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Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Inhibition of distal lung morphogenesis inNkx2.1(?/?) embryos
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Keeping it together: Pulmonary alveoli are maintained by a hierarchy of cellular programs
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Airway epithelial cell differentiation during lung organogenesis requires C/EBPα and C/EBPβ
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The Oxygen Environment at Birth Specifies the Population of Alveolar Epithelial Stem Cells in the Adult Lung
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Control of Alveolar Differentiation by the Lineage Transcription Factors GATA6 and HOPX Inhibits Lung Adenocarcinoma Metastasis
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Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming
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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
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Mapping the Mouse Cell Atlas by Microwell-Seq
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Mapping the Mouse Cell Atlas by Microwell-Seq
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Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
inferredcites →https://doi.org/10.1016/j.cell.2019.01.022openalex-snapshot
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics
inferredcites →https://doi.org/10.1016/j.cell.2019.02.026openalex-snapshot
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
inferredcites →https://doi.org/10.1016/j.cell.2019.05.031openalex-snapshot
Comprehensive Integration of Single-Cell Data
inferredcites →https://doi.org/10.1016/j.stem.2014.07.012openalex-snapshot
Repair and Regeneration of the Respiratory System: Complexity, Plasticity, and Mechanisms of Lung Stem Cell Function
inferredcites →https://doi.org/10.1016/j.stem.2016.10.004openalex-snapshot
Two-Way Conversion between Lipogenic and Myogenic Fibroblastic Phenotypes Marks the Progression and Resolution of Lung Fibrosis
inferredcites →https://doi.org/10.1016/j.stem.2017.03.011openalex-snapshot
Two-Way Conversion between Lipogenic and Myogenic Fibroblastic Phenotypes Marks the Progression and Resolution of Lung Fibrosis
inferredcites →https://doi.org/10.1016/j.stemcr.2019.02.013openalex-snapshot
IL-1 and TNFα Contribute to the Inflammatory Niche to Enhance Alveolar Regeneration
inferredcites →https://doi.org/10.1016/j.tcb.2014.09.003openalex-snapshot
Plasticity within stem cell hierarchies in mammalian epithelia
inferredcites →https://doi.org/10.1016/j.ydbio.2016.06.020openalex-snapshot
Foxp transcription factors suppress a non-pulmonary gene expression program to permit proper lung development
inferredcites →https://doi.org/10.1016/s1074-7613(01)00232-1openalex-snapshot
A Novel TNF Receptor Family Member Binds TWEAK and Is Implicated in Angiogenesis
inferredcites →https://doi.org/10.1038/nature12777openalex-snapshot
Dedifferentiation of committed epithelial cells into stem cells in vivo
inferredcites →https://doi.org/10.1038/nature13173openalex-snapshot
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
inferredcites →https://doi.org/10.1038/nature13903openalex-snapshot
p63+Krt5+ distal airway stem cells are essential for lung regeneration
inferredcites →https://doi.org/10.1038/nature14112openalex-snapshot
Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury
inferredcites →https://doi.org/10.1038/nature14984openalex-snapshot
Hedgehog actively maintains adult lung quiescence and regulates repair and regeneration
inferredcites →https://doi.org/10.1038/nature25786openalex-snapshot
Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor
inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
inferredcites →https://doi.org/10.1038/nbt.3192openalex-snapshot
Spatial reconstruction of single-cell gene expression data
inferredcites →https://doi.org/10.1038/nbt.4314openalex-snapshot
Dimensionality reduction for visualizing single-cell data using UMAP
inferredcites →https://doi.org/10.1038/ncb3580openalex-snapshot
Local lung hypoxia determines epithelial fate decisions during alveolar regeneration
inferredcites →https://doi.org/10.1038/ncomms8866openalex-snapshot
A draft network of ligand–receptor-mediated multicellular signalling in human
inferredcites →https://doi.org/10.1038/nmeth.2019openalex-snapshot
Fiji: an open-source platform for biological-image analysis
inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot
Diffusion pseudotime robustly reconstructs lineage branching
inferredcites →https://doi.org/10.1038/nri.2017.90openalex-snapshot
Type 2 immunity in tissue repair and fibrosis
inferredcites →https://doi.org/10.1038/s41467-018-07770-1openalex-snapshot
Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth
inferredcites →https://doi.org/10.1038/s41467-019-08831-9openalex-snapshot
An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
inferredcites →https://doi.org/10.1038/s41586-018-0393-7openalex-snapshot
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
inferredcites →https://doi.org/10.1038/s41586-018-0394-6openalex-snapshot
A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte
inferredcites →https://doi.org/10.1038/s41586-018-0414-6openalex-snapshot
RNA velocity of single cells
inferredcites →https://doi.org/10.1038/s41586-018-0590-4openalex-snapshot
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
inferredcites →https://doi.org/10.1038/s41586-018-0698-6openalex-snapshot
Single-cell reconstruction of the early maternal–fetal interface in humans
inferredcites →https://doi.org/10.1038/s41587-019-0071-9openalex-snapshot
A comparison of single-cell trajectory inference methods
inferredcites →https://doi.org/10.1038/s41587-019-0088-0openalex-snapshot
Inferring population dynamics from single-cell RNA-sequencing time series data
inferredcites →https://doi.org/10.1038/s41588-019-0346-6openalex-snapshot
Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction
inferredcites →https://doi.org/10.1038/s41590-018-0276-yopenalex-snapshot
Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
inferredcites →https://doi.org/10.1073/pnas.1621177114openalex-snapshot
Transcription factor Etv5 is essential for the maintenance of alveolar type II cells
inferredcites →https://doi.org/10.1084/jem.20162152openalex-snapshot
Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btz625openalex-snapshot
BBKNN: fast batch alignment of single cell transcriptomes
inferredcites →https://doi.org/10.1093/gigascience/giaa151openalex-snapshot
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1101/478503openalex-snapshot
Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species
inferredcites →https://doi.org/10.1101/gr.192237.115openalex-snapshot
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
inferredcites →https://doi.org/10.1126/science.aam6603openalex-snapshot
Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells
inferredcites →https://doi.org/10.1126/science.aax1971openalex-snapshot
A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution
inferredcites →https://doi.org/10.1126/scisignal.aao3469openalex-snapshot
Cadherin-11–mediated adhesion of macrophages to myofibroblasts establishes a profibrotic niche of active TGF-β
inferredcites →https://doi.org/10.1128/mcb.26.3.1109-1123.2006openalex-snapshot
Respiratory Failure Due to Differentiation Arrest and Expansion of Alveolar Cells following Lung-Specific Loss of the Transcription Factor C/EBPα in Mice
inferredcites →https://doi.org/10.1152/ajplung.00112.2013openalex-snapshot
Neonatal hyperoxia alters the host response to influenza A virus infection in adult mice through multiple pathways
inferredcites →https://doi.org/10.1152/ajplung.00408.2017openalex-snapshot
Distinct niches within the extracellular matrix dictate fibroblast function in (cell free) 3D lung tissue cultures
inferredcites →https://doi.org/10.1164/rccm.200712-1839ocopenalex-snapshot
Neonatal Hyperoxia Enhances the Inflammatory Response in Adult Mice Infected with Influenza A Virus
inferredcites →https://doi.org/10.1165/rcmb.2016-0150ocopenalex-snapshot
Alternative Progenitor Lineages Regenerate the Adult Lung Depleted of Alveolar Epithelial Type 2 Cells
inferredcites →https://doi.org/10.1165/rcmb.2018-0416tropenalex-snapshot
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease
inferredcites →https://doi.org/10.1172/jci.insight.123637openalex-snapshot
Single-cell RNA sequencing identifies TGF-β as a key regenerative cue following LPS-induced lung injury
inferredcites →https://doi.org/10.1172/jci.insight.128674openalex-snapshot
TAZ is required for lung alveolar epithelial cell differentiation after injury
inferredcites →https://doi.org/10.1172/jci.insight.90558openalex-snapshot
Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis
inferredcites →https://doi.org/10.1172/jci125014openalex-snapshot
Yap/Taz regulate alveolar regeneration and resolution of lung inflammation
inferredcites →https://doi.org/10.1172/jci68782openalex-snapshot
Type 2 alveolar cells are stem cells in adult lung
inferredcites →https://doi.org/10.1183/09031936.00183214openalex-snapshot
Preclinical validation and imaging of Wnt-induced repair in human 3D lung tissue cultures
inferredcites →https://doi.org/10.1186/1471-2105-13-s16-s12openalex-snapshot
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
inferredcites →https://doi.org/10.1186/gb-2014-15-2-r29openalex-snapshot
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
inferredcites →https://doi.org/10.1186/s13059-017-1382-0openalex-snapshot
SCANPY: large-scale single-cell gene expression data analysis
inferredcites →https://doi.org/10.1186/s13059-019-1663-xopenalex-snapshot
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
inferredcites →https://doi.org/10.1242/dev.00150openalex-snapshot
β-Catenin/Tcf-regulated transcription prior to the midblastula transition
inferredcites →https://doi.org/10.1242/dev.02273openalex-snapshot
C/EBPα is required for lung maturation at birth
inferredcites →https://doi.org/10.1242/dev.02846openalex-snapshot
Foxp2 and Foxp1 cooperatively regulate lung and esophagus development
inferredcites →https://doi.org/10.1242/dev.098186openalex-snapshot
Lung development: orchestrating the generation and regeneration of a complex organ
inferredcites →https://doi.org/10.1242/dev.129.9.2233openalex-snapshot
GATA6 regulates differentiation of distal lung epithelium
inferredcites →https://doi.org/10.1242/dev.130005openalex-snapshot
Development and plasticity of alveolar type 1 cells
inferredcites →https://doi.org/10.1242/dev.143784openalex-snapshot
Plasticity in the lung: making and breaking cell identity
inferredcites →https://doi.org/10.1242/dev.170506openalex-snapshot
Concepts and limitations for learning developmental trajectories from single cell genomics
inferredcites →https://doi.org/10.1242/dmm.019117openalex-snapshot
Enolase 1 and protein disulfide isomerase associated 3 regulate Wnt/β-catenin driven alveolar epithelial cell trans-differentiation
inferredcites →https://doi.org/10.12688/f1000research.9005.2openalex-snapshot
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 2; referees: 3 approved]
inferredcites →https://doi.org/10.12688/f1000research.9005.3openalex-snapshot
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
inferredcites →https://doi.org/10.15252/embr.201744816openalex-snapshot
Cell fate decisions: emerging roles for metabolic signals and cell morphology
inferredcites →https://doi.org/10.15252/msb.20156123openalex-snapshot
Time‐ and compartment‐resolved proteome profiling of the extracellular niche in lung injury and repair
inferredcites →https://doi.org/10.4049/jimmunol.171.10.5003openalex-snapshot
The Protease Inhibitor Cystatin C Is Differentially Expressed among Dendritic Cell Populations, but Does Not Control Antigen Presentation
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/b978-0-12-818422-6.00070-8openalex-snapshot
Lung tissue engineering
inferred← citeshttps://doi.org/10.1016/j.cellsig.2020.109588openalex-snapshot
Chronic WNT/β-catenin signaling induces cellular senescence in lung epithelial cells
inferred← citeshttps://doi.org/10.1016/j.stem.2019.12.014openalex-snapshot
Distinct Airway Epithelial Stem Cells Hide among Club Cells but Mobilize to Promote Alveolar Regeneration
inferred← citeshttps://doi.org/10.1038/s41556-020-0542-8openalex-snapshot
Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis
inferred← citeshttps://doi.org/10.1038/s41586-020-2882-8openalex-snapshot
Inhibition of LTβR signalling activates WNT-induced regeneration in lung
inferred← citeshttps://doi.org/10.1038/s41587-020-0591-3openalex-snapshot
Generalizing RNA velocity to transient cell states through dynamical modeling
inferred← citeshttps://doi.org/10.1038/s41598-020-77191-yopenalex-snapshot
Immortalisation of primary human alveolar epithelial lung cells using a non-viral vector to study respiratory bioreactivity in vitro
inferred← citeshttps://doi.org/10.1101/2020.05.28.121541openalex-snapshot
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
inferred← citeshttps://doi.org/10.1101/2020.06.06.136713openalex-snapshot
Human alveolar Type 2 epithelium transdifferentiates into metaplastic KRT5+ basal cells during alveolar repair
inferred← citeshttps://doi.org/10.1101/855155openalex-snapshot
Persistence of a novel regeneration-associated transitional cell state in pulmonary fibrosis
inferred← citeshttps://doi.org/10.1126/sciadv.aba1972openalex-snapshot
Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
inferred← citeshttps://doi.org/10.1136/bmjresp-2023-001762openalex-snapshot
Protective role of the HSP90 inhibitor, STA-9090, in lungs of SARS-CoV-2-infected Syrian golden hamsters
inferred← citeshttps://doi.org/10.1183/13993003.00646-2019openalex-snapshot
A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages
inferred← citeshttps://doi.org/10.1183/13993003.01326-2023openalex-snapshot
Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts
inferred← citeshttps://doi.org/10.1183/16000617.0060-2020openalex-snapshot
Breathing fresh air into respiratory research with single-cell RNA sequencing
inferred← citeshttps://doi.org/10.1183/16000617.0222-2020openalex-snapshot
Lung regeneration: implications of the diseased niche and ageing
inferred← citeshttps://doi.org/10.1183/20734735.0063-2020openalex-snapshot
Early Career Members at the ERS Lung Science Conference 2020: metabolic alterations in lung ageing and disease
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ERS International Congress, Madrid, 2019: highlights from the Basic and Translational Science Assembly
inferred← citeshttps://doi.org/10.1242/dmm.044404openalex-snapshot
Quantitative single-cell interactomes in normal and virus-infected mouse lungs
inferred← citeshttps://doi.org/10.15252/emmm.202012871openalex-snapshot
Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
inferred← citeshttps://doi.org/10.3389/fphys.2020.567675openalex-snapshot
A Novel Fibroblast Reporter Cell Line for in vitro Studies of Pulmonary Fibrosis
inferred← citeshttps://doi.org/10.3389/fphys.2021.649604openalex-snapshot
Chronic E-Cigarette Aerosol Inhalation Alters the Immune State of the Lungs and Increases ACE2 Expression, Raising Concern for Altered Response and Susceptibility to SARS-CoV-2
inferred← citeshttps://doi.org/10.3390/cells11020235openalex-snapshot
Differential LysoTracker Uptake Defines Two Populations of Distal Epithelial Cells in Idiopathic Pulmonary Fibrosis
inferred← citeshttps://doi.org/10.3390/cells11111820openalex-snapshot
Alveolar Basal Cells Differentiate towards Secretory Epithelial- and Aberrant Basaloid-like Cells In Vitro
inferred← citeshttps://doi.org/10.3390/diagnostics16101493openalex-snapshot
Pulmonary Fibrosis Beyond the Lung: Adipose Tissue as a Systemic Modifier of Fibrotic Remodeling
inferred← citeshttps://doi.org/10.3390/ijms21093188openalex-snapshot
Mechanisms of ATII-to-ATI Cell Differentiation during Lung Regeneration
inferred← citeshttps://doi.org/10.3390/ijms23126757openalex-snapshot
Regeneration-Associated Transitional State Cells in Pulmonary Fibrosis
inferred← citeshttps://doi.org/10.3390/ph18060812openalex-snapshot
Epithelial Cell Dysfunction in Pulmonary Fibrosis: Mechanisms, Interactions, and Emerging Therapeutic Targets
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Analysis of single cell gene expression reveals cellular heterogeneity and differentiation dynamics of an healthy airway epithelia
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