Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19

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

(2021) Xianwen Ren et al.   CELL

A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity

(2021) Sirui Zhou et al.   NATURE MEDICINE

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19

(2021) Md Rabiul Auwul et al.   BRIEFINGS IN BIOINFORMATICS

Integrative Genomics Analysis Reveals a 21q22.11 Locus Contributing Risk to COVID-19

(2021) Yunlong Ma et al.   HUMAN MOLECULAR GENETICS

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

(2021) Akira Cortal et al.   NATURE BIOTECHNOLOGY

Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19

(2021) Liam Gaziano et al.   NATURE MEDICINE

COVID-19 Quarantine Reveals Behavioral Changes Effect on Myopia Progression

(2021) Liangde Xu et al.   OPHTHALMOLOGY

scCODA is a Bayesian model for compositional single-cell data analysis

(2021) M. Büttner et al.   Nature Communications

Single cell sequencing analysis identifies genetics-modulated ORMDL3+ cholangiocytes having higher metabolic effects on primary biliary cholangitis

(2021) Bingyu Xiang et al.   JOURNAL OF NANOBIOTECHNOLOGY

Identification of 34 genes conferring genetic and pharmacological risk for the comorbidity of schizophrenia and smoking behaviors

(2020) Yunlong Ma et al.   Aging-US

Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China

(2020) Zunyou Wu et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

An interactive web-based dashboard to track COVID-19 in real time

(2020) Ensheng Dong et al.   LANCET INFECTIOUS DISEASES

Clinical Characteristics of Coronavirus Disease 2019 in China

(2020) Wei-jie Guan et al.   NEW ENGLAND JOURNAL OF MEDICINE

The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic

(2020)   EUROPEAN JOURNAL OF HUMAN GENETICS

Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area

(2020) Safiya Richardson et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical and immunological features of severe and moderate coronavirus disease 2019

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

SARS-CoV-2: a storm is raging

(2020) Savannah F. Pedersen et al.   JOURNAL OF CLINICAL INVESTIGATION

Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease

(2020) Julien Bryois et al.   NATURE GENETICS

Acute Pulmonary Embolism Associated with COVID-19 Pneumonia Detected by Pulmonary CT Angiography

(2020) Franck Grillet et al.   RADIOLOGY

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

Thrombocytopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A meta-analysis

(2020) Giuseppe Lippi et al.   CLINICA CHIMICA ACTA

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

Genomewide Association Study of Severe Covid-19 with Respiratory Failure

(2020) David Ellinghaus et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2020) Jérôme Hadjadj et al.   SCIENCE

Incidence of thrombotic complications in critically ill ICU patients with COVID-19

(2020) F.A. Klok et al.   THROMBOSIS RESEARCH

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

Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes

(2020) Asaf Poran et al.   Genome Medicine

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

Integrative genomics analysis identifies promising SNPs and genes implicated in tuberculosis risk based on multiple omics datasets

(2020) Mengqiu Xu et al.   Aging-US

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

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

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

Sex differences in immune responses that underlie COVID-19 disease outcomes

(2020) Takehiro Takahashi et al.   NATURE

An inflammatory cytokine signature predicts COVID-19 severity and survival

(2020) Diane Marie Del Valle et al.   NATURE MEDICINE

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

(2020) Maya Ghoussaini et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Prabhu S. Arunachalam et al.   SCIENCE

MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses

(2020) Anna Bruchez et al.   SCIENCE

Integrated genomics analysis highlights important SNPs and genes implicated in moderate-to-severe asthma based on GWAS and eQTL datasets

(2020) Zhouzhou Dong et al.   BMC Pulmonary Medicine

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

Cytokine Storm

(2020) David C. Fajgenbaum et al.   NEW ENGLAND JOURNAL OF MEDICINE

Network analysis and molecular mapping for SARS-CoV-2 to reveal drug targets and repurposing of clinically developed drugs

(2020) Shweta A. More et al.   VIROLOGY

Simultaneous parameter estimation and variable selection via the logit-normal continuous analogue of the spike-and-slab prior

(2019) W. Thomson et al.   Journal of the Royal Society Interface

Integrating predicted transcriptome from multiple tissues improves association detection

(2019) Alvaro N. Barbeira et al.   PLoS Genetics

A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data

(2019) Quan Wang et al.   NATURE NEUROSCIENCE

Interstitial-resident memory CD8+ T cells sustain frontline epithelial memory in the lung

(2019) Shiki Takamura et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CXCR6 regulates localization of tissue-resident memory CD8 T cells to the airways

(2019) Alexander N. Wein et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

(2018) Alvaro N. Barbeira et al.   Nature Communications

Understanding memory CD8 + T cells

(2017) Tasleem Samji et al.   IMMUNOLOGY LETTERS

Origin and differentiation of human memory CD8 T cells after vaccination

(2017) Rama S. Akondy et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

IRF3 and type I interferons fuel a fatal response to myocardial infarction

(2017) Kevin R King et al.   NATURE MEDICINE

DGIdb 3.0: a redesign and expansion of the drug–gene interaction database

(2017) Kelsy C Cotto et al.   NUCLEIC ACIDS RESEARCH

Establishment of a Strong Link Between Smoking and Cancer Pathogenesis through DNA Methylation Analysis

(2017) Yunlong Ma et al.   Scientific Reports

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

(2015)   NATURE NEUROSCIENCE

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

MAGMA: Generalized Gene-Set Analysis of GWAS Data

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

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

STAT2 deficiency and susceptibility to viral illness in humans

(2013) S. Hambleton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Inflammatory Monocytes Activate Memory CD8+ T and Innate NK Lymphocytes Independent of Cognate Antigen during Microbial Pathogen Invasion

(2012) Saïdi M'Homa Soudja et al.   IMMUNITY

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS