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

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

(2020) Chaolin Huang et al.   LANCET

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract

(2020) Yixuan J. Hou et al.   CELL

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

(2020) Daniel Blanco-Melo et al.   CELL

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

(2020) Pierre Bost 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

Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals

(2020) Ling Ni et al.   IMMUNITY

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

(2020) Waradon Sungnak et al.   NATURE MEDICINE

Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing

(2020) Wen Wen et al.   Cell Discovery

Platelet Gene Expression and Function in COVID-19 Patients

(2020) Bhanu Kanth Manne et al.   BLOOD

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

Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells

(2020) Yunlong Cao et al.   CELL

Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly

(2020) Xianwen Ren et al.   CELL RESEARCH

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

Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications

(2020) Divij Mathew et al.   SCIENCE

Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm

(2020) Chuang Guo et al.   Nature Communications

A human circulating immune cell landscape in aging and COVID-19

(2020) Yingfeng Zheng et al.   Protein & Cell

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

CoV-AbDab: the Coronavirus Antibody Database

(2020) Matthew I J Raybould et al.   BIOINFORMATICS

Phenotypical and functional alteration of unconventional T cells in severe COVID-19 patients

(2020) Youenn Jouan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Pulmonary Megakaryocytes in Coronavirus Disease 2019 (COVID-19): Roles in Thrombi and Fibrosis

(2020) Jecko Thachil et al.   SEMINARS IN THROMBOSIS AND HEMOSTASIS

A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors

(2020) Manvendra Singh et al.   Cell Reports

Single-cell Transcriptomic Landscape of Human Blood Cells

(2020) Xiaowei Xie et al.   National Science Review

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

(2020) Yapeng Su et al.   CELL

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

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

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

FPR1 is the plague receptor on host immune cells

(2019) Patrick Osei-Owusu et al.   NATURE

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

An elaborate landscape of the human antibody repertoire against enterovirus 71 infection is revealed by phage display screening and deep sequencing

(2016) Zhe Chen et al.   mAbs

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

(2013) N. Jiang et al.   Science Translational Medicine

Leukocyte recruitment in the brain in sepsis: involvement of the annexin 1-FPR2/ALX anti-inflammatory system

(2012) Felicity N. E. Gavins et al.   FASEB JOURNAL

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

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

Interferon-stimulated genes and their antiviral effector functions

(2011) John W Schoggins et al.   Current Opinion in Virology

XBP1 governs late events in plasma cell differentiation and is not required for antigen-specific memory B cell development

(2009) Derrick J. Todd et al.   JOURNAL OF EXPERIMENTAL MEDICINE