Using single-cell RNA sequencing to unravel cell lineage relationships in the respiratory tract

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

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

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

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures

(2019) Sandra Ruiz García et al.   DEVELOPMENT

Ontogeny and Biology of Human Small Airway Epithelial Club Cells

(2018) Wu-Lin Zuo et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

(2018) Kelly Street et al.   BMC GENOMICS

Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury

(2018) Aleksandra Tata et al.   Cell Stem Cell

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

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

(2018) Lindsey W. Plasschaert et al.   NATURE

Allergic inflammatory memory in human respiratory epithelial progenitor cells

(2018) Jose Ordovas-Montanes et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

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

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth

(2018) Minzhe Guo et al.   Nature Communications

CDC20B is required for deuterosome-mediated centriole production in multiciliated cells

(2018) Diego R. Revinski et al.   Nature Communications

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

(2017) Bhupinder Pal et al.   Nature Communications

Dual SMAD Signaling Inhibition Enables Long-Term Expansion of Diverse Epithelial Basal Cells

(2016) Hongmei Mou et al.   Cell Stem Cell

SLICE: determining cell differentiation and lineage based on single cell entropy

(2016) Minzhe Guo et al.   NUCLEIC ACIDS RESEARCH

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Injury Induces Direct Lineage Segregation of Functionally Distinct Airway Basal Stem/Progenitor Cell Subpopulations

(2015) Ana Pardo-Saganta et al.   Cell Stem Cell

Notch3-Jagged signaling controls the pool of undifferentiated airway progenitors

(2015) M. Mori et al.   DEVELOPMENT

Clonal Dynamics Reveal Two Distinct Populations of Basal Cells in Slow-Turnover Airway Epithelium

(2015) Julie K. Watson et al.   Cell Reports

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

(2014) Brigid L.M. Hogan et al.   Cell Stem Cell

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

(2014) Barbara Treutlein et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Lung regeneration: mechanisms, applications and emerging stem cell populations

(2014) Darrell N Kotton et al.   NATURE MEDICINE

Bronchial epithelium as a target for innovative treatments in asthma

(2013) Delphine Gras et al.   PHARMACOLOGY & THERAPEUTICS

Stochastic homeostasis in human airway epithelium is achieved by neutral competition of basal cell progenitors

(2013) Vitor H Teixeira et al.   eLife

Tracheal Basal Cells

(2010) Brook B. Cole et al.   AMERICAN JOURNAL OF PATHOLOGY

Advances in Mucous Cell Metaplasia

(2009) David R. Curran et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

The Role of Scgb1a1+ Clara Cells in the Long-Term Maintenance and Repair of Lung Airway, but Not Alveolar, Epithelium

(2009) Emma L. Rawlins et al.   Cell Stem Cell

SPDEF is required for mouse pulmonary goblet cell differentiation and regulates a network of genes associated with mucus production

(2009) Gang Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Basal cells as stem cells of the mouse trachea and human airway epithelium

(2009) J. R. Rock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA