{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T10:18:04Z","timestamp":1792750684377,"version":"4.5.0"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"7904","license":[{"start":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T00:00:00Z","timestamp":1648598400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T00:00:00Z","timestamp":1648598400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2022,4,7]]},"DOI":"10.1038\/s41586-022-04541-3","type":"journal-article","created":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T12:39:06Z","timestamp":1648643946000},"page":"111-119","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":358,"title":["Human distal lung maps and lineage hierarchies reveal a bipotent progenitor"],"prefix":"10.1038","volume":"604","author":[{"given":"Preetish","family":"Kadur Lakshminarasimha Murthy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8532-7680","authenticated-orcid":false,"given":"Vishwaraj","family":"Sontake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandra","family":"Tata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshihiko","family":"Kobayashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Macadlo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9341-2730","authenticated-orcid":false,"given":"Kenichi","family":"Okuda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2385-6712","authenticated-orcid":false,"given":"Ansley S.","family":"Conchola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoko","family":"Nakano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Gregory","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa A.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7869-3992","authenticated-orcid":false,"given":"Jason R.","family":"Spence","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2389-9277","authenticated-orcid":false,"given":"John F.","family":"Engelhardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard C.","family":"Boucher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason R.","family":"Rock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott H.","family":"Randell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4837-0337","authenticated-orcid":false,"given":"Purushothama Rao","family":"Tata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,3,30]]},"reference":[{"key":"4541_CR1","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1016\/S2213-2600(19)30356-X","volume":"8","author":"SE Verleden","year":"2020","unstructured":"Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573\u2013584 (2020).","journal-title":"Lancet Respir. Med."},{"key":"4541_CR2","first-page":"433","volume":"10","author":"JC Hogg","year":"1967","unstructured":"Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen Emphysema Conf. https:\/\/europepmc.org\/article\/med\/5610792\u00a010, 433\u2013441 (1967).","journal-title":"Aspen Emphysema Conf."},{"key":"4541_CR3","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1164\/rccm.201602-0278OC","volume":"195","author":"N Tanabe","year":"2017","unstructured":"Tanabe, N. et al. Micro-computed tomography comparison of preterminal bronchioles in centrilobular and panlobular emphysema. Am. J. Respir. Crit. Care Med. 195, 630\u2013638 (2017).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"4541_CR4","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1126\/science.137.3530.577","volume":"137","author":"ER Weibel","year":"1962","unstructured":"Weibel, E. R. & Gomez, D. M. Architecture of the human lung. Use of quantitative methods establishes fundamental relations between size and number of lung structures. Science 137, 577\u2013585 (1962).","journal-title":"Science"},{"key":"4541_CR5","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1038\/s41556-020-0542-8","volume":"22","author":"Y Kobayashi","year":"2020","unstructured":"Kobayashi, Y. et al. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat. Cell Biol. 22, 934\u2013946 (2020).","journal-title":"Nat. Cell Biol."},{"key":"4541_CR6","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17358-3","volume":"11","author":"M Strunz","year":"2020","unstructured":"Strunz, M. et al. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis. Nat. Commun. 11, 3559 (2020).","journal-title":"Nat. Commun."},{"key":"4541_CR7","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1016\/j.stem.2020.06.020","volume":"27","author":"J Choi","year":"2020","unstructured":"Choi, J. et al. Inflammatory signals induce AT2 cell-derived damage-associated transient progenitors that mediate alveolar regeneration. Cell Stem Cell 27, 366\u2013382 (2020).","journal-title":"Cell Stem Cell"},{"key":"4541_CR8","doi-asserted-by":"publisher","first-page":"e27041","DOI":"10.7554\/eLife.27041","volume":"6","author":"A Regev","year":"2017","unstructured":"Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).","journal-title":"eLife"},{"key":"4541_CR9","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202\u20131214 (2015).","journal-title":"Cell"},{"key":"4541_CR10","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","volume":"161","author":"AM Klein","year":"2015","unstructured":"Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187\u20131201 (2015).","journal-title":"Cell"},{"key":"4541_CR11","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1038\/s41586-020-2922-4","volume":"587","author":"KJ Travaglini","year":"2020","unstructured":"Travaglini, K. J. et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 587, 619\u2013625 (2020).","journal-title":"Nature"},{"key":"4541_CR12","doi-asserted-by":"publisher","first-page":"eaba1972","DOI":"10.1126\/sciadv.aba1972","volume":"6","author":"AC Habermann","year":"2020","unstructured":"Habermann, A. C. et al. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci. Adv. 6, eaba1972 (2020).","journal-title":"Sci. Adv."},{"key":"4541_CR13","doi-asserted-by":"publisher","first-page":"eaba1983","DOI":"10.1126\/sciadv.aba1983","volume":"6","author":"TS Adams","year":"2020","unstructured":"Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci. Adv. 6, eaba1983 (2020).","journal-title":"Sci. Adv."},{"key":"4541_CR14","doi-asserted-by":"publisher","first-page":"1540","DOI":"10.1164\/rccm.201904-0792OC","volume":"202","author":"G Carraro","year":"2020","unstructured":"Carraro, G. et al. Single-cell reconstruction of human basal cell diversity in normal and idiopathic pulmonary fibrosis lungs. Am. J. Respir. Crit. Care Med. 202, 1540\u20131550 (2020).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"4541_CR15","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1164\/rccm.202008-3198OC","volume":"203","author":"K Okuda","year":"2021","unstructured":"Okuda, K. et al. Secretory cells dominate airway CFTR expression and function in human airway superficial epithelia. Am. J. Respir. Crit. Care Med. 203, 1275\u20131289 (2021).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"4541_CR16","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/s41586-018-0394-6","volume":"560","author":"LW Plasschaert","year":"2018","unstructured":"Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377\u2013381 (2018).","journal-title":"Nature"},{"key":"4541_CR17","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","volume":"560","author":"DT Montoro","year":"2018","unstructured":"Montoro, D. T. et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 560, 319\u2013324 (2018).","journal-title":"Nature"},{"key":"4541_CR18","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1038\/s41591-019-0468-5","volume":"25","author":"FA Vieira Braga","year":"2019","unstructured":"Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153\u20131163 (2019).","journal-title":"Nat. Med."},{"key":"4541_CR19","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1056\/NEJM196806202782501","volume":"278","author":"JC Hogg","year":"1968","unstructured":"Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. Site and nature of airway obstruction in chronic obstructive lung disease. N. Engl. J. Med. 278, 1355\u20131360 (1968).","journal-title":"N. Engl. J. Med."},{"key":"4541_CR20","doi-asserted-by":"publisher","first-page":"2645","DOI":"10.1056\/NEJMoa032158","volume":"350","author":"JC Hogg","year":"2004","unstructured":"Hogg, J. C. et al. The nature of small-airway obstruction in chronic obstructive pulmonary disease. N. Engl. J. Med. 350, 2645\u20132653 (2004).","journal-title":"N. Engl. J. Med."},{"key":"4541_CR21","doi-asserted-by":"publisher","first-page":"1277","DOI":"10.1056\/NEJM197806082982303","volume":"298","author":"M Cosio","year":"1978","unstructured":"Cosio, M. et al. The relations between structural changes in small airways and pulmonary-function tests. N. Engl. J. Med. 298, 1277\u20131281 (1978).","journal-title":"N. Engl. J. Med."