Cell type- and replication stage-specific influenza virus responses in vivo

Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection

(2020) Chang Wang et al.   mBio

Comparative analysis of African and Asian lineage-derived Zika Virus strains reveals differences in activation of and sensitivity to antiviral innate immunity.

(2019) Katharina Esser-Nobis et al.   JOURNAL OF VIROLOGY

Single-cell virus sequencing of influenza infections that trigger innate immunity

(2019) Alistair B. Russell et al.   JOURNAL OF VIROLOGY

Structural snapshots of actively transcribing influenza polymerase

(2019) Tomas Kouba et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

IRF1 Maintains Optimal Constitutive Expression of Antiviral Genes and Regulates the Early Antiviral Response

(2019) Debasis Panda et al.   Frontiers in Immunology

Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1

(2019) Irene Ramos et al.   JOURNAL OF VIROLOGY

An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity

(2019) Nora Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-term surviving influenza infected cells evade CD8+ T cell mediated clearance

(2019) Jessica K. Fiege et al.   PLoS Pathogens

Visualizing the Selectivity and Dynamics of Interferon Signaling In Vivo

(2019) Sebastian A. Stifter et al.   Cell Reports

Interferon-Independent Innate Responses to Cytomegalovirus

(2019) Caroline L. Ashley et al.   Frontiers in Immunology

RIG-I and Other RNA Sensors in Antiviral Immunity

(2018) Kwan T. Chow et al.   Annual Review of Immunology

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

(2018) Vineet D. Menachery et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pulmonary alveolar type I cell population consists of two distinct subtypes that differ in cell fate

(2018) Yanjie Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extreme heterogeneity of influenza virus infection in single cells

(2018) Alistair B Russell et al.   eLife

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Distinct antiviral signatures revealed by the magnitude and round of influenza virus replication in vivo

(2018) Louisa E. Sjaastad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mini viral RNAs act as innate immune agonists during influenza virus infection

(2018) Aartjan J. W. te Velthuis et al.   Nature Microbiology

Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses

(2017) M. J Killip et al.   JOURNAL OF GENERAL VIROLOGY

Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis

(2016) Aartjan J. W. te Velthuis et al.   NATURE REVIEWS MICROBIOLOGY

Club cells surviving influenza A virus infection induce temporary nonspecific antiviral immunity

(2016) Jennifer R. Hamilton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RIG-I Signaling Is Essential for Influenza B Virus-Induced Rapid Interferon Gene Expression

(2015) Sanna M. Mäkelä et al.   JOURNAL OF VIROLOGY

Generation of a variety of stable Influenza A reporter viruses by genetic engineering of the NS gene segment

(2015) Peter Reuther et al.   Scientific Reports

In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus

(2015) Asiel A. Benitez et al.   Cell Reports

Long-term survival of influenza virus infected club cells drives immunopathology

(2014) Nicholas S. Heaton et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Activation of the Interferon Induction Cascade by Influenza A Viruses Requires Viral RNA Synthesis and Nuclear Export

(2014) M. J. Killip et al.   JOURNAL OF VIROLOGY

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

IFITM3 Restricts Influenza A Virus Entry by Blocking the Formation of Fusion Pores following Virus-Endosome Hemifusion

(2014) Tanay M. Desai et al.   PLoS Pathogens

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

(2013) Y. Liao et al.   BIOINFORMATICS

Incoming RNA Virus Nucleocapsids Containing a 5′-Triphosphorylated Genome Activate RIG-I and Antiviral Signaling

(2013) Michaela Weber et al.   Cell Host & Microbe

Visualizing the Beta Interferon Response in Mice during Infection with Influenza A Viruses Expressing or Lacking Nonstructural Protein 1

(2013) C. Kallfass et al.   JOURNAL OF VIROLOGY

Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus

(2013) A. York et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity

(2013) Karla Tapia et al.   PLoS Pathogens

Hepatic STAMP2 decreases hepatitis B virus X protein-associated metabolic deregulation

(2012) Hye Young Kim et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Incoming Influenza A Virus Evades Early Host Recognition, while Influenza B Virus Induces Interferon Expression Directly upon Entry

(2012) P. Osterlund et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

The 3′ Untranslated Regions of Influenza Genomic Sequences Are 5′PPP-Independent Ligands for RIG-I

(2012) William G. Davis et al.   PLoS One

Membrane Perturbation Elicits an IRF3-Dependent, Interferon-Independent Antiviral Response

(2011) R. S. Noyce et al.   JOURNAL OF VIROLOGY

IFITM3 Inhibits Influenza A Virus Infection by Preventing Cytosolic Entry

(2011) Eric M. Feeley et al.   PLoS Pathogens

RIG-I Detects Viral Genomic RNA during Negative-Strand RNA Virus Infection

(2010) Jan Rehwinkel et al.   CELL

Transcription Factor Redundancy Ensures Induction of the Antiviral State

(2010) Sonja Schmid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Double-Stranded RNA Adenosine Deaminase ADAR-1-Induced Hypermutated Genomes among Inactivated Seasonal Influenza and Live Attenuated Measles Virus Vaccines

(2010) R. Suspene et al.   JOURNAL OF VIROLOGY

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

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