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Inference and analysis of cell-cell communication using CellChat

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Cross-tissue organization of the fibroblast lineage

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Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics

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In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution

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Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study

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Single Cell Reconstruction of Human Basal Cell Diversity in Normal and IPF Lung

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A Single-cell Atlas of the Human Healthy Airways

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Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration

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Generalizing RNA velocity to transient cell states through dynamical modeling

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Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

(2020) Maximilian Strunz et al.   Nature Communications

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

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Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

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Single-cell transcriptomic atlas of primate cardiopulmonary aging

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Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2 mediated interferon responses and pneumocyte dysfunction

(2020) Hiroaki Katsura et al.   Cell Stem Cell

Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia

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A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

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The single-cell transcriptional landscape of mammalian organogenesis

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Comprehensive Integration of Single-Cell Data

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A cellular census of human lungs identifies novel cell states in health and in asthma

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Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung

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scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data

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Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

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The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Automated cell-type classification in intact tissues by single-cell molecular profiling

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Transcriptome profiling reveals the complexity of pirfenidone effects in IPF

(2018) Grazyna Kwapiszewska et al.   EUROPEAN RESPIRATORY JOURNAL

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

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A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Nonhuman Primate Models of Respiratory Disease: Past, Present, and Future

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SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

The Human Cell Atlas

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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

A retrospective of lung morphometry: from 1963 to present

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Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

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Long-term pulmonary outcomes of patients with bronchopulmonary dysplasia

(2013) Anita Bhandari et al.   SEMINARS IN PERINATOLOGY

Distal Airway Stem Cells Yield Alveoli In Vitro and during Lung Regeneration following H1N1 Influenza Infection

(2011) Pooja A. Kumar et al.   CELL

Asymmetric cell divisions promote Notch-dependent epidermal differentiation

(2011) Scott E. Williams et al.   NATURE

Ectopic respiratory epithelial cell differentiation in bronchiolised distal airspaces in idiopathic pulmonary fibrosis

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The porcine lung as a potential model for cystic fibrosis

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