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

Hepatitis C virus–specific CD4+ T cell phenotype and function in different infection outcomes

(2020) Diana Y. Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

COVID-19 pneumonia: what has CT taught us?

(2020) Elaine Y P Lee et al.   LANCET INFECTIOUS DISEASES

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

Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets

(2019) Frédéric Pont et al.   NUCLEIC ACIDS RESEARCH

Origin and ontogeny of lung macrophages: from mice to humans

(2019) Elza Evren et al.   IMMUNOLOGY

Developmental control of macrophage function

(2018) Johnny Bonnardel et al.   CURRENT OPINION IN IMMUNOLOGY

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

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage Responses Cause Lethal Pneumonia in SARS-CoV-Infected Mice

(2016) Rudragouda Channappanavar et al.   Cell Host & Microbe

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Virus-Specific Memory CD8 T Cells Provide Substantial Protection from Lethal Severe Acute Respiratory Syndrome Coronavirus Infection

(2014) R. Channappanavar et al.   JOURNAL OF VIROLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

T Cell Responses Are Required for Protection from Clinical Disease and for Virus Clearance in Severe Acute Respiratory Syndrome Coronavirus-Infected Mice

(2010) J. Zhao et al.   JOURNAL OF VIROLOGY