In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients

(2020) Lirong Zou et al.   NEW ENGLAND JOURNAL OF MEDICINE

Why does COVID-19 disproportionately affect older people?

(2020) Amber L. Mueller et al.   Aging-US

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

(2020) Daniel Blanco-Melo et al.   CELL

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

(2020) Joseph R. Fauver 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

An Infectious cDNA Clone of SARS-CoV-2

(2020) Xuping Xie et al.   Cell Host & Microbe

Clinical and immunological features of severe and moderate coronavirus disease 2019

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

Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit

(2020) Arun K. Nalla et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Triple combination of interferon beta-1b, lopinavir–ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: an open-label, randomised, phase 2 trial

(2020) Ivan Fan-Ngai Hung et al.   LANCET

Virological assessment of hospitalized patients with COVID-2019

(2020) Roman Wölfel et al.   NATURE

Temporal dynamics in viral shedding and transmissibility of COVID-19

(2020) Xi He et al.   NATURE MEDICINE

Effective treatment of severe COVID-19 patients with tocilizumab

(2020) Xiaoling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex-specific clinical characteristics and prognosis of coronavirus disease-19 infection in Wuhan, China: A retrospective study of 168 severe patients

(2020) Yifan Meng et al.   PLoS Pathogens

The immune response to influenza in older humans: beyond immune senescence

(2020) Janet E. McElhaney et al.   Immunity & Ageing

Validation of SARS-CoV-2 detection across multiple specimen types

(2020) Garrett A. Perchetti et al.   JOURNAL OF CLINICAL VIROLOGY

Viral dynamics in mild and severe cases of COVID-19

(2020) Yang Liu et al.   LANCET INFECTIOUS DISEASES

A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape

(2019) Philipp Hubel et al.   NATURE IMMUNOLOGY

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Human Coronavirus: Host-Pathogen Interaction

(2019) To Sing Fung et al.   Annual Review of Microbiology

Age related human T cell subset evolution and senescence

(2019) Mingde Li et al.   Immunity & Ageing

The endonucleolytic RNA cleavage function of nsp1 of Middle East respiratory syndrome coronavirus promotes the production of infectious virus particles in specific human cell lines

(2018) Keisuke Nakagawa et al.   JOURNAL OF VIROLOGY

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage Responses Cause Lethal Pneumonia in SARS-CoV-Infected Mice

(2016) Rudragouda Channappanavar et al.   Cell Host & Microbe

Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

(2016) Alexander L. Greninger et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence

(2016) Giselle M. Boukhaled et al.   Cell Reports

SeXX Matters in Infectious Disease Pathogenesis

(2016) Landon G. vom Steeg et al.   PLoS Pathogens

Middle East Respiratory Syndrome Coronavirus nsp1 Inhibits Host Gene Expression by Selectively Targeting mRNAs Transcribed in the Nucleus while Sparing mRNAs of Cytoplasmic Origin

(2015) Kumari G. Lokugamage et al.   JOURNAL OF VIROLOGY

Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

(2014) Guangchuang Yu et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses

(2014) V. D. Menachery et al.   mBio

The impact of ageing on natural killer cell function and potential consequences for health in older adults

(2013) Jon Hazeldine et al.   AGEING RESEARCH REVIEWS

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

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

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

Mechanisms of Severe Acute Respiratory Syndrome Pathogenesis and Innate Immunomodulation

(2008) M. Frieman et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS