Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

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

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

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens

(2021) Efthymia Papalexi et al.   NATURE GENETICS

Deciphering the state of immune silence in fatal COVID-19 patients

(2021) Pierre Bost et al.   Nature Communications

A neutrophil activation signature predicts critical illness and mortality in COVID-19

(2021) Matthew L. Meizlish et al.   Blood Advances

Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses

(2021) Hong Zheng et al.   IMMUNITY

Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19

(2021) Corleone S. Delaveris et al.   ACS Central Science

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

(2020) Shobana V Stassen et al.   BIOINFORMATICS

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

(2020) Chaolin Huang et al.   LANCET

An immune-cell signature of bacterial sepsis

(2020) Miguel Reyes et al.   NATURE MEDICINE

Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics

(2020) Hamad Alshetaiwi et al.   Science Immunology

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

(2020) Daniel Blanco-Melo et al.   CELL

Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure

(2020) Evangelos J. Giamarellos-Bourboulis et al.   Cell Host & Microbe

A Dynamic Immune Response Shapes COVID-19 Progression

(2020) Eugenia Ziying Ong et al.   Cell Host & Microbe

CD24Fc protects against viral pneumonia in simian immunodeficiency virus-infected Chinese rhesus monkeys

(2020) Ren-Rong Tian et al.   Cellular & Molecular Immunology

Elevated exhaustion levels and reduced functional diversity of T cells in peripheral blood may predict severe progression in COVID-19 patients

(2020) Hong-Yi Zheng et al.   Cellular & Molecular Immunology

COVID-19: A New Virus, but a Familiar Receptor and Cytokine Release Syndrome

(2020) Toshio Hirano et al.   IMMUNITY

Targeting potential drivers of COVID-19: Neutrophil extracellular traps

(2020) Betsy J. Barnes et al.   JOURNAL OF EXPERIMENTAL MEDICINE

COVID-19: consider cytokine storm syndromes and immunosuppression

(2020) Puja Mehta et al.   LANCET

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

(2020) Samuel W. Kazer et al.   NATURE MEDICINE

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

(2020) Mingfeng Liao et al.   NATURE MEDICINE

Reduction and Functional Exhaustion of T Cells in Patients With Coronavirus Disease 2019 (COVID-19)

(2020) Bo Diao et al.   Frontiers in Immunology

Neutrophil Extracellular Traps (NETs) Contribute to Immunothrombosis in COVID-19 Acute Respiratory Distress Syndrome

(2020) Elizabeth A Middleton 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

May IL-17 have a role in COVID-19 infection?

(2020) Matteo Megna et al.   MEDICAL HYPOTHESES

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’

(2020) Enrico Lavezzo et al.   NATURE

Longitudinal analyses reveal immunological misfiring in severe COVID-19

(2020) Carolina Lucas et al.   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection

(2020) Xuemei Xie 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

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

(2020) Divij Mathew et al.   SCIENCE

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

(2020) Jérôme Hadjadj et al.   SCIENCE

Type III interferons disrupt the lung epithelial barrier upon viral recognition

(2020) Achille Broggi et al.   SCIENCE

The Role of Dendritic Cells During Infections Caused by Highly Prevalent Viruses

(2020) Jorge A. Soto et al.   Frontiers in Immunology

Neutrophil extracellular traps in COVID-19

(2020) Yu Zuo et al.   JCI Insight

Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis

(2020) Jennifer G. Wilson et al.   JCI Insight

Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity

(2020) Carolyn Rydyznski Moderbacher et al.   CELL

Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2

(2020) Sandra C.A. Nielsen et al.   Cell Host & Microbe

Unique immunological profile in patients with COVID-19

(2020) Stefania Varchetta et al.   Cellular & Molecular Immunology

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

(2020) Travis K. Hughes et al.   IMMUNITY

Neutrophil extracellular traps infiltrate the lung airway, interstitial, and vascular compartments in severe COVID-19

(2020) Coraline Radermecker et al.   JOURNAL OF EXPERIMENTAL MEDICINE

SARS-CoV-2–triggered neutrophil extracellular traps mediate COVID-19 pathology

(2020) Flavio Protasio Veras et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A dynamic COVID-19 immune signature includes associations with poor prognosis

(2020) Adam G. Laing et al.   NATURE MEDICINE

Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans

(2020) Prabhu S. Arunachalam et al.   SCIENCE

Excessive Neutrophils and Neutrophil Extracellular Traps in COVID-19

(2020) Jun Wang et al.   Frontiers in Immunology

Large-Scale Multi-omic Analysis of COVID-19 Severity

(2020) Katherine A. Overmyer et al.   Cell Systems

Natural killer cell immunotypes related to COVID-19 disease severity

(2020) Christopher Maucourant et al.   Science Immunology

Functional SARS-CoV-2-Specific Immune Memory Persists after Mild COVID-19

(2020) Lauren B. Rodda et al.   CELL

Genetic mechanisms of critical illness in Covid-19

(2020) Erola Pairo-Castineira et al.   NATURE

Profiling of the Human Natural Killer Cell Receptor-Ligand Repertoire

(2020) Elena Vendrame et al.   Jove-Journal of Visualized Experiments

Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome

(2020) Katharina Röltgen et al.   Science Immunology

Bats and Coronaviruses

(2019) Arinjay Banerjee et al.   Viruses-Basel

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

Neutrophil activation and NETosis are the major drivers of thrombosis in heparin-induced thrombocytopenia

(2019) José Perdomo et al.   Nature Communications

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

(2019) Maria Gutierrez-Arcelus et al.   Nature Communications

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

Coexpression of CD163 and CD141 identifies human circulating IL-10-producing dendritic cells (DC-10)

(2019) Michela Comi et al.   Cellular & Molecular Immunology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

DNAM-1 Activating Receptor and Its Ligands: How Do Viruses Affect the NK Cell-Mediated Immune Surveillance during the Various Phases of Infection?

(2019) Loredana Cifaldi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Nuclear hnRNPA2B1 initiates and amplifies the innate immune response to DNA viruses

(2019) Lei Wang et al.   SCIENCE

CD83: Activation Marker for Antigen Presenting Cells and Its Therapeutic Potential

(2019) Ziduo Li et al.   Frontiers in Immunology

The Role of Innate Leukocytes during Influenza Virus Infection

(2019) Prem P. Lamichhane et al.   Journal of Immunology Research

CytoNorm: A Normalization Algorithm for Cytometry Data

(2019) Sofie Van Gassen et al.   CYTOMETRY PART A

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

CD24 and Fc fusion protein protects SIVmac239-infected Chinese rhesus macaque against progression to AIDS

(2018) Ren-Rong Tian et al.   ANTIVIRAL RESEARCH

Dysregulated myelopoiesis and hematopoietic function following acute physiologic insult

(2018) Tyler J. Loftus et al.   CURRENT OPINION IN HEMATOLOGY

Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions

(2018) Maximilien Evrard et al.   IMMUNITY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

The Immunomodulatory Effects of Macrolides—A Systematic Review of the Underlying Mechanisms

(2018) Petra Zimmermann et al.   Frontiers in Immunology

CD161 Defines a Functionally Distinct Subset of Pro-Inflammatory Natural Killer Cells

(2018) Ayako Kurioka et al.   Frontiers in Immunology

Respiratory Mononuclear Phagocytes in Human Influenza A Virus Infection: Their Role in Immune Protection and As Targets of the Virus

(2018) Sindhu Vangeti et al.   Frontiers in Immunology

A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum

(2018) Robert A. Carter et al.   CURRENT BIOLOGY

Monocytes and Macrophages as Viral Targets and Reservoirs

(2018) Ekaterina Nikitina et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Identification of a Human Clonogenic Progenitor with Strict Monocyte Differentiation Potential: A Counterpart of Mouse cMoPs

(2017) Shunsuke Kawamura et al.   IMMUNITY

Regulation of NKG2D-Dependent NK Cell Functions: The Yin and the Yang of Receptor Endocytosis

(2017) Rosa Molfetta et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Extensive diversity of coronaviruses in bats from China

(2017) Xian-Dan Lin et al.   VIROLOGY

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

(2017) Songjoon Baek et al.   Cell Reports

Pyruvate Kinase M2 Is Required for the Expression of the Immune Checkpoint PD-L1 in Immune Cells and Tumors

(2017) Eva M. Palsson-McDermott et al.   Frontiers in Immunology

Acute Respiratory Distress Syndrome Neutrophils Have a Distinct Phenotype and Are Resistant to Phosphoinositide 3-Kinase Inhibition

(2016) Jatinder K. Juss et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

The Chemokine Receptor CX3CR1 Defines Three Antigen-Experienced CD8 T Cell Subsets with Distinct Roles in Immune Surveillance and Homeostasis

(2016) Carmen Gerlach et al.   IMMUNITY

Neutrophil elastase-deficient mice form neutrophil extracellular traps in an experimental model of deep vein thrombosis

(2016) K. Martinod et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

MCEMP1 — a new prognostic and diagnostic biomarker for stroke?

(2016) Heather Wood   Nature Reviews Neurology

Peripheral BloodMCEMP1Gene Expression as a Biomarker for Stroke Prognosis

(2016) Kripa Raman et al.   STROKE

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Mechanotransduction in neutrophil activation and deactivation

(2015) Andrew E. Ekpenyong et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

CDK6 Levels Regulate Quiescence Exit in Human Hematopoietic Stem Cells

(2015) Elisa Laurenti et al.   Cell Stem Cell

The role of FcεRI expressed in dendritic cells and monocytes

(2015) Jeoung-Sook Shin et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses

(2015) Marta Andres-Terre et al.   IMMUNITY

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

(2015) Eli R Zunder et al.   Nature Protocols

The intricate interplay between RNA viruses and NF-κB

(2014) M. Lienhard Schmitz et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Mi-2/NuRD chromatin remodeling complexes regulate B and T-lymphocyte development and function

(2014) Carissa Dege et al.   IMMUNOLOGICAL REVIEWS

CD4 Ligation on Human Blood Monocytes Triggers Macrophage Differentiation and Enhances HIV Infection

(2014) A. Zhen et al.   JOURNAL OF VIROLOGY

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

IFN-γ-Stimulated Neutrophils Suppress Lymphocyte Proliferation through Expression of PD-L1

(2013) Stan de Kleijn et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The role of SRY-related HMG box transcription factor 4 (SOX4) in tumorigenesis and metastasis: friend or foe?

(2012) S J Vervoort et al.   ONCOGENE

Influenza Virus A Infection of Human Monocyte and Macrophage Subpopulations Reveals Increased Susceptibility Associated with Cell Differentiation

(2012) Marieke A. Hoeve et al.   PLoS One

YBX1 expression and function in early hematopoiesis and leukemic cells

(2011) Jasjeet Bhullar et al.   IMMUNOGENETICS

PAD4-Mediated Neutrophil Extracellular Trap Formation Is Not Required for Immunity against Influenza Infection

(2011) Saskia Hemmers et al.   PLoS One

PAD4 is essential for antibacterial innate immunity mediated by neutrophil extracellular traps

(2010) Pingxin Li et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cutting Edge: Bacterial Infection Induces Hematopoietic Stem and Progenitor Cell Expansion in the Absence of TLR Signaling

(2010) Philip O. Scumpia et al.   JOURNAL OF IMMUNOLOGY

Primary Human Tumor Cells Expressing CD155 Impair Tumor Targeting by Down-Regulating DNAM-1 on NK Cells

(2009) M. Carlsten et al.   JOURNAL OF IMMUNOLOGY

CD24 and Siglec-10 Selectively Repress Tissue Damage-Induced Immune Responses

(2009) G.-Y. Chen et al.   SCIENCE

NF- B in the Immune Response of Drosophila

(2009) C. Hetru et al.   Cold Spring Harbor Perspectives in Biology

The Nuclear Factor NF- B Pathway in Inflammation

(2009) T. Lawrence   Cold Spring Harbor Perspectives in Biology

Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis

(2008) Giorgia Salvagiotto et al.   EXPERIMENTAL HEMATOLOGY

The role of the chromatin remodeler Mi-2  in hematopoietic stem cell self-renewal and multilineage differentiation

(2008) T. Yoshida et al.   GENES & DEVELOPMENT