Local and systemic responses to SARS-CoV-2 infection in children and adults

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

(2021) Rogan A. Grant et al.   NATURE

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

(2021) Anna C. Aschenbrenner et al.   Genome Medicine

COVID-19 and the human innate immune system

(2021) Joachim L. Schultze et al.   CELL

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

(2021) Christoph Muus et al.   NATURE MEDICINE

Diverse Functional Autoantibodies in Patients with COVID-19

(2021) Eric Y. Wang et al.   NATURE

Single-cell RNA sequencing of blood antigen-presenting cells in severe COVID-19 reveals multi-process defects in antiviral immunity

(2021) Melissa Saichi et al.   NATURE CELL BIOLOGY

Single-cell multi-omics analysis of the immune response in COVID-19

(2021) Emily Stephenson et al.   NATURE MEDICINE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

(2021) Carly G.K. Ziegler et al.   CELL

Deaths from COVID ‘incredibly rare’ among children

(2021) Heidi Ledford   NATURE

Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

(2021) J. Loske et al.   NATURE BIOTECHNOLOGY

A map of transcriptional heterogeneity and regulatory variation in human microglia

(2021) Adam M. H. Young et al.   NATURE GENETICS

Age-related Differences in the Nasal Mucosal Immune Response to SARS-CoV-2

(2021) Clarissa M. Koch et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

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

(2020) Daniel Blanco-Melo et al.   CELL

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

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

(2020) Markus Hoffmann et al.   CELL

Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

(2020) Fengting Yu et al.   CLINICAL INFECTIOUS DISEASES

Nasal Gene Expression of Angiotensin-Converting Enzyme 2 in Children and Adults

(2020) Supinda Bunyavanich et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical and immunological features of severe and moderate coronavirus disease 2019

(2020) Guang Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2020) Mingfeng Liao et al.   NATURE MEDICINE

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

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

(2020) Haynes Heaton et al.   NATURE METHODS

Severe Covid-19

(2020) David A. Berlin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents

(2020) Riccardo Castagnoli et al.   JAMA Pediatrics

Expression of SARS-CoV-2 receptor, ACE2, and TMPRSS2 in the lung airways is lower in children compared to adults and increases due to smoking and COPD

(2020) Narjes Saheb Sharif-Askari et al.   Molecular Therapy-Methods & Clinical Development

A Single-cell Atlas of the Human Healthy Airways

(2020) Marie Deprez et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data

(2020) Gregor Sturm et al.   BIOINFORMATICS

Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19

(2020) Aymeric Silvin et al.   CELL

Distinct stem/progenitor cells proliferate to regenerate the trachea, intrapulmonary airways and alveoli in COVID-19 patients

(2020) Yinshan Fang et al.   CELL RESEARCH

Acute SARS-CoV-2 Infection Impairs Dendritic Cell and T Cell Responses

(2020) Runhong Zhou et al.   IMMUNITY

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

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

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

Single-cell landscape of immunological responses in patients with COVID-19

(2020) Ji-Yuan Zhang et al.   NATURE IMMUNOLOGY

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

(2020) Aaron J. Wilk et al.   NATURE MEDICINE

Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients

(2020) Jérôme Hadjadj et al.   SCIENCE

Type I and III interferons disrupt lung epithelial repair during recovery from viral infection

(2020) Jack Major et al.   SCIENCE

Type III interferons disrupt the lung epithelial barrier upon viral recognition

(2020) Achille Broggi et al.   SCIENCE

Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19

(2020) Jeong Seok Lee et al.   Science Immunology

Distinct clinical and immunological features of SARS–CoV-2–induced multisystem inflammatory syndrome in children

(2020) Pui Y. Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

Type I interferon susceptibility distinguishes SARS-CoV-2 from SARS-CoV.

(2020) Kumari G. Lokugamage et al.   JOURNAL OF VIROLOGY

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

Immune responses to SARS-CoV-2 infection in hospitalized pediatric and adult patients

(2020) Carl A. Pierce et al.   Science Translational Medicine

Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study

(2020) Olivia V Swann et al.   BMJ-British Medical Journal

Influence of aging on deterioration of patients with COVID-19

(2020) Limin Pang et al.   Aging-US

Untuned antiviral immunity in COVID-19 revealed by temporal type I/III interferon patterns and flu comparison

(2020) Ioanna-Evdokia Galani et al.   NATURE IMMUNOLOGY

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

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

Interferon-Stimulated Genes: What Do They All Do?

(2019) John W. Schoggins   Annual Review of Virology

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

(2019) Sandra Ruiz García et al.   DEVELOPMENT

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Human T Cell Development, Localization, and Function throughout Life

(2018) Brahma V. Kumar et al.   IMMUNITY

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Gene expression variability across cells and species shapes innate immunity

(2018) Tzachi Hagai et al.   NATURE

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The developing immune system - from foetus to toddler

(2011) Sofia Ygberg et al.   ACTA PAEDIATRICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS