SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

Collapse induration of alveoli is an ultrastructural finding in a COVID-19 patient

(2021) Matthias Ochs et al.   EUROPEAN RESPIRATORY JOURNAL

6-month consequences of COVID-19 in patients discharged from hospital: a cohort study

(2021) Chaolin Huang et al.   LANCET

Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

(2021) Rogan A. Grant et al.   NATURE

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys

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Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19

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Inference and analysis of cell-cell communication using CellChat

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Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells

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The COVID-19 puzzle: deciphering pathophysiology and phenotypes of a new disease entity

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Tofacitinib in Patients Hospitalized with Covid-19 Pneumonia

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Estimating infectiousness throughout SARS-CoV-2 infection course

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SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals

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Initial CT findings and temporal changes in patients with the novel coronavirus pneumonia (2019-nCoV): a study of 63 patients in Wuhan, China

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Blood monocyte counts as a potential prognostic marker for IPF: Analysis from the Australian IPF registry

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Transforming growth factor–β in tissue fibrosis

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SciPy 1.0: fundamental algorithms for scientific computing in Python

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Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

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Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

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SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

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Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area

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Legumain promotes fibrogenesis in chronic pancreatitis via activation of transforming growth factor β1

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COVID-19: consider cytokine storm syndromes and immunosuppression

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Virological assessment of hospitalized patients with COVID-2019

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Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

(2020) Mingfeng Liao et al.   NATURE MEDICINE

Temporal dynamics in viral shedding and transmissibility of COVID-19

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Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

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Pulmonary fibrosis secondary to COVID-19: a call to arms?

(2020) Paolo Spagnolo et al.   Lancet Respiratory Medicine

Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy

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Chemokine Receptor 2-targeted Molecular Imaging in Pulmonary Fibrosis

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Severe COVID-19 is marked by a dysregulated myeloid cell compartment

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Rapid onset honeycombing fibrosis in spontaneously breathing patient with Covid-19

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Studying the pathophysiology of coronavirus disease 2019: a protocol for the Berlin prospective COVID-19 patient cohort (Pa-COVID-19)

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Fatal pulmonary fibrosis: a post-COVID-19 autopsy case

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Poor survival with extracorporeal membrane oxygenation in acute respiratory distress syndrome (ARDS) due to coronavirus disease 2019 (COVID-19): Pooled analysis of early reports

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Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study

(2020) Luca Carsana et al.   LANCET INFECTIOUS DISEASES

A systematic review of pathological findings in COVID-19: a pathophysiological timeline and possible mechanisms of disease progression

(2020) Samuel B. Polak et al.   MODERN PATHOLOGY

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

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Is a “Cytokine Storm” Relevant to COVID-19?

(2020) Pratik Sinha et al.   JAMA Internal Medicine

COVID-19-associated acute respiratory distress syndrome: is a different approach to management warranted?

(2020) Eddy Fan et al.   Lancet Respiratory Medicine

Mortality in COVID-19 patients with acute respiratory distress syndrome and corticosteroids use: a systematic review and meta-analysis

(2020) Syed Shahzad Hasan et al.   Expert Review of Respiratory Medicine

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

(2020) Christoph B. Messner et al.   Cell Systems

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

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

Severe immunosuppression and not a cytokine storm characterize COVID-19 infections

(2020) Kenneth E. Remy et al.   JCI Insight

CASE REPORT OF SEVERE PULMONARY FIBROSIS AS A SEQUELAE OF COVID-19 INFECTION

(2020) Shiva Arjun et al.   CHEST

COVID-19 and myeloid cells: complex interplay correlates with lung severity

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Extracorporeal membrane oxygenation support in COVID-19: an international cohort study of the Extracorporeal Life Support Organization registry

(2020) Ryan P Barbaro et al.   LANCET

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Neuropilin-1 is a host factor for SARS-CoV-2 infection

(2020) James L. Daly et al.   SCIENCE

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

(2020) Ludovico Cantuti-Castelvetri et al.   SCIENCE

Cytokine elevation in severe and critical COVID-19: a rapid systematic review, meta-analysis, and comparison with other inflammatory syndromes

(2020) Daniel E Leisman et al.   Lancet Respiratory Medicine

Fibrosis: from mechanisms to medicines

(2020) Neil C. Henderson et al.   NATURE

Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19

(2020) Jenny Meinhardt et al.   NATURE NEUROSCIENCE

Lung transplantation for patients with severe COVID-19

(2020) Ankit Bharat et al.   Science Translational Medicine

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study

(2019) Madeleine K D Scott et al.   Lancet Respiratory Medicine

Macrophage-Derived Legumain Promotes Pulmonary Hypertension by Activating the MMP (Matrix Metalloproteinase)-2/TGF (Transforming Growth Factor)-β1 Signaling

(2019) Peiyuan Bai et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

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Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

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ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Elevation of pulmonary CD163+ and CD204+ macrophages is associated with the clinical course of idiopathic pulmonary fibrosis patients

(2019) Takashi Nouno et al.   Journal of Thoracic Disease

Viral Infection Increases the Risk of Idiopathic Pulmonary Fibrosis

(2019) Gaohong Sheng et al.   CHEST

A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signaling in monocyte-derived alveolar macrophages

(2019) Nikita Joshi et al.   EUROPEAN RESPIRATORY JOURNAL

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant

(2019) Boris Bogdanow et al.   Nature Communications

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

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rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics

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Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

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Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

(2018) Karolin Holzwarth et al.   CYTOMETRY PART A

The papain-like protease determines a virulence trait that varies among members of the SARS-coronavirus species

(2018) Daniela Niemeyer et al.   PLoS Pathogens

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

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Deep generative modeling for single-cell transcriptomics

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Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

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(2017) Troy D. Cline et al.   JOURNAL OF GENERAL VIROLOGY

Quantitative Proteomic Approach Identifies Vpr Binding Protein as Novel Host Factor Supporting Influenza A Virus Infections in Human Cells

(2017) Anne Sadewasser et al.   MOLECULAR & CELLULAR PROTEOMICS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Acute Respiratory Distress Syndrome

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QuPath: Open source software for digital pathology image analysis

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Identification of an atypical monocyte and committed progenitor involved in fibrosis

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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

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Macrophage Activation in Acute Exacerbation of Idiopathic Pulmonary Fibrosis

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Macrophages Produce TGF- -Induced ( -ig-h3) following Ingestion of Apoptotic Cells and Regulate MMP14 Levels and Collagen Turnover in Fibroblasts

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Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages

(2014) Christoph Schneider et al.   NATURE IMMUNOLOGY

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Highly Pathogenic H5N1 Influenza A Virus Strains Provoke Heterogeneous IFN-α/β Responses That Distinctively Affect Viral Propagation in Human Cells

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Liver X receptor and peroxisome proliferator-activated receptor as integrators of lipid homeostasis and immunity

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Fiji: an open-source platform for biological-image analysis

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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

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Ly6ChiMonocytes Direct Alternatively Activated Profibrotic Macrophage Regulation of Lung Fibrosis

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Viral Infection in Acute Exacerbation of Idiopathic Pulmonary Fibrosis

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Osteopontin in macrophage function

(2011) Susan R. Rittling   EXPERT REVIEWS IN MOLECULAR MEDICINE

Osteopontin, an oxidant stress sensitive cytokine, up-regulates collagen-I via integrin αVβ3 engagement and PI3K/pAkt/NFκB signaling

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Viral infection and aging as cofactors for the development of pulmonary fibrosis

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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