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

TooManyCells identifies and visualizes relationships of single-cell clades

(2020) Gregory W. Schwartz et al.   NATURE METHODS

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

(2020) Taylor S. Adams et al.   Science Advances

ABL kinase inhibition promotes lung regeneration through expansion of an SCGB1A1+ SPC+ cell population following bacterial pneumonia

(2019) Aaditya Khatri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction

(2019) Qiaozhen Liu et al.   NATURE GENETICS

Bronchioalveolar stem cells are a main source for regeneration of distal lung epithelia in vivo

(2019) Isabelle Salwig et al.   EMBO JOURNAL

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

(2019) Christina Morse et al.   EUROPEAN RESPIRATORY JOURNAL

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

(2019) Felipe A. Vieira Braga et al.   NATURE MEDICINE

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

(2018) Kelly Street et al.   BMC GENOMICS

Idiopathic pulmonary fibrosis: Epithelial-mesenchymal interactions and emerging therapeutic targets

(2018) Justin C. Hewlett et al.   MATRIX BIOLOGY

Idiopathic Pulmonary Fibrosis

(2018) David J. Lederer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2018) Lindsey W. Plasschaert et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

(2018) Davide Risso et al.   PLoS Computational Biology

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Local lung hypoxia determines epithelial fate decisions during alveolar regeneration

(2017) Ying Xi et al.   NATURE CELL BIOLOGY

MicroRNA-138 Inhibits Cell Growth, Invasion, and EMT of Non-Small Cell Lung Cancer Via SOX4/p53 Feedback Loop

(2017) Dandan Li et al.   ONCOLOGY RESEARCH

Cellular senescence mediates fibrotic pulmonary disease

(2017) Marissa J. Schafer et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis

(2017) Milica Vukmirovic et al.   BMC Pulmonary Medicine

Extensive Phenotyping of Individuals at Risk for Familial Interstitial Pneumonia Reveals Clues to the Pathogenesis of Interstitial Lung Disease

(2015) Jonathan A. Kropski et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

A Novel Genomic Signature with Translational Significance for Human Idiopathic Pulmonary Fibrosis

(2015) Yasmina Bauer et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

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

The genetic basis of idiopathic pulmonary fibrosis

(2015) Jonathan A. Kropski et al.   EUROPEAN RESPIRATORY JOURNAL

Classification of usual interstitial pneumonia in patients with interstitial lung disease: assessment of a machine learning approach using high-dimensional transcriptional data

(2015) Su Yeon Kim et al.   Lancet Respiratory Medicine

p63+Krt5+ distal airway stem cells are essential for lung regeneration

(2014) Wei Zuo et al.   NATURE

Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury

(2014) Andrew E. Vaughan et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Cellular senescence: from physiology to pathology

(2014) Daniel Muñoz-Espín et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An Official American Thoracic Society/European Respiratory Society Statement: Update of the International Multidisciplinary Classification of the Idiopathic Interstitial Pneumonias

(2013) William D. Travis et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Animal Models of Fibrotic Lung Disease

(2013) Bethany B. Moore et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Type 2 alveolar cells are stem cells in adult lung

(2013) Christina E. Barkauskas et al.   JOURNAL OF CLINICAL INVESTIGATION

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis

(2013) Tasha E Fingerlin et al.   NATURE GENETICS

Sox9 plays multiple roles in the lung epithelium during branching morphogenesis

(2013) B. E. Rockich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis

(2013) Ivana V Yang et al.   THORAX

Acellular Normal and Fibrotic Human Lung Matrices as a Culture System forIn VitroInvestigation

(2012) Adam J. Booth et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

The Role of Sox Genes in Lung Morphogenesis and Cancer

(2012) Yongzhao Zhu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Interactions Between β-Catenin and Transforming Growth Factor-β Signaling Pathways Mediate Epithelial-Mesenchymal Transition and Are Dependent on the Transcriptional Co-activator cAMP-response Element-binding Protein (CREB)-binding Protein (CBP)

(2012) Beiyun Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Alveolar epithelial cells express mesenchymal proteins in patients with idiopathic pulmonary fibrosis

(2011) Cecilia Marmai et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Alveolar Epithelial Cells Undergo Epithelial-to-Mesenchymal Transition in Response to Endoplasmic Reticulum Stress

(2011) Harikrishna Tanjore et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A CommonMUC5BPromoter Polymorphism and Pulmonary Fibrosis

(2011) Max A. Seibold et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis

(2009) Kazuhisa Konishi et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Contribution of Epithelial-derived Fibroblasts to Bleomycin-induced Lung Fibrosis

(2009) Harikrishna Tanjore et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Genetic Defects in Surfactant Protein A2 Are Associated with Pulmonary Fibrosis and Lung Cancer

(2008) Yongyu Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MMP1 and MMP7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis

(2008) Ivan O Rosas et al.   PLOS MEDICINE