., Hwang, D., Lee, H., Baek, S.H., 2015. Pontin functions as an essential coactivator for Oct4-dependent lincRNA expression in mouse embryonic stem cells. Nature communications 6, 6810.
[2014]
Tian, Y.*, Simanshu, D.K.*, Ma, J.-B., Park, J.-E., Heo, I., Narry Kim, V., Patel, D.J., 2014. A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer. Molecular Cell. 53, 606-616.
Kim, Y.*, Lee, J.H., Park, J.-E., Cho, J., Yi, H., Kim, V.N., 2014. PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator. Genes Dev. 28, 1310–1322.
[2012]
Heo, I.*, Ha, M.*, Lim, J., Yoon, M.-J., Park, J.-E., Kwon, S.C., Chang, H., Kim, V.N., 2012. Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 151, 521–532.
[2011]
Park, J.-E.*, Heo, I.*, Tian, Y., Simanshu, D.K., Chang, H., Jee, D., Patel, D.J., Kim, V.N., 2011. Dicer recognizes the 5’ end of RNA for efficient and accurate processing. Nature 475, 201–205.