Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

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

(2020) Yoshihiko Kobayashi et al.   NATURE CELL BIOLOGY

A transitional stem cell state in the lung

(2020) Jamie M. Verheyden 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

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

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

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

(2020) Arun C. Habermann et al.   Science Advances

LifeTime and improving European healthcare through cell-based interceptive medicine

(2020) Nikolaus Rajewsky et al.   NATURE

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

(2020) Matthew D Young et al.   GigaScience

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

(2019) Ilias Angelidis et al.   Nature Communications

Progress in Understanding and Treating Idiopathic Pulmonary Fibrosis

(2019) Jonathan A. Kropski et al.   Annual Review of Medicine

The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease

(2019) Herbert B Schiller et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Diagnostic Likelihood Thresholds that Define a Working Diagnosis of Idiopathic Pulmonary Fibrosis

(2019) Simon L.F. Walsh et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

Biomarkers of extracellular matrix turnover in patients with idiopathic pulmonary fibrosis given nintedanib (INMARK study): a randomised, placebo-controlled study

(2019) Toby M Maher et al.   Lancet Respiratory Medicine

Plasma Proteome Profiling to detect and avoid sample‐related biases in biomarker studies

(2019) Philipp E Geyer et al.   EMBO Molecular Medicine

Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis

(2019) Richard J Allen et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Viral Infection Increases the Risk of Idiopathic Pulmonary Fibrosis

(2019) Gaohong Sheng et al.   CHEST

18F-AzaFol for Detection of Folate Receptor-β Positive Macrophages in Experimental Interstitial Lung Disease—A Proof-of-Concept Study

(2019) Janine Schniering et al.   Frontiers in Immunology

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Global Gene Expression Analysis in an in vitro Fibroblast Model of Idiopathic Pulmonary Fibrosis Reveals Potential Role for CXCL14/CXCR4

(2018) Luis R. Rodriguez et al.   Scientific Reports

Prognostic and predictive biomarkers for patients with idiopathic pulmonary fibrosis treated with pirfenidone: post-hoc assessment of the CAPACITY and ASCEND trials

(2018) Margaret Neighbors et al.   Lancet Respiratory Medicine

BAL Cell Gene Expression is Indicative of Outcome and Airway Basal Cell Involvement in IPF

(2018) Antje Prasse et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

Visualisation of interstitial lung disease by molecular imaging of integrin αvβ3 and somatostatin receptor 2

(2018) Janine Schniering et al.   ANNALS OF THE RHEUMATIC DISEASES

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial function

(2017) Guoying Yu et al.   NATURE MEDICINE

Transcription factor Etv5 is essential for the maintenance of alveolar type II cells

(2017) Zhen Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CXCL14 is a candidate biomarker for Hedgehog signalling in idiopathic pulmonary fibrosis

(2017) Guiquan Jia et al.   THORAX

An epithelial biomarker signature for idiopathic pulmonary fibrosis: an analysis from the multicentre PROFILE cohort study

(2017) Toby M Maher et al.   Lancet Respiratory Medicine

Daily Home Spirometry: An Effective Tool for Detecting Progression in Idiopathic Pulmonary Fibrosis

(2016) Anne-Marie Russell et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Acute Exacerbation of Idiopathic Pulmonary Fibrosis. An International Working Group Report

(2016) Harold R. Collard et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Age-driven developmental drift in the pathogenesis of idiopathic pulmonary fibrosis

(2016) Moisés Selman et al.   EUROPEAN RESPIRATORY JOURNAL

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Plasma Proteome Profiling to Assess Human Health and Disease

(2016) Philipp E. Geyer et al.   Cell Systems

An Official ATS/ERS/JRS/ALAT Clinical Practice Guideline: Treatment of Idiopathic Pulmonary Fibrosis. An Update of the 2011 Clinical Practice Guideline

(2015) Ganesh Raghu et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

(2015) Evan Z. Macosko et al.   CELL

Perivascular Gli1+ Progenitors Are Key Contributors to Injury-Induced Organ Fibrosis

(2015) Rafael Kramann et al.   Cell Stem Cell

Quantitative Proteomics of Bronchoalveolar Lavage Fluid in Idiopathic Pulmonary Fibrosis

(2015) Matthew W. Foster et al.   JOURNAL OF PROTEOME RESEARCH

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair

(2015) H. B. Schiller et al.   Molecular Systems Biology

Complement System in Lung Disease

(2014) Pankita H. Pandya et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Crosstalk between TGF-β1 and complement activation augments epithelial injury in pulmonary fibrosis

(2014) Hongmei Gu et al.   FASEB JOURNAL

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

Implicating Exudate Macrophages and Ly-6Chigh Monocytes in CCR2-Dependent Lung Fibrosis following Gene-Targeted Alveolar Injury

(2013) J. J. Osterholzer et al.   JOURNAL OF IMMUNOLOGY

Dimerization of complement factor H-related proteins modulates complement activation in vivo

(2013) E. Goicoechea de Jorge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PAI-1 promotes the accumulation of exudate macrophages and worsens pulmonary fibrosis following type II alveolar epithelial cell injury

(2012) John J Osterholzer et al.   JOURNAL OF PATHOLOGY

SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components

(2012) Richard A. Scheltema et al.   JOURNAL OF PROTEOME RESEARCH

Interstitial lung disease in connective tissue disorders

(2012) Aryeh Fischer et al.   LANCET

Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer

(2011) T. R. Cox et al.   Disease Models & Mechanisms

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

Regulated gene expression in cultured type II cells of adult human lung

(2010) Philip L. Ballard et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Plasma biomarker profiles in acute exacerbation of idiopathic pulmonary fibrosis

(2010) Harold R. Collard et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

CARPs enhance p53 turnover by degrading 14-3-3σ and stabilizing MDM2

(2010) Wensheng Yang et al.   CELL CYCLE

68Ga-DOTANOC PET/CT Allows Somatostatin Receptor Imaging in Idiopathic Pulmonary Fibrosis: Preliminary Results

(2010) V. Ambrosini et al.   JOURNAL OF NUCLEAR MEDICINE

Serum Surfactant Protein-A Is a Strong Predictor of Early Mortality in Idiopathic Pulmonary Fibrosis

(2009) Brent W. Kinder et al.   CHEST

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY