Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

(2022) David J. Ahern et al.   CELL

DOCK2 is involved in the host genetics and biology of severe COVID-19

(2022) Ho Namkoong et al.   NATURE

A first update on mapping the human genetic architecture of COVID-19

(2022) et al.   NATURE

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

(2022) Martin Jinye Zhang et al.   NATURE GENETICS

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Ethnic differences in SARS-CoV-2 infection and COVID-19-related hospitalisation, intensive care unit admission, and death in 17 million adults in England: an observational cohort study using the OpenSAFELY platform

(2021) Rohini Mathur et al.   LANCET

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

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

(2021) Benjamin Krämer et al.   IMMUNITY

Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease

(2021) Kevin Mulder et al.   IMMUNITY

Mapping the human genetic architecture of COVID-19

(2021)   NATURE

Protection of BNT162b2 Vaccine Booster against Covid-19 in Israel

(2021) Yinon M. Bar-On et al.   NEW ENGLAND JOURNAL OF MEDICINE

Trans-ethnic genome-wide association study of severe COVID-19

(2021) Peng Wu et al.   Communications Biology

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

(2021) Masahiro Yoshida et al.   NATURE

Differential abundance testing on single-cell data using k-nearest neighbor graphs

(2021) Emma Dann et al.   NATURE BIOTECHNOLOGY

Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus

(2021) Damien J. Downes et al.   NATURE GENETICS

Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors

(2021) Amanda L. Gavin et al.   Nature Communications

MAIT Cells in Health and Disease

(2020) Nicholas M. Provine et al.   Annual Review of Immunology

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

(2020) Chaolin Huang et al.   LANCET

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

COVID-19: Pathogenesis, cytokine storm and therapeutic potential of interferons

(2020) Shivraj Hariram Nile et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Clinical and immunological features of severe and moderate coronavirus disease 2019

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

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

(2020) Gregor Sturm et al.   BIOINFORMATICS

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

(2020) Jonas Schulte-Schrepping et al.   CELL

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

(2020) Aymeric Silvin et al.   CELL

Decrease of non‐classical and intermediate monocyte subsets in severe acute SARS‐CoV ‐2 infection

(2020) Arianna Gatti et al.   CYTOMETRY PART A

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen 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

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

(2020)   NEW ENGLAND JOURNAL OF MEDICINE

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

(2020) Jérôme Hadjadj et al.   SCIENCE

Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19

(2020) Benjamin J. Meckiff et al.   CELL

Human germinal centres engage memory and naive B cells after influenza vaccination

(2020) Jackson S. Turner et al.   NATURE

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

(2020) Maya Ghoussaini et al.   NUCLEIC ACIDS RESEARCH

Predicting cell-to-cell communication networks using NATMI

(2020) Rui Hou et al.   Nature Communications

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19

(2020) Yapeng Su et al.   CELL

Genetic mechanisms of critical illness in Covid-19

(2020) Erola Pairo-Castineira et al.   NATURE

Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine

(2020) Fernando P. Polack et al.   NEW ENGLAND JOURNAL OF MEDICINE

Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients

(2020) Changfu Yao et al.   Cell Reports

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

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

scds: computational annotation of doublets in single-cell RNA sequencing data

(2019) Abha S Bais et al.   BIOINFORMATICS

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

(2019) Dmitry V Bagaev et al.   NUCLEIC ACIDS RESEARCH

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

(2018) Yukinori Okada et al.   Nature Communications

The fate and lifespan of human monocyte subsets in steady state and systemic inflammation

(2017) Amit A. Patel et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Monocyte Conversion During Inflammation and InjuryHighlights

(2016) Rachel M. Kratofil et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

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

Herc5 Attenuates Influenza A Virus by Catalyzing ISGylation of Viral NS1 Protein

(2010) Y. Tang et al.   JOURNAL OF IMMUNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS