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

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

(2020) Chaolin Huang et al.   LANCET

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

(2020) Bo Shen et al.   CELL

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

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

Functional exhaustion of antiviral lymphocytes in COVID-19 patients

(2020) Meijuan Zheng et al.   Cellular & Molecular Immunology

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

(2020) Yapeng Su et al.   Nature Communications

Liver injury in COVID-19: The current evidence

(2020) Saleh A Alqahtani et al.   United European Gastroenterology Journal

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

(2020) Bo Diao et al.   Frontiers in Immunology

Hypotension, Systemic Inflammatory Response Syndrome, and COVID-19: A Clinical Conundrum

(2020) Dusan Hanidziar et al.   ANESTHESIA AND ANALGESIA

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

Longitudinal analyses reveal immunological misfiring in severe COVID-19

(2020) Carolina Lucas et al.   NATURE

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

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

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

Immunological and inflammatory profiles in mild and severe cases of COVID-19

(2020) Jin-Wen Song et al.   Nature Communications

Comprehensive mapping of immune perturbations associated with severe COVID-19

(2020) Leticia Kuri-Cervantes et al.   Science Immunology

COVID-19 infection alters kynurenine and fatty acid metabolism, correlating with IL-6 levels and renal status

(2020) Tiffany Thomas et al.   JCI Insight

Loss of Bcl-6-Expressing T Follicular Helper Cells and Germinal Centers in COVID-19

(2020) Naoki Kaneko et al.   CELL

An inflammatory cytokine signature predicts COVID-19 severity and survival

(2020) Diane Marie Del Valle 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

Natural killer cell immunotypes related to COVID-19 disease severity

(2020) Christopher Maucourant et al.   Science Immunology

Natural killer cell expression of Ki67 is associated with elevated serum IL-15, disease activity and nephritis in systemic lupus erythematosus

(2019) K. Hudspeth et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

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

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

Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance

(2019) Yapeng Su et al.   PLoS Computational Biology

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

(2019) Peter A. Szabo et al.   Nature Communications

Orchestrating single-cell analysis with Bioconductor

(2019) Robert A. Amezquita et al.   NATURE METHODS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

B cell MHC class II signaling: A story of life and death

(2018) Divya Sai Katikaneni et al.   HUMAN IMMUNOLOGY

KLRG1 + Effector CD8 + T Cells Lose KLRG1, Differentiate into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity

(2018) Dietmar Herndler-Brandstetter et al.   IMMUNITY

Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells

(2018) Bertram Bengsch et al.   IMMUNITY

A Multi-omic Association Study of Trimethylamine N-Oxide

(2018) Ohad Manor et al.   Cell Reports

Ki67 is a Graded Rather than a Binary Marker of Proliferation versus Quiescence

(2018) Iain Miller et al.   Cell Reports

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

The Emerging Role of CD244 Signaling in Immune Cells of the Tumor Microenvironment

(2018) Laura Agresta et al.   Frontiers in Immunology

Differential Requirements for Tcf1 Long Isoforms in CD8+and CD4+T Cell Responses to Acute Viral Infection

(2017) Jodi A. Gullicksrud et al.   JOURNAL OF IMMUNOLOGY

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Polyfunctional natural killer cells with a low activation profile in response to Toll-like receptor 3 activation in HIV-1-exposed seronegative subjects

(2017) Josenilson F. Lima et al.   Scientific Reports

CD8+ T-cell mediated anti-malaria protection induced by malaria vaccines; assessment of hepatic CD8+ T cells by SCBC assay

(2017) Jing Zhou et al.   Human Vaccines & Immunotherapeutics

Cytotoxic CD4 T Cells—Friend or Foe during Viral Infection?

(2017) Jennifer A. Juno et al.   Frontiers in Immunology

The Other Function: Class II-Restricted Antigen Presentation by B Cells

(2017) Lital N. Adler et al.   Frontiers in Immunology

CD57 in human natural killer cells and T-lymphocytes

(2016) Hassen Kared et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Adaptive immunity in the liver

(2016) Zongwen Shuai et al.   Cellular & Molecular Immunology

Lag-3, Tim-3, and TIGIT: Co-inhibitory Receptors with Specialized Functions in Immune Regulation

(2016) Ana C. Anderson et al.   IMMUNITY

Blimp-1/PRDM1 regulates the transcription of human CS1 (SLAMF7) gene in NK and B cells

(2016) Jong R. Kim et al.   IMMUNOBIOLOGY

Early CCR6 expression on B cells modulates germinal centre kinetics and efficient antibody responses

(2016) Dorothea Reimer et al.   IMMUNOLOGY AND CELL BIOLOGY

Fc Receptor–like 5 Expression Distinguishes Two Distinct Subsets of Human Circulating Tissue–like Memory B Cells

(2016) Huifang Li et al.   JOURNAL OF IMMUNOLOGY

Clec4A4 is a regulatory receptor for dendritic cells that impairs inflammation and T-cell immunity

(2016) Tomofumi Uto et al.   Nature Communications

CD23 can negatively regulate B-cell receptor signaling

(2016) Chaohong Liu et al.   Scientific Reports

FOXP3+ regulatory T cells and their functional regulation

(2015) Zhiyuan Li et al.   Cellular & Molecular Immunology

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

(2015) Yao Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

T Follicular Helper Cell Differentiation, Function, and Roles in Disease

(2014) Shane Crotty   IMMUNITY

Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition

(2014) S. Zadran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Multifunctional T-cell Analyses to Study Response and Progression in Adoptive Cell Transfer Immunotherapy

(2013) Chao Ma et al.   Cancer Discovery

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

Progenitor and Terminal Subsets of CD8+ T Cells Cooperate to Contain Chronic Viral Infection

(2012) M. A. Paley et al.   SCIENCE

Pro- and anti-apoptotic CD95 signaling in T cells

(2011) Maren Paulsen et al.   Cell Communication and Signaling

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

The Novel Tuberculosis Vaccine, AERAS-402, Induces Robust and Polyfunctional CD4+and CD8+T Cells in Adults

(2010) Brian Abel et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

IL-7 Enhances Survival of Human CD56bright NK Cells

(2010) Annie Michaud et al.   JOURNAL OF IMMUNOTHERAPY

Kynurenine is an endothelium-derived relaxing factor produced during inflammation

(2010) Yutang Wang et al.   NATURE MEDICINE

Information-theoretic analysis of phenotype changes in early stages of carcinogenesis

(2010) F. Remacle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PD-1 signaling in primary T cells

(2009) James L. Riley   IMMUNOLOGICAL REVIEWS

The Transcriptome of Human Cytotoxic T Cells: Similarities and Disparities Among Allostimulated CD4+CTL, CD8+CTL and NK cells

(2008) L. G. Hidalgo et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Functions of natural killer cells

(2008) Eric Vivier et al.   NATURE IMMUNOLOGY