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An integrated cell ...
An integrated cell atlas of the lung in health and disease
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- Sikkema, Lisa (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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- Ramírez-Suástegui, Ciro (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA, La Jolla
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- Strobl, Daniel C. (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
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- Gillett, Tessa E. (author)
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands; Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Zappia, Luke (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Department of Mathematics, Technical University of Munich, Garching, Germany
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- Madissoon, Elo (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- Markov, Nikolay S. (author)
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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- Zaragosi, Laure Emmanuelle (author)
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France
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- Ji, Yuge (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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- Ansari, Meshal (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Arguel, Marie Jeanne (author)
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France
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- Apperloo, Leonie (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Banchero, Martin (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Bécavin, Christophe (author)
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France
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- Berg, Marijn (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Chichelnitskiy, Evgeny (author)
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
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- Chung, Mei i. (author)
- Translational Genomics Research Institute, Phoenix, AZ, USA
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- Collin, Antoine (author)
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France; 3IA Côte d’Azur, Nice, France
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- Gay, Aurore C.A. (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Gote-Schniering, Janine (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Hooshiar Kashani, Baharak (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Inecik, Kemal (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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- Jain, Manu (author)
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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- Kapellos, Theodore S. (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany; Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
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- Kole, Tessa M. (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Leroy, Sylvie (author)
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, Nice, France
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- Mayr, Christoph H. (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Oliver, Amanda J. (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- von Papen, Michael (author)
- Research, Development and Innovation, Comma Soft, Bonn, Germany
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- Peter, Lance (author)
- Translational Genomics Research Institute, Phoenix, AZ, USA
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- Taylor, Chase J. (author)
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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- Walzthoeni, Thomas (author)
- Core Facility Genomics, Helmholtz Center Munich, Munich, Germany
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- Xu, Chuan (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- Bui, Linh T. (author)
- Translational Genomics Research Institute, Phoenix, AZ, USA
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- De Donno, Carlo (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
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- Dony, Leander (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany; Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
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- Faiz, Alen (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
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- Guo, Minzhe (author)
- Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
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- Gutierrez, Austin J. (author)
- Translational Genomics Research Institute, Phoenix, AZ, USA
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- Heumos, Lukas (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany; Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Huang, Ni (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- Ibarra, Ignacio L. (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
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- Jackson, Nathan D. (author)
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
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- Kadur Lakshminarasimha Murthy, Preetish (author)
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA; Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
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- Lotfollahi, Mohammad (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- Tabib, Tracy (author)
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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- Talavera-López, Carlos (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
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- Travaglini, Kyle J. (author)
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Allen Institute for Brain Science, Seattle, WA, USA
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- Wilbrey-Clark, Anna (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- Worlock, Kaylee B. (author)
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
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- Yoshida, Masahiro (author)
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
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- Chen, Yuexin (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Hagood, James S. (author)
- Department of Pediatrics (Pulmonology), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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- Agami, Ahmed (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Horvath, Peter (author)
- Biological Research Centre, Szeged, Hungary; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
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- Lundeberg, Joakim (author)
- KTH,Genteknologi
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- Marquette, Charles Hugo (author)
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, Nice, France
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- Pryhuber, Gloria (author)
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
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- Samakovlis, Chistos (author)
- Lab and Department of Molecular Bioscience, Stockholm University, Stockholm, Sweden
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- Sun, Xin (author)
- University of California, San Diego, La Jolla, CA, USA, La Jolla
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- Ware, Lorraine B. (author)
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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- Zhang, Kun (author)
- University of California, San Diego, La Jolla, CA, USA, La Jolla
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- van den Berge, Maarten (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Bossé, Yohan (author)
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
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- Desai, Tushar J. (author)
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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- Eickelberg, Oliver (author)
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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- Kaminski, Naftali (author)
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
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- Krasnow, Mark A. (author)
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
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- Lafyatis, Robert (author)
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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- Nikolic, Marko Z. (author)
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
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- Powell, Joseph E. (author)
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
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- Rajagopal, Jayaraj (author)
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
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- Rojas, Mauricio (author)
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
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- Rozenblatt-Rosen, Orit (author)
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
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- Seibold, Max A. (author)
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA; Department of Pediatrics, National Jewish Health, Denver, CO, USA; Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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- Sheppard, Dean (author)
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
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- Shepherd, Douglas P. (author)
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
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- Sin, Don D. (author)
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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- Timens, Wim (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Tsankov, Alexander M. (author)
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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- Whitsett, Jeffrey (author)
- Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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- Xu, Yan (author)
- Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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- Banovich, Nicholas E. (author)
- Translational Genomics Research Institute, Phoenix, AZ, USA
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- Barbry, Pascal (author)
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and Centre National de la Recherche Scientifique, Valbonne, France; 3IA Côte d’Azur, Nice, France
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- Duong, Thu Elizabeth (author)
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA, La Jolla
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- Falk, Christine S. (author)
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
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- Meyer, Kerstin B. (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge
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- Kropski, Jonathan A. (author)
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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- Pe’er, Dana (author)
- Howard Hughes Medical Institute, Chevy Chase, MD, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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- Schiller, Herbert B. (author)
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Tata, Purushothama Rao (author)
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
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- Schultze, Joachim L. (author)
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
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- Teichmann, Sara A. (author)
- Wellcome Sanger Institute, Hinxton, Cambridge, UK, Cambridge; Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
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- Misharin, Alexander V. (author)
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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- Nawijn, Martijn C. (author)
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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- Luecken, Malte D. (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
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- Theis, Fabian J. (author)
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany; TUM School of Life Sciences, Technical University of Munich, Munich, Germany; Department of Mathematics, Technical University of Munich, Garching, Germany
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(creator_code:org_t)
- Springer Nature, 2023
- 2023
- English.
