ArticleNature medicine2023
An integrated cell atlas of the lung in health and disease.
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Article in Nature medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 559 papers.
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559citing papers in PubMed
105.9field-weighted citation impact, top 1% of its field
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Who cites it
559 citing papers in PubMed, 684 citations in OpenAlex.
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- Nasal Epithelial Immune Signatures Are Associated With Age-Dependent Asthma Trajectories in Early Life.Allergy · 2026Observational
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- Mechanosignaling promotes macrophage apoptosis resistance in pulmonary fibrosisbioRxiv : the preprint server for biology · 2026Article
- Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet.Nature communications · 2026Article
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- The Role of the Nervous System in Lung Disease.Current neurology and neuroscience reports · 2026Review
- Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence.bioRxiv : the preprint server for biology · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade.eLife · 2026Article
- Scale-Invariant, Robust Sparse PCA for Large Data via Differentiable Penalties.Transactions on machine learning research · 2026Article
499 more citing papers are in PubMed but not listed here.
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Authors and funding
87 authors at 20 institutions in 10 countries.
Lisa SikkemaDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.ORCID 0000-0001-9686-6295
Ciro Ramírez-Suástegui *Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Daniel C Strobl *Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Tessa E Gillett *Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands.ORCID 0000-0002-5447-1727
Luke Zappia *Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.ORCID 0000-0001-7744-8565
Elo Madissoon *Wellcome Sanger Institute, Hinxton, Cambridge, UK.
Nikolay S Markov *Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.ORCID 0000-0002-3659-4387
Laure-Emmanuelle Zaragosi *Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.ORCID 0000-0001-6747-7928
Yuge JiDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Meshal AnsariDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Marie-Jeanne ArguelInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.ORCID 0000-0002-8725-2555
Leonie ApperlooGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Martin BancheroGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Christophe BécavinInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.ORCID 0000-0003-1555-3153
Marijn BergGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Evgeny ChichelnitskiyInstitute for Transplant Immunology, Hannover Medical School, Hannover, Germany.
Mei-I ChungTranslational Genomics Research Institute, Phoenix, AZ, USA.
Antoine CollinInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.
Aurore C A GayGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.ORCID 0000-0002-1593-2674
Janine Gote-SchnieringInstitute 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.
Baharak Hooshiar KashaniInstitute 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.
Kemal InecikDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.ORCID 0000-0001-7379-9093
Manu JainDivision of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Theodore S KapellosInstitute 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.
Tessa M KoleGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Sylvie LeroyPulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.
Christoph H MayrInstitute 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.
Amanda J OliverWellcome Sanger Institute, Hinxton, Cambridge, UK.ORCID 0000-0003-1690-9027
Michael von PapenResearch, Development and Innovation, Comma Soft, Bonn, Germany.ORCID 0000-0001-5030-1643
Lance PeterTranslational Genomics Research Institute, Phoenix, AZ, USA.
Chase J TaylorDivision of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Thomas WalzthoeniCore Facility Genomics, Helmholtz Center Munich, Munich, Germany.
Chuan XuWellcome Sanger Institute, Hinxton, Cambridge, UK.
Linh T BuiTranslational Genomics Research Institute, Phoenix, AZ, USA.ORCID 0000-0003-3152-8978
Carlo De DonnoDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Leander DonyDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.ORCID 0000-0001-5697-6991
Alen FaizGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Minzhe GuoDivision of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.ORCID 0000-0002-5502-9172
Austin J GutierrezTranslational Genomics Research Institute, Phoenix, AZ, USA.ORCID 0000-0003-2977-2189
Lukas HeumosDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Ni HuangWellcome Sanger Institute, Hinxton, Cambridge, UK.
Ignacio L IbarraDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.ORCID 0000-0002-0582-002X
Nathan D JacksonCenter for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
Preetish Kadur Lakshminarasimha MurthyDepartment of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
Mohammad LotfollahiDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.ORCID 0000-0001-6858-7985
Tracy TabibDivision of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Carlos Talavera-LópezDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Kyle J TravagliniDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0003-3164-6448
Anna Wilbrey-ClarkWellcome Sanger Institute, Hinxton, Cambridge, UK.
Kaylee B WorlockDepartment of Respiratory Medicine, Division of Medicine, University College London, London, UK.ORCID 0000-0002-5656-7634
Masahiro YoshidaDepartment of Respiratory Medicine, Division of Medicine, University College London, London, UK.ORCID 0000-0002-3521-5322
Lung Biological Network Consortium
Maarten van den BergeGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
Yohan BosséInstitut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada.ORCID 0000-0002-3067-3711
Tushar J DesaiDepartment of Medicine, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-8794-5319
Oliver EickelbergDivision of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Naftali KaminskiPulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.ORCID 0000-0001-5917-4601
Mark A KrasnowDepartment of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-1976-5471
Robert LafyatisDivision of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.ORCID 0000-0002-9398-5034
Marko Z NikolicDepartment of Respiratory Medicine, Division of Medicine, University College London, London, UK.ORCID 0000-0001-6304-6848
Joseph E PowellGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Jayaraj RajagopalCenter for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA.
Mauricio RojasDepartment of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA.
Orit Rozenblatt-RosenKlarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0001-6313-3570
Max A SeiboldCenter for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.ORCID 0000-0002-8685-4263
Dean SheppardDivision of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA.ORCID 0000-0002-6277-2036
Douglas P ShepherdDepartment of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA.
Don D SinCentre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.ORCID 0000-0002-0756-6643
Wim TimensGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.ORCID 0000-0002-4146-6363
Alexander M TsankovDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Jeffrey WhitsettDivision of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.ORCID 0000-0003-1668-5174
Yan XuDivision of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.ORCID 0000-0003-2025-027X
Nicholas E BanovichTranslational Genomics Research Institute, Phoenix, AZ, USA.
Pascal BarbryInstitut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France.ORCID 0000-0001-9632-6483
Thu Elizabeth DuongDepartment of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0001-7122-4448
Christine S FalkInstitute for Transplant Immunology, Hannover Medical School, Hannover, Germany.
Kerstin B MeyerWellcome Sanger Institute, Hinxton, Cambridge, UK.ORCID 0000-0001-5906-1498
Jonathan A KropskiDivision of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID 0000-0002-8923-1344
Dana Pe'erHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID 0000-0002-9259-8817
Herbert B SchillerInstitute 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.ORCID 0000-0001-9498-7034
Purushothama Rao TataDepartment of Cell Biology, Duke University School of Medicine, Durham, NC, USA.ORCID 0000-0003-4837-0337
Joachim L SchultzeDepartment of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
Sara A TeichmannWellcome Sanger Institute, Hinxton, Cambridge, UK.ORCID 0000-0002-6294-6366
Alexander V MisharinDivision of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.ORCID 0000-0003-2879-3789
Martijn C NawijnGroningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.ORCID 0000-0003-3372-6521
Malte D LueckenDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany. malte.luecken@helmholtz-munich.de.ORCID 0000-0001-7464-7921
Fabian J TheisDepartment of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany. fabian.theis@helmholtz-munich.de.ORCID 0000-0002-2419-1943
Helmholtz Zentrum München · DEUniversity Medical Center Groningen · NLWellcome Sanger Institute · GBGerman Center for Lung Research · DECentre National de la Recherche Scientifique · FRTranslational Genomics Research Institute · USCincinnati Children's Hospital Medical Center · USNorthwestern University · USUniversity College London · GBUniversity of California San Diego · USUniversity of Pittsburgh · USDuke University · USMedizinische Hochschule Hannover · DENational Jewish Health · USUniversité Côte d'Azur · FRUniversity of Bonn · DEVanderbilt University Medical Center · USAllen Institute for Brain Science · USArizona State University · USBroad Institute · US
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4MYale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9MTissue resident macrophages regulate proteostasis in the aging lungP01AG049665 · NIA · NORTHWESTERN UNIVERSITY AT CHICAGO · PI GR Scott Budinger · 2015 to 2026
$26.9MTechnology CoreU19AI135964 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI JUSTIN B. STARREN · 2018 to 2026
$24.7MRole of miRNAs in Th2-Driven inflammation in AsthmaP01HL107202 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FAHY, JOHN V · 2012 to 2023
$23.3MTranslational studies for identifying and targeting novel pathways in systemic sclerosis pathogenesisP50AR060780 · NIAMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LAFYATIS, ROBERT A. · 2011 to 2021
$14.9MTriState SenNET (Lung and Heart) Tissue Map and Atlas consortiumU54AG075931 · NIA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI TOREN FINKEL, Melanie Koenigshoff · 2021 to 2026
$14.0MMidwest Murine-Tissue Mapping Center (MM-TMC)U54AG079754 · NIA · UNIVERSITY OF MINNESOTA · PI GR Scott Budinger, Sundeep Khosla · 2022 to 2026
$11.5MBioRepository for INvestigation of Diseases of the Lung (BRINDL) - Phase IIIU01HL148861 · NHLBI · UNIVERSITY OF ROCHESTER · PI GLORIA S PRYHUBER · 2019 to 2026
$9.7MSystems Biology CoreP50AR080612 · NIAMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI ROBERT A. LAFYATIS · 2022 to 2026
$9.5MThe Airway Functional Genomics of Bronchodilator Drug Response in Minority Children with AsthmaR01HL117004 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, SEIBOLD, MAX A · 2013 to 2022
$9.3MTranscriptomic and Genetic Endotyping of Exacerbation-Prone AsthmaticsP01HL132821 · NHLBI · NATIONAL JEWISH HEALTH · PI SEIBOLD, MAX A · 2017 to 2021
$9.0MMedical Research Council MR/R015635/1NCATS NIH HHS UL1 TR001863NCI NIH HHS P30 CA008748NHLBI NIH HHS P01 HL107202NHLBI NIH HHS P01 HL132821NHLBI NIH HHS R01 HL068702NHLBI NIH HHS R01 HL117004NHLBI NIH HHS R01 HL123766NHLBI NIH HHS R01 HL126176NHLBI NIH HHS R01 HL127349NHLBI NIH HHS R01 HL128439NHLBI NIH HHS R01 HL135156NHLBI NIH HHS R01 HL141380NHLBI NIH HHS R01 HL141852NHLBI NIH HHS R01 HL142568NHLBI NIH HHS R01 HL145372NHLBI NIH HHS R01 HL146519NHLBI NIH HHS R01 HL146557NHLBI NIH HHS R01 HL153045NHLBI NIH HHS R01 HL153312NHLBI NIH HHS R01 HL153375NHLBI NIH HHS R01 HL158139NHLBI NIH HHS R21 HL156124NHLBI NIH HHS R21 HL161760NHLBI NIH HHS R56 HL157632NHLBI NIH HHS U01 HL145567NHLBI NIH HHS U01 HL148856NHLBI NIH HHS U01 HL148861NHLBI NIH HHS U54 HL145608NHLBI NIH HHS U54 HL165443NIAID NIH HHS U19 AI135964NIAMS NIH HHS P50 AR060780NIAMS NIH HHS P50 AR080612NIA NIH HHS P01 AG049665NIA NIH HHS U54 AG075931NIA NIH HHS U54 AG079754NICHD NIH HHS K12 HD105271NIEHS NIH HHS R01 ES034350NIMHD NIH HHS R01 MD010443Wellcome Trust
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
Indexed as
COVID-19Lung NeoplasmsPulmonary FibrosisHumansLungMacrophages
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