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@ARTICLE{Sikkema:258918,
      author       = {Sikkema, Lisa and Ramírez-Suástegui, Ciro and Strobl,
                      Daniel C and Gillett, Tessa E and Zappia, Luke and
                      Madissoon, Elo and Markov, Nikolay S and Zaragosi,
                      Laure-Emmanuelle and Ji, Yuge and Ansari, Meshal and Arguel,
                      Marie-Jeanne and Apperloo, Leonie and Banchero, Martin and
                      Bécavin, Christophe and Berg, Marijn and Chichelnitskiy,
                      Evgeny and Chung, Mei-I and Collin, Antoine and Gay, Aurore
                      C A and Gote-Schniering, Janine and Hooshiar Kashani,
                      Baharak and Inecik, Kemal and Jain, Manu and Kapellos,
                      Theodore S and Kole, Tessa M and Leroy, Sylvie and Mayr,
                      Christoph H and Oliver, Amanda J and von Papen, Michael and
                      Peter, Lance and Taylor, Chase J and Walzthoeni, Thomas and
                      Xu, Chuan and Bui, Linh T and De Donno, Carlo and Dony,
                      Leander and Faiz, Alen and Guo, Minzhe and Gutierrez, Austin
                      J and Heumos, Lukas and Huang, Ni and Ibarra, Ignacio L and
                      Jackson, Nathan D and Kadur Lakshminarasimha Murthy,
                      Preetish and Lotfollahi, Mohammad and Tabib, Tracy and
                      Talavera-López, Carlos and Travaglini, Kyle J and
                      Wilbrey-Clark, Anna and Worlock, Kaylee B and Yoshida,
                      Masahiro and van den Berge, Maarten and Bossé, Yohan and
                      Desai, Tushar J and Eickelberg, Oliver and Kaminski, Naftali
                      and Krasnow, Mark A and Lafyatis, Robert and Nikolic, Marko
                      Z and Powell, Joseph E and Rajagopal, Jayaraj and Rojas,
                      Mauricio and Rozenblatt-Rosen, Orit and Seibold, Max A and
                      Sheppard, Dean and Shepherd, Douglas P and Sin, Don D and
                      Timens, Wim and Tsankov, Alexander M and Whitsett, Jeffrey
                      and Xu, Yan and Banovich, Nicholas E and Barbry, Pascal and
                      Duong, Thu Elizabeth and Falk, Christine S and Meyer,
                      Kerstin B and Kropski, Jonathan A and Pe'er, Dana and
                      Schiller, Herbert B and Tata, Purushothama Rao and Schultze,
                      Joachim L and Teichmann, Sara A and Misharin, Alexander V
                      and Nawijn, Martijn C and Luecken, Malte D and Theis, Fabian
                      J},
      collaboration = {Consortium, Lung Biological Network},
      othercontributors = {Chen, Yuexin and Hagood, James S and Agami, Ahmed and
                          Horvath, Peter and Lundeberg, Joakim and Marquette,
                          Charles-Hugo and Pryhuber, Gloria and Samakovlis, Chistos
                          and Sun, Xin and Ware, Lorraine B and Zhang, Kun},
      title        = {{A}n integrated cell atlas of the lung in health and
                      disease.},
      journal      = {Nature medicine},
      volume       = {29},
      number       = {6},
      issn         = {1078-8956},
      address      = {New York, NY},
      publisher    = {Nature America Inc.},
      reportid     = {DZNE-2023-00690},
      pages        = {1563 - 1577},
      year         = {2023},
      abstract     = {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.},
      keywords     = {Humans / COVID-19 / Lung / Pulmonary Fibrosis / Lung
                      Neoplasms: genetics / Macrophages},
      cin          = {Schultze - PRECISE / $R\&D$ PRECISE},
      ddc          = {610},
      cid          = {I:(DE-2719)1013031 / I:(DE-2719)5000031},
      pnm          = {354 - Disease Prevention and Healthy Aging (POF4-354) / 352
                      - Disease Mechanisms (POF4-352)},
      pid          = {G:(DE-HGF)POF4-354 / G:(DE-HGF)POF4-352},
      experiment   = {EXP:(DE-2719)PRECISE-20190321},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37291214},
      pmc          = {pmc:PMC10287567},
      doi          = {10.1038/s41591-023-02327-2},
      url          = {https://pub.dzne.de/record/258918},
}