The DOI matches its Crossref record; 138 of the 138 references it cites were found in a registry or an index.
An integrated cell atlas of the lung in health and disease
Open accessAbstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1 + profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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1 retracted
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Self-citationIntegrated analysis of multimodal single-cell data
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Fast, sensitive and accurate integration of single-cell data with Harmony
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Hill, W., Lim, E. L., Weeden, C. E., Lee, C., Augustine, M., Chen, K., Kuan, F.-C., Marongiu, F., Evans, E. J., Moore, D. A., et al. (2023) · Nature · doi:10.1038/s41586-023-05874-3 · Cited by 808
Self-citationProgram, C. C. S., Abdulla, S., Aevermann, B., Assis, P., Badajoz, S., Bell, S. M., Bezzi, E., Cakir, B., Chaffer, J., Chambers, S., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1142 · Cited by 399
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Persad, S., Choo, Z.-N., Dien, C., Sohail, N., Masilionis, I., Chaligné, R., Nawy, T., Brown, C. C., Sharma, R., Pe’er, I., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01716-9 · Cited by 222
Self-citationA spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Madissoon, E., Oliver, A. J., Kleshchevnikov, V., Wilbrey-Clark, A., Polanski, K., Richoz, N., Ribeiro Orsi, A., Mamanova, L., Bolt, L., Elmentaite, R., et al. (2023) · Nature Genetics · doi:10.1038/s41588-022-01243-4 · Cited by 219
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Metadata
- Authors
- Sikkema, L., Ramírez-Suástegui, C., Strobl, D. C., Gillett, T. E., Zappia, L., Madissoon, E., Markov, N. S., Zaragosi, L.-E., Ji, Y., Ansari, M., Arguel, M.-J., Apperloo, L., Banchero, M., Bécavin, C., Berg, M., Chichelnitskiy, E., Chung, M.-I., Collin, A., Gay, A. C. A., Gote-Schniering, J., Hooshiar Kashani, B., Inecik, K., Jain, M., Kapellos, T. S., Kole, T. M., Leroy, S., Mayr, C. H., Oliver, A. J., von Papen, M., Peter, L., Taylor, C. J., Walzthoeni, T., Xu, C., Bui, L. T., De Donno, C., Dony, L., Faiz, A., Guo, M., Gutierrez, A. J., Heumos, L., Huang, N., Ibarra, I. L., Jackson, N. D., Kadur Lakshminarasimha Murthy, P., Lotfollahi, M., Tabib, T., Talavera-López, C., Travaglini, K. J., Wilbrey-Clark, A., Worlock, K. B., Yoshida, M., Lung Biological Network Consortium, Chen, Y., Hagood, J. S., Agami, A., Horvath, P., Lundeberg, J., Marquette, C.-H., Pryhuber, G., Samakovlis, C., Sun, X., Ware, L. B., Zhang, K., van den Berge, M., Bossé, Y., Desai, T. J., Eickelberg, O., Kaminski, N., Krasnow, M. A., Lafyatis, R., Nikolic, M. Z., Powell, J. E., Rajagopal, J., Rojas, M., Rozenblatt-Rosen, O., Seibold, M. A., Sheppard, D., Shepherd, D. P., Sin, D. D., Timens, W., Tsankov, A. M., Whitsett, J., Xu, Y., Banovich, N. E., Barbry, P., Duong, T. E., Falk, C. S., Meyer, K. B., Kropski, J. A., Pe’er, D., Schiller, H. B., Tata, P. R., Schultze, J. L., Teichmann, S. A., Misharin, A. V., Nawijn, M. C., Luecken, M. D., & Theis, F. J.
- Venue
- Nature Medicine
- Published
- 2023-06
- Volume
- 29
- Issue
- 6
- Pages
- 1563-1577
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- OpenAlex
- W4379879135
- Cited by
- 854
- References
- 138
- FWCI
- 62.46
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Sikkema, L., Ramírez-Suástegui, C., Strobl, D. C., Gillett, T. E., Zappia, L., Madissoon, E., Markov, N. S., Zaragosi, L.-E., Ji, Y., Ansari, M., Arguel, M.-J., Apperloo, L., Banchero, M., Bécavin, C., Berg, M., Chichelnitskiy, E., Chung, M.-I., Collin, A., Gay, A. C. A., . . . Theis, F. J. (2023). An integrated cell atlas of the lung in health and disease. Nature Medicine. https://doi.org/10.1038/s41591-023-02327-2
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