ArticleNature communications2023
Guided construction of single cell reference for human and mouse lung.
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Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers.
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130citing papers in PubMed
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Who cites it
130 citing papers in PubMed.
- Single-cell RNA sequencing reveals dysregulation of innate immune signaling in early-life respiratory syncytial virus infection with subsequent low-level cadmium exposure.Toxicology reports · 2026Article
- Mapping Embryonic Mouse Lung Development Using Enhanced Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Decreased Endothelial Cell Retinoic Acid Signaling Accelerates Progression of Single Ventricle Pulmonary Vascular Malformations.JACC. Basic to translational science · 2026Article
- Pervasive tissue specificity of driver genes revealed by mutational analysis of 265 cancer types.iScience · 2026Article
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- In situ structure of the human ciliary transition zone links linker defects to primary ciliary dyskinesia.Science (New York, N.Y.) · 2026Article
- LATS1/2 inactivation drives a distinct venous endothelial cell response that contributes to fibrotic remodeling of the lung.Science advances · 2026Article
- SARS-CoV-2 infection produces an IL-33-dependent chronic eosinophilic pneumonia and muco-inflammatory airways disease in Scnn1b-Tg mice.JCI insight · 2026Article
- Neural crest cell signatures drive tumorigenesis in tuberous sclerosis complex and lymphangioleiomyomatosis.JCI insight · 2026Article
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- Cellular hallmarks and aging clock of the human lung parenchyma.Nature communications · 2026Article
- E2F1 Drives Endothelial Arterial Programming in Pulmonary Arterial Hypertension.bioRxiv : the preprint server for biology · 2026Article
- Genetic Determinants of Pulmonary Artery Size in over 50,000 Subjects with and without COPD.medRxiv : the preprint server for health sciences · 2026Article
- ITGA5 as a Dual Regulator of Epithelial-Mesenchymal Transition and Epithelial Cell Anoikis Resistance: Functional Validation and Drug Prediction.Cell proliferation · 2026Article
- Integrated stress response couples mitochondrial fitness with lineage reprogramming to drive cancer evolution.Nature cell biology · 2026Article
- Single-nucleus RNA sequencing identifies conserved structural cell programs in allergic lung inflammation.The journal of allergy and clinical immunology. Global · 2026Article
- Functional Role of Piezo1 in Regulating Whole-Lung Vascular Reactivity.Pulmonary circulation · 2026Article
- The lung tissue environment inbioRxiv : the preprint server for biology · 2026Article
- Extra gene coding capacity of SARS-CoV-2 provides a virus engineering platform for in vitro and in vivo applications.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Excessive postnatal smooth muscle differentiation in a lung-specific model of TBX4-related pulmonary hypertension.JCI insight · 2026Article
70 more citing papers are in PubMed but not listed here.
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Authors and funding
33 authors.
Minzhe GuoThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA. minzhe.guo@cchmc.org.ORCID 0000-0002-5502-9172
Michael P MorleyDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Cheng JiangThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Yixin WuThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Guangyuan LiDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.ORCID 0000-0002-0628-2454
Yina DuThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Shuyang ZhaoThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.ORCID 0000-0001-6570-949X
Andrew WagnerThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Adnan Cihan CakarThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Michal KourilDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.ORCID 0000-0002-4786-7934
Kang JinDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.ORCID 0000-0001-5638-040X
Nathan GaddisRTI International, Durham, NC, 27709, USA.
Joseph A KitzmillerThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Kathleen StewartDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Maria C BasilDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Susan M LinDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Yun YingDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Apoorva BabuDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Kathryn A Wikenheiser-BrokampThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.ORCID 0000-0002-2932-3095
Kyu Shik MunDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
Anjaparavanda P NarenDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
Geremy ClairBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.ORCID 0000-0003-0478-8520
Joshua N AdkinsBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.ORCID 0000-0003-0399-0700
Gloria S PryhuberDepartment of Pediatrics Division of Neonatology, University of Rochester Medical Center, Rochester, NY, 14642, USA.ORCID 0000-0002-9185-3994
Ravi S MisraDepartment of Pediatrics Division of Neonatology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
Bruce J AronowDepartment of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.ORCID 0000-0001-5109-6514
Timothy L TickleData Sciences Platform, The Broad Institute, Cambridge, MA, 02142, USA.ORCID 0000-0002-6592-6272
Nathan SalomonisDepartment of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.ORCID 0000-0001-9689-2469
Xin SunDepartment of Pediatrics, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
Edward E MorriseyDepartment of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Jeffrey A WhitsettThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.ORCID 0000-0003-1668-5174
NHLBI LungMAP Consortium
Yan XuThe Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA. yan.xu@cchmc.org.ORCID 0000-0003-2025-027X
Funding
The LungMAP Data Coordination Center for Next Gen Systems Biology of RespirationU24HL148865 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI Bruce J Aronow, Nathan G. Salomonis · 2019 to 2026
$12.4MPilot and Feasibility ProgramP30DK117467 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI Raouf S. Amin · 2018 to 2026
$11.4MBioRepository for INvestigation of Diseases of the Lung (BRINDL) - Phase IIIU01HL148861 · NHLBI · UNIVERSITY OF ROCHESTER · PI GLORIA S PRYHUBER · 2019 to 2026
$9.7MEditing Alveolar Progenitor Cells for Correction of Monogenic DiseaseU01HL134745 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI KOTTON, DARRELL N., MORRISEY, EDWARD E · 2016 to 2022
$8.3MBiorepository for Investigation of Neonatal Diseases of Lung-Normal (BRINDL-NL)U01HL122700 · NHLBI · UNIVERSITY OF ROCHESTER · PI PRYHUBER, GLORIA S · 2014 to 2018
$6.1MResearch Center for Spatiotemporal Lung Imaging and OmicsU01HL148860 · NHLBI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI ADKINS, JOSHUA N., CARSON, JAMES PAUL · 2019 to 2023
$4.7MLungMap Phase II - Building a multidimensional map of developing human lungU01HL148856 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI WHITSETT, JEFFREY A, XU, YAN · 2019 to 2023
$4.5MMulti-modal characterization of three human lung niches at the single cell levelU01HL148857 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MORRISEY, EDWARD E · 2019 to 2023
$4.4MDecoding the Cellular Niches Critical for Lung Maturation and PathogenesisU01HL148867 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUN, XIN · 2019 to 2023
$4.4M"Lung MAP" Atlas Research CenterU01HL122642 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI POTTER, S. STEVEN, WHITSETT, JEFFREY A · 2014 to 2018
$3.9MUterine signaling networks in the pathogenesis of pulmonary lymphangioleiomyomatosis (LAM)R01HL153045 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI XU, YAN, YU, JANE · 2020 to 2023
$3.1MMolecular regulation of cell fate and progenitor function in the distal human respiratory airwaysK08HL163398 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI Maria Ciocca Basil · 2022 to 2026
$834kNHLBI NIH HHS K08 HL163398NHLBI NIH HHS R01 HL153045NHLBI NIH HHS R01HL153045NHLBI NIH HHS U01 HL122642NHLBI NIH HHS U01HL122642NHLBI NIH HHS U01 HL122700NHLBI NIH HHS U01 HL134745NHLBI NIH HHS U01HL134745NHLBI NIH HHS U01 HL148856NHLBI NIH HHS U01HL148856NHLBI NIH HHS U01 HL148857NHLBI NIH HHS U01 HL148860NHLBI NIH HHS U01 HL148861NHLBI NIH HHS U01 HL148867NHLBI NIH HHS U24 HL148865NIDDK NIH HHS P30 DK117467NIDDK NIH HHS P30DK117467
Abstract
Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.
Indexed as
Gene Expression ProfilingInformation DisseminationAnimalsHumansMiceSingle-Cell AnalysisTranscriptome
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