Transitional cell states sculpt tissue topology during lung regeneration

Efficient AAV Mediated Transgenesis in Alveolar Stem Cells and Associated Niches

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LGR5 expressing skin fibroblasts define a major cellular hub perturbed in scleroderma

(2022) Chamutal Gur et al.   CELL

Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

(2022) Preetish Kadur Lakshminarasimha Murthy et al.   NATURE

Human distal airways contain a multipotent secretory cell that can regenerate alveoli

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Syndrome of Combined Pulmonary Fibrosis and Emphysema: An Official ATS/ERS/JRS/ALAT Research Statement

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Wound healing, fibroblast heterogeneity, and fibrosis

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Incidence and Progression of Fibrotic Lung Disease in an At-Risk Cohort

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Multi-apical polarity of alveolar stem cells and their dynamics during lung development and regeneration

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Lung Cell Atlases in Health and Disease

(2022) Taylor S. Adams et al.   Annual Review of Physiology

Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing

(2021) Sepideh Abbasi et al.   Cell Stem Cell

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Democratising deep learning for microscopy with ZeroCostDL4Mic

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Respiratory dysfunction in a mouse model of spinocerebellar ataxia type 7

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Organ remodeling: The molecular choreography of a dance of destruction

(2021) Greg J. Beitel   CURRENT BIOLOGY

Control of hormone-driven organ disassembly by ECM remodeling and Yorkie-dependent apoptosis

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A census of the lung: CellCards from LungMAP

(2021) Xin Sun et al.   DEVELOPMENTAL CELL

Lung Regeneration: Cells, Models, and Mechanisms

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The Cellular and Physiological Basis for Lung Repair and Regeneration: Past, Present, and Future

(2020) Maria C. Basil et al.   Cell Stem Cell

Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis

(2020) Tatsuya Tsukui et al.   Nature Communications

Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis

(2020) Yoshihiko Kobayashi et al.   NATURE CELL BIOLOGY

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

(2020) Maximilian Strunz et al.   Nature Communications

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

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

(2020) Travis K. Hughes et al.   IMMUNITY

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

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Cellpose: a generalist algorithm for cellular segmentation

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

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IL-1 and TNFα Contribute to the Inflammatory Niche to Enhance Alveolar Regeneration

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Mechanisms of physiological tissue remodeling in animals: Manipulating tissue, organ, and organism morphology

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Comprehensive Integration of Single-Cell Data

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Resolving the fibrotic niche of human liver cirrhosis at single-cell level

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Stem cell–driven lymphatic remodeling coordinates tissue regeneration

(2019) Shiri Gur-Cohen et al.   SCIENCE

Niche-mediated BMP/SMAD signaling regulates lung alveolar stem cell proliferation and differentiation

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Extracellular matrix in lung development, homeostasis and disease

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

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Runt-Related Transcription Factor 1 (RUNX1) Promotes TGF-β-Induced Renal Tubular Epithelial-to-Mesenchymal Transition (EMT) and Renal Fibrosis through the PI3K Subunit p110δ

(2018) Tong Zhou et al.   EBioMedicine

Positional Stability and Membrane Occupancy Define Skin Fibroblast Homeostasis In Vivo

(2018) Edward Marsh et al.   CELL

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Lung morphometry: the link between structure and function

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In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

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

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Repair and Regeneration of the Respiratory System: Complexity, Plasticity, and Mechanisms of Lung Stem Cell Function

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RUNX1 is essential for mesenchymal stem cell proliferation and myofibroblast differentiation

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A retrospective of lung morphometry: from 1963 to present

(2013) Ewald R. Weibel   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Genetic studies provide clues on the pathogenesis of idiopathic pulmonary fibrosis

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Multiple stromal populations contribute to pulmonary fibrosis without evidence for epithelial to mesenchymal transition

(2011) J. R. Rock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interconversion Between Intestinal Stem Cell Populations in Distinct Niches

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Extracellular Matrix Degradation and Remodeling in Development and Disease

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Assessment of air space size characteristics by intercept (chord) measurement: an accurate and efficient stereological approach

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A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

(2009) Linda Madisen et al.   NATURE NEUROSCIENCE

Efficient temporally-controlled targeted mutagenesis in smooth muscle cells of the adult mouse

(2008) Olivia Wendling et al.   GENESIS

Extracellular matrix dynamics in development and regenerative medicine

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