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.

[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.