},{"key":"4541_CR22","doi-asserted-by":"publisher","first-page":"L405","DOI":"10.1152\/ajplung.00169.2013","volume":"305","author":"ER Weibel","year":"2013","unstructured":"Weibel, E. R. A retrospective of lung morphometry: from 1963 to present. Am. J. Physiol. Lung Cell. Mol. Physiol. 305, L405\u2013L408 (2013).","journal-title":"Am. J. Physiol. Lung Cell. Mol. Physiol."},{"key":"4541_CR23","doi-asserted-by":"publisher","first-page":"1636","DOI":"10.1164\/rccm.201911-2199OC","volume":"202","author":"M Deprez","year":"2020","unstructured":"Deprez, M. et al. A single-cell atlas of the human healthy airways. Am. J. Respir. Crit. Care Med. 202, 1636\u20131645 (2020).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"4541_CR24","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1038\/s41586-021-03549-5","volume":"593","author":"MB Buechler","year":"2021","unstructured":"Buechler, M. B. et al. Cross-tissue organization of the fibroblast lineage. Nature 593, 575\u2013579 (2021).","journal-title":"Nature"},{"key":"4541_CR25","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1007\/s00441-016-2545-0","volume":"367","author":"JC Schittny","year":"2017","unstructured":"Schittny, J. C. Development of the lung. Cell Tissue Res. 367, 427\u2013444 (2017).","journal-title":"Cell Tissue Res."},{"key":"4541_CR26","doi-asserted-by":"publisher","DOI":"10.1186\/s13326-019-0209-1","volume":"10","author":"H Pan","year":"2019","unstructured":"Pan, H., Deutsch, G. H. & Wert, S. E. Comprehensive anatomic ontologies for lung development: a comparison of alveolar formation and maturation within mouse and human lung. J. Biomed. Semant. 10, 18 (2019).","journal-title":"J. Biomed. Semant."},{"key":"4541_CR27","doi-asserted-by":"publisher","first-page":"S174","DOI":"10.1164\/ajrccm.157.5.rsaa-1","volume":"157","author":"PK Jeffrey","year":"1998","unstructured":"Jeffrey, P. K. The development of large and small airways. Am. J. Respir. Crit. Care Med. 157, S174\u2013S180 (1998).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"4541_CR28","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.devcel.2020.01.033","volume":"53","author":"AJ Miller","year":"2020","unstructured":"Miller, A. J. et al. In vitro and in vivo development of the human airway at single-cell resolution. Dev. Cell 53, 117\u2013128 (2020).","journal-title":"Dev. Cell"},{"key":"4541_CR29","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","volume":"560","author":"G La Manno","year":"2018","unstructured":"La Manno, G. et al. RNA velocity of single cells. Nature 560, 494\u2013498 (2018).","journal-title":"Nature"},{"key":"4541_CR30","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4772-0","volume":"19","author":"K Street","year":"2018","unstructured":"Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).","journal-title":"BMC Genomics"},{"key":"4541_CR31","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1038\/s41587-020-0591-3","volume":"38","author":"V Bergen","year":"2020","unstructured":"Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408\u20131414 (2020).","journal-title":"Nat. Biotechnol."},{"key":"4541_CR32","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","volume":"566","author":"J Cao","year":"2019","unstructured":"Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496\u2013502 (2019).","journal-title":"Nature"},{"key":"4541_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1663-x","volume":"20","author":"FA Wolf","year":"2019","unstructured":"Wolf, F. A. et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 59 (2019).","journal-title":"Genome Biol."},{"key":"4541_CR34","doi-asserted-by":"publisher","first-page":"2077","DOI":"10.1093\/bioinformatics\/bty058","volume":"34","author":"S Jin","year":"2018","unstructured":"Jin, S., MacLean, A. L., Peng, T. & Nie, Q. scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. Bioinformatics 34, 2077\u20132086 (2018).","journal-title":"Bioinformatics"},{"key":"4541_CR35","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25548-w","volume":"12","author":"P Zhou","year":"2021","unstructured":"Zhou, P., Wang, S., Li, T. & Nie, Q. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics. Nat. Commun. 12, 5609 (2021).","journal-title":"Nat. Commun."},{"key":"4541_CR36","doi-asserted-by":"publisher","first-page":"890","DOI":"10.1016\/j.stem.2020.10.005","volume":"27","author":"H Katsura","year":"2020","unstructured":"Katsura, H. et al. Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2-mediated interferon responses and pneumocyte dysfunction. Cell Stem Cell 27, 890\u2013904 (2020).","journal-title":"Cell Stem Cell"},{"key":"4541_CR37","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1136\/thx.2010.151555","volume":"66","author":"L Plantier","year":"2011","unstructured":"Plantier, L. et al. Ectopic respiratory epithelial cell differentiation in bronchiolised distal airspaces in idiopathic pulmonary fibrosis. Thorax 66, 651\u2013657 (2011).","journal-title":"Thorax"},{"key":"4541_CR38","doi-asserted-by":"crossref","unstructured":"Weibel, E. R. Morphometry of the Human Lung (Springer-Verlag, 1963).","DOI":"10.1007\/978-3-642-87553-3"},{"key":"4541_CR39","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1002\/aja.1001420108","volume":"142","author":"WL Castleman","year":"1975","unstructured":"Castleman, W. L., Dungworth, D. L. & Tyler, W. S. Intrapulmonary airway morphology in three species of monkeys: a correlated scanning and transmission electron microscopic study. Am. J. Anat. 142, 107\u2013121 (1975).","journal-title":"Am. J. Anat."},{"key":"4541_CR40","first-page":"457","volume":"108","author":"KE Pinkerton","year":"2000","unstructured":"Pinkerton, K. E. & Joad, J. P. The mammalian respiratory system and critical windows of exposure for children\u2019s health. Environ. Health Perspect. 108, 457\u2013462 (2000). Suppl 3.","journal-title":"Environ. Health Perspect."},{"key":"4541_CR41","first-page":"891","volume":"3","author":"DM Hyde","year":"1979","unstructured":"Hyde, D. M., Samuelson, D. A., Blakeney, W. H. & Kosch, P. C. A correlative light microscopy, transmission and scanning electron microscopy study of the ferret lung. Scan. Electron Microsc. 3, 891\u2013898 (1979).","journal-title":"Scan. Electron Microsc."},{"key":"4541_CR42","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1093\/ilar\/ilx030","volume":"58","author":"LA Miller","year":"2017","unstructured":"Miller, L. A., Royer, C. M., Pinkerton, K. E. & Schelegle, E. S. Nonhuman primate models of respiratory disease: past, present, and future. ILAR J. 58, 269\u2013280 (2017).","journal-title":"ILAR J."},{"key":"4541_CR43","doi-asserted-by":"crossref","unstructured":"Rogers, C. S. et al. The porcine lung as a potential model for cystic fibrosis. Am. J. Physiol. Lung Cell Mol. Physiol. 295, L240\u2013L263 (2008).","DOI":"10.1152\/ajplung.90203.2008"},{"key":"4541_CR44","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1002\/aja.1001840104","volume":"184","author":"CG Plopper","year":"1989","unstructured":"Plopper, C. G., Heidsiek, J. G., Weir, A. J., George, J. A. & Hyde, D. M. Tracheobronchial epithelium in the adult rhesus monkey: a quantitative histochemical and ultrastructural study. Am. J. Anat. 184, 31\u201340 (1989).","journal-title":"Am. J. Anat."},{"key":"4541_CR45","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/s41422-020-00412-6","volume":"31","author":"S Ma","year":"2021","unstructured":"Ma, S. et al. Single-cell transcriptomic atlas of primate cardiopulmonary aging. Cell Res. 31, 415\u2013432 (2021).","journal-title":"Cell Res."},{"key":"4541_CR46","doi-asserted-by":"publisher","first-page":"1941","DOI":"10.1056\/NEJMra1813799","volume":"380","author":"RC Boucher","year":"2019","unstructured":"Boucher, R. C. Muco-obstructive lung diseases. N. Engl. J. Med. 380, 1941\u20131953 (2019).","journal-title":"N. Engl. J. Med."},{"key":"4541_CR47","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1053\/j.semperi.2013.01.010","volume":"37","author":"A Bhandari","year":"2013","unstructured":"Bhandari, A. & McGrath-Morrow, S. Long-term pulmonary outcomes of patients with bronchopulmonary dysplasia. Semin. Perinatol. 37, 132\u2013137 (2013).","journal-title":"Semin. Perinatol."},{"key":"4541_CR48","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-41777-y","volume":"9","author":"Y Jiang","year":"2019","unstructured":"Jiang, Y. et al. Alteration of cystic airway mesenchyme in congenital pulmonary airway malformation. Sci. Rep. 9, 5296 (2019).","journal-title":"Sci. Rep."},{"key":"4541_CR49","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1016\/j.cell.2005.03.032","volume":"121","author":"CFB Kim","year":"2005","unstructured":"Kim, C. F. B. et al. Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell 121, 823\u2013835 (2005).","journal-title":"Cell"},{"key":"4541_CR50","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/S0002-9440(10)64169-7","volume":"161","author":"A Giangreco","year":"2002","unstructured":"Giangreco, A., Reynolds, S. D. & Stripp, B. R. Terminal bronchioles harbor a unique airway stem cell population that localizes to the bronchoalveolar duct junction. Am. J. Pathol. 161, 173\u2013182 (2002).","journal-title":"Am. J. Pathol."},{"key":"4541_CR51","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nature09793","volume":"470","author":"SE Williams","year":"2011","unstructured":"Williams, S. E., Beronja, S., Pasolli, H. A. & Fuchs, E. Asymmetric cell divisions promote Notch-dependent epidermal differentiation. Nature 470, 353\u2013358 (2011).","journal-title":"Nature"},{"key":"4541_CR52","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.cell.2011.10.001","volume":"147","author":"PA Kumar","year":"2011","unstructured":"Kumar, P. A. et al. Distal airway stem cells yield alveoli in vitro and during lung regeneration following H1N1 influenza infection. Cell\u00a0147, 525\u2013538 (2011).","journal-title":"Cell"},{"key":"4541_CR53","doi-asserted-by":"publisher","first-page":"e30510","DOI":"10.7554\/eLife.30510","volume":"7","author":"M Nagendran","year":"2018","unstructured":"Nagendran, M., Riordan, D. P., Harbury, P. B. & Desai, T. J. Automated cell-type classification in intact tissues by single-cell molecular profiling. eLife 7, e30510 (2018).","journal-title":"eLife"},{"key":"4541_CR54","doi-asserted-by":"publisher","first-page":"800564","DOI":"10.1183\/13993003.00564-2018","volume":"52","author":"G Kwapiszewska","year":"2018","unstructured":"Kwapiszewska, G. et al. Transcriptome profiling reveals the complexity of pirfenidone effects in idiopathic pulmonary fibrosis. Eur. Respir. J. 52, 800564 (2018).","journal-title":"Eur. Respir. J."},{"key":"4541_CR55","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888\u20131902 (2019).","journal-title":"Cell"},{"key":"4541_CR56","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa151","volume":"9","author":"MD Young","year":"2020","unstructured":"Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience 9, giaa151 (2020).","journal-title":"Gigascience"},{"key":"4541_CR57","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1874-1","volume":"20","author":"C Hafemeister","year":"2019","unstructured":"Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).","journal-title":"Genome Biol."},{"key":"4541_CR58","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-128","volume":"14","author":"EY Chen","year":"2013","unstructured":"Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).","journal-title":"BMC Bioinformatics"},{"key":"4541_CR59","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1016\/j.cell.2018.01.029","volume":"172","author":"SA Lambert","year":"2018","unstructured":"Lambert, S. A. et al. The human transcription factors. Cell 172, 650\u2013665 (2018).","journal-title":"Cell"},{"key":"4541_CR60","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1038\/nmeth.4463","volume":"14","author":"S Aibar","year":"2017","unstructured":"Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083\u20131086 (2017).","journal-title":"Nat. Methods"},{"key":"4541_CR61","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21246-9","volume":"12","author":"S Jin","year":"2021","unstructured":"Jin, S. et al. Inference and analysis of cell\u2013cell communication using CellChat. Nat. Commun. 12, 1088 (2021).","journal-title":"Nat. Commun."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04541-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04541-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04541-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T08:10:56Z","timestamp":1649751056000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04541-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3,30]]},"references-count":61,"journal-issue":{"issue":"7904","published-print":{"date-parts":[[2022,4,7]]}},"alternative-id":["4541"],"URL":"https:\/\/doi.org\/10.1038\/s41586-022-04541-3","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,3,30]]},"assertion":[{"value":"21 June 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 February 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 March 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"P.R.T. serves as a consultant for Surrozen, Cellarity and Celldom on work not related to the contents of this manuscript. J.R.R. is an employee of Genentech. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}