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In: Nature Medicine. - : Springer Nature. - 1078-8956 .- 1546-170X. ; 29:6, s. 1563-1577
- Related links:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
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- 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
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- By the author/editor
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Sikkema, Lisa
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Ramírez-Suástegu ...
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Strobl, Daniel C ...
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Gillett, Tessa E ...
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Zappia, Luke
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Madissoon, Elo
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show more...
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Markov, Nikolay ...
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Zaragosi, Laure ...
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Ji, Yuge
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Ansari, Meshal
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Arguel, Marie Je ...
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Apperloo, Leonie
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Banchero, Martin
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Bécavin, Christo ...
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Berg, Marijn
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Chichelnitskiy, ...
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Chung, Mei i.
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Collin, Antoine
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Gay, Aurore C.A.
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Gote-Schniering, ...
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Hooshiar Kashani ...
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Inecik, Kemal
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Jain, Manu
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Kapellos, Theodo ...
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Kole, Tessa M.
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Leroy, Sylvie
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Mayr, Christoph ...
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Oliver, Amanda J ...
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von Papen, Micha ...
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Peter, Lance
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Taylor, Chase J.
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Walzthoeni, Thom ...
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Xu, Chuan
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Bui, Linh T.
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De Donno, Carlo
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Dony, Leander
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Faiz, Alen
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Guo, Minzhe
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Gutierrez, Austi ...
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Heumos, Lukas
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Huang, Ni
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Ibarra, Ignacio ...
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Jackson, Nathan ...
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Kadur Lakshminar ...
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Lotfollahi, Moha ...
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Tabib, Tracy
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Talavera-López, ...
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Travaglini, Kyle ...
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Wilbrey-Clark, A ...
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Worlock, Kaylee ...
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Yoshida, Masahir ...
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Chen, Yuexin
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Hagood, James S.
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Agami, Ahmed
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Horvath, Peter
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Lundeberg, Joaki ...
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Marquette, Charl ...
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Pryhuber, Gloria
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Samakovlis, Chis ...
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Sun, Xin
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Ware, Lorraine B ...
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Zhang, Kun
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van den Berge, M ...
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Bossé, Yohan
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Desai, Tushar J.
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Eickelberg, Oliv ...
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Kaminski, Naftal ...
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Krasnow, Mark A.
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Lafyatis, Robert
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Nikolic, Marko Z ...
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Powell, Joseph E ...
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Rajagopal, Jayar ...
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Rojas, Mauricio
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Rozenblatt-Rosen ...
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Seibold, Max A.
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Sheppard, Dean
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Shepherd, Dougla ...
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Sin, Don D.
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Timens, Wim
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Tsankov, Alexand ...
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Whitsett, Jeffre ...
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Xu, Yan
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Banovich, Nichol ...
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Barbry, Pascal
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Duong, Thu Eliza ...
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Falk, Christine ...
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Meyer, Kerstin B ...
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Kropski, Jonatha ...
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Pe’er, Dana
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Schiller, Herber ...
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Tata, Purushotha ...
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Schultze, Joachi ...
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Teichmann, Sara ...
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Misharin, Alexan ...
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Nawijn, Martijn ...
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Luecken, Malte D ...
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Theis, Fabian J.
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Cell and Molecul ...
- Articles in the publication
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Nature Medicine
- By the university
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Royal Institute of Technology