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

Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures

(2021) Jacob D. Galson et al.   Frontiers in Immunology

Gene-Set Integrative Analysis of Multi-Omics Data Using Tensor-based Association Test

(2021) Sheng-Mao Chang et al.   BIOINFORMATICS

Immune checkpoint inhibition in COVID-19: risks and benefits

(2021) Parmida Sadat Pezeshki et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

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

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

Interleukin-6 Receptor Antagonists in Critically Ill Patients with Covid-19

(2021)   NEW ENGLAND JOURNAL OF MEDICINE

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

(2021) Pierre Bost et al.   Nature Communications

Parallels in Sepsis and COVID-19 Conditions: Implications for Managing Severe COVID-19

(2021) Charles Ochieng’ Olwal et al.   Frontiers in Immunology

Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

(2021) Obbina Abani et al.   LANCET

Diverse Functional Autoantibodies in Patients with COVID-19

(2021) Eric Y. Wang et al.   NATURE

Influenza virus and SARS-CoV-2: pathogenesis and host responses in the respiratory tract

(2021) Tim Flerlage et al.   NATURE REVIEWS MICROBIOLOGY

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

(2021) Florian Wimmers et al.   CELL

Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19

(2021) Maojun You et al.   NATURE CELL BIOLOGY

Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients

(2021) Jonathan Youngs et al.   PLoS Pathogens

Immune checkpoint blockade sensitivity and progression-free survival associates with baseline CD8 + T cell clone size and cytotoxicity

(2021) Robert A. Watson et al.   Science Immunology

Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

(2020) Benjamin P. Fairfax et al.   NATURE MEDICINE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Cytokine release syndrome in severe COVID-19

(2020) John B. Moore et al.   SCIENCE

Prediction models for diagnosis and prognosis of covid-19: systematic review and critical appraisal

(2020) Laure Wynants et al.   BMJ-British Medical Journal

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

(2020) Bo Diao et al.   Frontiers in Immunology

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

Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor

(2020) Immanuel Kwok et al.   IMMUNITY

Single-Cell Sequencing of Peripheral Mononuclear Cells Reveals Distinct Immune Response Landscapes of COVID-19 and Influenza Patients

(2020) Linnan Zhu et al.   IMMUNITY

p38 MAPK inhibition: A promising therapeutic approach for COVID-19

(2020) Joseph M. Grimes et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

(2020) Fengchao Yu et al.   MOLECULAR & CELLULAR PROTEOMICS

Factors associated with COVID-19-related death using OpenSAFELY

(2020) Elizabeth J. Williamson et al.   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

AP-1 imprints a reversible transcriptional programme of senescent cells

(2020) Ricardo Iván Martínez-Zamudio et al.   NATURE CELL BIOLOGY

Philosopher: a versatile toolkit for shotgun proteomics data analysis

(2020) Felipe da Veiga Leprevost et al.   NATURE METHODS

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

(2020) Bo Li et al.   NATURE METHODS

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

(2020)   NEW ENGLAND JOURNAL OF 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

Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

(2020) Philip J. M. Brouwer et al.   SCIENCE

Activation and evasion of type I interferon responses by SARS-CoV-2

(2020) Xiaobo Lei et al.   Nature Communications

Comprehensive mapping of immune perturbations associated with severe COVID-19

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

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

Sepsis and Coronavirus Disease 2019

(2020) Jesús Beltrán-García et al.   CRITICAL CARE MEDICINE

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

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

Kinase inhibition in autoimmunity and inflammation

(2020) Ali A. Zarrin et al.   NATURE REVIEWS DRUG DISCOVERY

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

(2020) Prabhu S. Arunachalam et al.   SCIENCE

MAIT cell activation and dynamics associated with COVID-19 disease severity

(2020) Tiphaine Parrot et al.   Science Immunology

Longitudinal immune profiling reveals key myeloid signatures associated with COVID-19

(2020) Elizabeth R. Mann et al.   Science Immunology

Baricitinib treatment resolves lower-airway macrophage inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques

(2020) Timothy N. Hoang et al.   CELL

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

(2020) Joana P. Bernardes et al.   IMMUNITY

Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19

(2020) Andre C. Kalil et al.   NEW ENGLAND JOURNAL OF MEDICINE

Coronavirus Disease 2019–Associated Thrombosis and Coagulopathy: Review of the Pathophysiological Characteristics and Implications for Antithrombotic Management

(2020) Luis Ortega‐Paz et al.   Journal of the American Heart Association

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer

(2019) Anna Seigal et al.   Journal of the Royal Society Interface

Derivation, Validation, and Potential Treatment Implications of Novel Clinical Phenotypes for Sepsis

(2019) Christopher W. Seymour et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Distinct fibroblast subsets drive inflammation and damage in arthritis

(2019) Adam P. Croft et al.   NATURE

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

(2019) Leticia De Mattos-Arruda et al.   Cell Reports

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

SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses

(2019) Adriana Tomic et al.   JOURNAL OF IMMUNOLOGY

A genetics-led approach defines the drug target landscape of 30 immune-related traits

(2019) Hai Fang et al.   NATURE GENETICS

Analysis of the B cell receptor repertoire in six immune-mediated diseases

(2019) R. J. M. Bashford-Rogers et al.   NATURE

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

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

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

c-Jun overexpression in CAR T cells induces exhaustion resistance

(2019) Rachel C. Lynn et al.   NATURE

Orchestrating single-cell analysis with Bioconductor

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

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

A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

(2018) Nicolai Bache et al.   MOLECULAR & CELLULAR PROTEOMICS

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis

(2018) Hendrik Nolte et al.   Scientific Reports

Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization

(2018) Hadi Fanaee-T et al.   BIOINFORMATICS

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

A complete tool set for molecular QTL discovery and analysis

(2017) Olivier Delaneau et al.   Nature Communications

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types

(2017) Vincent van Unen et al.   Nature Communications

Heparin reduces nonspecific eosinophil staining artifacts in mass cytometry experiments

(2016) Adeeb H. Rahman et al.   CYTOMETRY PART A

Tensor decomposition for multiple-tissue gene expression experiments

(2016) Victoria Hore et al.   NATURE GENETICS

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

(2016) Hai Fang et al.   Genome Medicine

Identification and characterization of VEGF-A-responsive neutrophils expressing CD49d, VEGFR1, and CXCR4 in mice and humans

(2015) S. Massena et al.   BLOOD

Algebraic Systems Biology: A Case Study for the Wnt Pathway

(2015) Elizabeth Gross et al.   BULLETIN OF MATHEMATICAL BIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing

(2015) Mark Klinger et al.   PLoS One

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis

(2014) Alexandre Zougman et al.   PROTEOMICS

Why have clinical trials in sepsis failed?

(2014) John C. Marshall   TRENDS IN MOLECULAR MEDICINE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Viral population analysis and minority-variant detection using short read next-generation sequencing

(2013) S. J. Watson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

(2013) Andrew D. Fernandes et al.   PLoS One

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

A diverse range of gene products are effectors of the type I interferon antiviral response

(2011) John W. Schoggins et al.   NATURE

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

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

Antiinflammatory Effects of the ETS Factor ERG in Endothelial Cells Are Mediated Through Transcriptional Repression of the Interleukin-8 Gene

(2009) Lei Yuan et al.   CIRCULATION RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS