Sources, attribution & editorial method

This site exposes the reviewed knowledge base as a connected scholarly resource.

Corpus and scope

The collection contains 63 publication records, six research areas, 34 themes, 14 discoveries, and 129 explicit publication relationships. It spans 2003–2025 and is a selected corpus, not a complete bibliography or a statement about all current laboratory activity.

The supplied review reports full-text assessment and identifier verification against Crossref and NCBI. This website preserves those records and their source mappings. No original publication PDFs were included in the supplied archive. Open-access links point to PubMed Central where recorded; publisher access and PDF delivery are controlled by the source.

Attribution and evidence

The corpus classifies 37 papers as lab-led, 10 as co-led, 14 as collaborative, and two as training-period work. These classifications follow contribution statements in the reviewed records. Discovery pages distinguish demonstrated findings, interpretation, cross-paper synthesis, and limitations.

Publication relationships are included only when documented in the reviewed records. Sharing a pathogen or a method creates a browsing connection, not a claim of scientific derivation. Directed edges retain their original direction and evidence.

Historical boundaries

Statements that a line of work stopped or was not revisited refer only to the supplied corpus. They do not establish the present status of unpublished or later research. The RNAi and Drosha accounts retain both negative and positive findings and the laboratory’s revisions.

Sources and machine-readable access

Each publication page includes its citation and authoritative identifiers. The data catalog exposes original records, source mappings, controlled vocabulary, and derived relationships. Scientific articles retain their original rights; this site does not redistribute publisher PDFs or grant rights to their contents.

Controlled vocabulary

What this document is

The 63 publication records carry six descriptive fields written independently by eleven contributors, and the fields are inconsistent. Before the filters on this site or the machine-readable data can be trusted, those strings have to be resolved into a controlled vocabulary. This document records the result and the reasoning, so that a later curator can see why two strings were merged and reverse the decision if it was wrong.

This document and data/vocabulary.json were produced from one mapping in a single pass, so the two cannot disagree, and the entries below carry the full mapping in readable form. Every publication list was checked programmatically against the files in content/publications, and every canonical term has at least one publication.

Scale of the problem

Field	Surface forms	Canonical terms
technologies	338	145
pathogens	59	43
viral_families	20	20
host_species	30	21
biological_systems	240	197
key_concepts	542	154

Principles applied

Normalisation was not done by lowercasing and deduplicating, because that gets both directions wrong. Genuinely identical things are sometimes spelled very differently, and genuinely different things are sometimes spelled almost the same.

Things merged despite very different spellings. The small RNA blot appears as "small RNA Northern blot", "small RNA northern blot" and "small RNA Northern blotting" and is one method. Bulk transcriptome profiling appears as "RNA sequencing", "bulk RNA sequencing", "bulk mRNA sequencing", "mRNA sequencing", "messenger RNA sequencing", "mRNA deep sequencing" and "ribosomal RNA-depleted total RNA sequencing", and no record uses the variation to mark a distinction. The BHK line appears as "BHK cells", "BHK-21 cells", "BHK21 cells" and "baby hamster kidney cells". Hosts appear as "dog" and "canine" and "canine cells", and as "golden hamster" and "hamster" and "hamster cells".

Things kept apart despite similar spellings. "northern blot" and "small RNA northern blot" are separate entries, because the second denotes a denaturing polyacrylamide system for species under about 40 nucleotides and the two are used for different claims in the same papers. "Vero cells" and "Vero E6 cells" are separate lines. "coimmunoprecipitation", "Argonaute immunoprecipitation" and "RNA immunoprecipitation" are three different experiments. "SARS-CoV" and "SARS-CoV-2" are two different viruses, and the strings "SARS-CoV-1" and "severe acute respiratory syndrome coronavirus" were folded into the former, not the latter. "in vivo RNAi screening" and "genome-wide CRISPR knockout screening" are both forward genetic screens and remain separate, because they differ in delivery, selection and readout.

Strain strings were folded into the species and preserved as aliases, so that "influenza A virus H5N1 A/Vietnam/1203/04" and "SARS-CoV-2 USA-WA1/2020" remain findable without fragmenting the species counts.

Group terms were kept as entries in their own right. "poxviruses", "herpesviruses", "RNA viruses" and "DNA viruses" appear only in review articles, where they denote categories rather than agents, and merging them into a member species would misattribute a claim.

Platform statements were separated from assays. "SOLiD sequencing", "Illumina MiSeq" and "Illumina deep sequencing" name instruments rather than experiments and sit in a single entry for sequencing platforms, leaving the assay entries to describe what was sequenced.

Engineered derivatives were kept distinct from their parents where the genotype is the point of the experiment, so NoDice HEK293T cells, ADAR1 knockout A549 cells and RELA knockout HeLa-ACE2 cells each have their own entry, while variants that differ only in spelling were merged.

Known ambiguities left in place

Three decisions are judgement calls that a later curator may want to revisit.

The string "luciferase reporter assay" is used in this corpus for two different experiments, a promoter reporter measuring transcriptional induction and a target site reporter measuring post-transcriptional silencing. It is mapped to the promoter reporter entry by default, and several records that use it, notably Perez 2009, use it in the second sense. Where a record spelled the silencing use out, as in "luciferase 3-prime UTR reporter assay" or "reporter-based post-transcriptional silencing assay", it was mapped to the silencing entry instead. The ambiguity cannot be resolved from the frontmatter alone.

The strings "quantitative PCR" and "quantitative RT-PCR" were merged. In every record where the underlying experiment can be identified, the template is RNA and the step is reverse transcription followed by quantitative PCR, so the shorter string appears to be an abbreviation rather than a different assay.

The host annotation "hamster" in the earlier small RNA papers denotes BHK-21 baby hamster kidney cells and not an animal experiment. Merging it with "golden hamster" makes the host count for hamster read higher than the number of studies that used the animal. The animal enters the corpus with Hoagland 2021 and the records that follow it.

A caution about key concepts

The key_concepts field is the least consistent of the six, with 542 surface forms across 63 records and most of them appearing once. Merging there is thematic rather than strictly synonymous, and the resulting 154 entries should be read as a browsing index rather than as an ontology. Grouping "IKK-related kinases", "IKKepsilon", "TBK1" and "virus-activated kinase" into one term is defensible for a filter and wrong for a claim. The alias lists below preserve every original string, so any grouping here can be undone.

Technologies

145 canonical terms from 338 surface forms. Grouped by family, then ordered by number of publications.

Animal, organoid and tissue models

Route-controlled in vivo infection and delivery (in-vivo-infection-route)

Surface forms. "intranasal and intravenous infection of mice", "intranasal delivery", "intranasal infection of hamsters", "intranasal interferon administration", "intranasal mouse infection", "intravenous infection"

Publications. In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Animal transmission models (animal-transmission-model)

Surface forms. "cohousing transmission model", "ferret transmission study", "hamster challenge and transmission models", "nebulized aerosol exposure"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Behavioural and sensory testing (behavioural-and-sensory-testing)

Surface forms. "buried food finding test", "Hargreaves thermal testing", "locomotor beam break assay", "marble burying assay", "von Frey monofilament testing"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Cre-LoxP lineage tracing of infected cells (cre-lox-lineage-tracing)

Surface forms. "Cre-lox lineage tracing", "Cre-LoxP lineage tracing", "tdTomato reporter mice"

Publications. Long-term survival of influenza virus infected club cells drives immunopathology, Synthetic Virology: Building Viruses to Better Understand Them

Directed differentiation of human pluripotent stem cells (hpsc-directed-differentiation)

Surface forms. "directed differentiation of human pluripotent stem cells", "directed trilineage differentiation", "embryoid body cardiomyocyte differentiation", "hPSC ScoreCard assay"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Air-liquid interface culture (ali-culture)

Surface forms. "air-liquid interface culture"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Epithelial barrier permeability measurement (barrier-permeability)

Surface forms. "barrier permeability measurement"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Kidney capsule xenotransplantation (xenotransplantation)

Surface forms. "kidney capsule xenotransplantation"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Organ-on-a-chip microfluidics (organ-on-chip)

Surface forms. "organ-on-a-chip microfluidics"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Organoid culture (organoid-culture)

Surface forms. "organoid culture"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Pharmacokinetic analysis (pharmacokinetics)

Surface forms. "pharmacokinetic analysis"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Pharmacological immunosuppression (immunosuppression-treatment)

Surface forms. "dexamethasone immunosuppression"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Serum transfer with ultraviolet inactivation (serum-transfer)

Surface forms. "serum transfer with ultraviolet inactivation"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Targeted cell ablation (cell-ablation)

Surface forms. "diphtheria toxin receptor depletion"

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

Functional genomics and screening

Site-directed and alanine scanning mutagenesis (site-directed-mutagenesis)

Surface forms. "alanine scanning mutagenesis", "site-directed mutagenesis", "site-directed promoter mutagenesis", "site-directed splice site mutagenesis"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, MicroRNA-mediated species-specific attenuation of influenza A virus, A Small-RNA Enhancer of Viral Polymerase Activity, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Adenoviral vector delivery (adenoviral-vector)

Surface forms. "adenoviral overexpression", "adenoviral reconstitution", "adenoviral vector delivery", "adenoviral vector transduction"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

CRISPR-Cas9 knockout cell lines (crispr-knockout)

Surface forms. "CRISPR Cas9 gene disruption", "CRISPR knockout", "CRISPR knockout cell lines", "CRISPR-Cas9 knockout"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Lentiviral transduction (lentiviral-transduction)

Surface forms. "lentiviral microRNA transduction", "lentiviral transduction", "lentiviral vectors"

Publications. Transcription Factor Redundancy Ensures Induction of the Antiviral State, RNA viruses and the host microRNA machinery, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Conditional and inducible gene knockout (conditional-knockout)

Surface forms. "conditional gene knockout", "conditional knockout with Cre-expressing adenoviral vectors", "tamoxifen-inducible conditional knockout mouse"

Publications. Evidence for a cytoplasmic microprocessor of pri-miRNAs, Drosha as an interferon-independent antiviral factor, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Genome-wide CRISPR-Cas9 knockout screening (genome-wide-crispr-screen)

Surface forms. "GeCKO library", "GeCKOv2 library", "genome-scale CRISPR-Cas9 knockout screening", "genome-wide CRISPR knockout screening", "MAGeCK analysis", "robust rank aggregation"

Publications. Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

In vivo RNAi screening through viral fitness (in-vivo-rnai-screen)

Surface forms. "artificial microRNA libraries", "artificial microRNA library", "in vivo RNAi screening"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Synthetic Virology: Building Viruses to Better Understand Them

Knockout mouse infection (knockout-mice)

Surface forms. "gene knockout mice", "knockout mouse infection"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus

Doxycycline-inducible lentiviral expression (inducible-expression)

Surface forms. "doxycycline-inducible lentiviral expression", "lentiviral doxycycline-inducible expression"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Engineered transcription factor constructs (engineered-tf-constructs)

Surface forms. "chimeric VPR transcriptional activators", "constitutively active IRF7 truncation"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Adeno-associated virus vectors (aav-vector)

Surface forms. "adeno-associated virus vectors"

Publications. RNA viruses and the host microRNA machinery

Agroinfiltration of plant tissue (agroinfiltration)

Surface forms. "agroinfiltration"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

cDNA complementation of knockouts (genetic-complementation)

Surface forms. "cDNA complementation"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

Expression screening of codon-optimised heterologous proteins (heterologous-protein-expression-screen)

Surface forms. "expression screening of codon-optimized proteins"

Publications. Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Head-to-head competition assay (competition-assay)

Surface forms. "in vitro competition assay"

Publications. The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

Single-cell CRISPR screening with ECCITE-seq (single-cell-crispr-screen)

Surface forms. "ECCITE-seq single-cell CRISPR screening"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Trans-complementation infection assay (trans-complementation-assay)

Surface forms. "trans-complementation infection assay"

Publications. The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Genome engineering

Cellular reprogramming to pluripotency (cellular-reprogramming)

Surface forms. "cellular reprogramming with OCT4 SOX2 KLF4 and c-MYC"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells

mSwAP-In iterative genome writing (mswap-in-genome-writing)

Surface forms. "CRISPR-Cas9 assisted homologous recombination", "mSwAP-In genome writing", "yeast assembly of large DNA"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Tetraploid blastocyst complementation (tetraploid-complementation)

Surface forms. "tetraploid blastocyst complementation"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Imaging and histology

Immunofluorescence and confocal microscopy (immunofluorescence-microscopy)

Surface forms. "confocal immunofluorescence", "immunofluorescence", "immunofluorescence confocal microscopy", "immunofluorescence microscopy", "immunofluorescence microscopy and colocalization analysis"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Homologous recombination is an intrinsic defense against antiviral RNA interference, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Histopathology (histopathology)

Surface forms. "haematoxylin and eosin histology", "histology and immunohistochemistry", "histopathology", "lung histology", "lung histopathology scoring"

Publications. Long-term survival of influenza virus infected club cells drives immunopathology, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Immunohistochemistry (immunohistochemistry)

Surface forms. "immunohistochemistry"

Publications. SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, Mouse genome rewriting and tailoring of three important disease loci

RNA in situ hybridisation (rna-in-situ-hybridization)

Surface forms. "RNA in situ hybridization", "RNAscope in situ hybridization"

Publications. Evidence for a cytoplasmic microprocessor of pri-miRNAs, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Cell viability and cell death assays (cell-death-assays)

Surface forms. "cell viability assay", "Sytox and caspase activity cell death assays", "TUNEL staining"

Publications. A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Electron microscopy (electron-microscopy)

Surface forms. "scanning electron microscopy", "transmission electron microscopy"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Fluorescent fusion protein localisation (fluorescent-fusion-localization)

Surface forms. "GFP fusion localization"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway

High-content microscopy (high-content-imaging)

Surface forms. "high-content microscopy"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Lectin staining of surface glycans (lectin-staining)

Surface forms. "lectin staining"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

Immunology assays

Flow cytometry (flow-cytometry)

Surface forms. "flow cytometry", "flow cytometry DNA content analysis", "flow cytometry immune profiling", "flow cytometry with cross-reactive antibodies", "imaging cytometry"

Publications. Engineered RNA viral synthesis of microRNAs, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

ELISA (elisa)

Surface forms. "anti-RBD ELISA", "ELISA"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Mouse genome rewriting and tailoring of three important disease loci

Multiplexed cytokine measurement (multiplex-cytokine-assay)

Surface forms. "cytokine multiplex assay", "ELISA cytokine profiling", "Luminex cytokine panel", "multiplex bead cytokine array", "multiplexed ELISA"

Publications. Long-term survival of influenza virus infected club cells drives immunopathology, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Cell and nuclei sorting (cell-sorting)

Surface forms. "fluorescence-activated cell sorting", "fluorescence-activated nuclei sorting", "magnetic-activated cell sorting"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Long-term survival of influenza virus infected club cells drives immunopathology, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Antigen-specific B cell detection (antigen-specific-b-cell-detection)

Surface forms. "antigen-specific B cell staining", "biotinylated antigen B cell probe"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A diminished immune response underlies age-related SARS-CoV-2 pathologies

Dye dilution cell division tracking (cell-division-tracking)

Surface forms. "CellTrace Violet labeling", "CFSE cell division tracking"

Publications. Evidence for a cytoplasmic microprocessor of pri-miRNAs, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission

Plaque reduction neutralisation test (neutralization-assay)

Surface forms. "plaque reduction neutralization test"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A diminished immune response underlies age-related SARS-CoV-2 pathologies

Adoptive cell transfer (adoptive-transfer)

Surface forms. "adoptive cell transfer"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission

Hemagglutination inhibition assay (hemagglutination-inhibition)

Surface forms. "hemagglutination inhibition assay"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus

Interferon bioassay (interferon-bioassay)

Surface forms. "interferon bioassay"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

MHC class I tetramer staining (tetramer-staining)

Surface forms. "MHC class I tetramer staining"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

MHC epitope prediction (epitope-prediction)

Surface forms. "MHC epitope prediction"

Publications. The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Peptide restimulation of T cells (t-cell-restimulation)

Surface forms. "peptide restimulation assay"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission

T cell hybridoma antigen presentation assay (antigen-presentation-assay)

Surface forms. "CD8 T cell hybridoma antigen presentation assay"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

Proteomics and biochemistry

Luciferase promoter reporter assay (luciferase-promoter-reporter)

Surface forms. "interferon-stimulated response element luciferase reporter", "luciferase promoter reporter assay", "luciferase reporter assay", "luciferase reporter assays", "promoter reporter assays"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, MicroRNA-mediated species-specific attenuation of influenza A virus, Transcription Factor Redundancy Ensures Induction of the Antiviral State, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Immunoblotting (immunoblotting)

Surface forms. "immunoblotting", "western blot", "western blotting"

Publications. A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Type I interferon response impairs differentiation potential of pluripotent stem cells, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Electrophoretic mobility shift assay (emsa)

Surface forms. "electrophoretic mobility shift assay"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors

In vitro reconstitution with purified components (in-vitro-reconstitution)

Surface forms. "cell-free IRF3 dimerization assay", "in vitro minus-strand synthesis assay", "in vitro RNA polymerase assay", "in vitro RNase cleavage assay", "polymerase reconstitution assay", "reconstituted influenza replication complex"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Coimmunoprecipitation (co-ip)

Surface forms. "coimmunoprecipitation", "immunoprecipitation"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors

In vitro kinase assay (in-vitro-kinase-assay)

Surface forms. "in vitro kinase assay", "in vitro kinase assays", "radiolabeled ATP incorporation", "recombinant kinase assay"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Mass spectrometry proteomics (mass-spectrometry-proteomics)

Surface forms. "mass spectrometry", "mass spectrometry proteomics", "quantitative mass spectrometry", "quantitative mass spectrometry proteomics"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Minigenome, minireplicon and replicon reporters (minigenome-assay)

Surface forms. "minigenome assay", "minireplicon systems", "Sindbis replicon and luciferase reporters"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors, Synthetic Virology: Building Viruses to Better Understand Them, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Radiolabelling and translation measurement (translation-measurement)

Surface forms. "in vivo radiolabeling", "puromycin incorporation translation assay", "radiolabeled amino acid tracing"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Phosphoproteomics (phosphoproteomics)

Surface forms. "data-independent acquisition phosphoproteomics", "phosphoproteomics by liquid chromatography mass spectrometry"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Phosphospecific immunoblotting and phosphatase treatment (phospho-immunoblotting)

Surface forms. "phosphatase treatment", "phosphospecific immunoblotting"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

Subcellular fractionation (subcellular-fractionation)

Surface forms. "subcellular fractionation"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity, Drosha as an interferon-independent antiviral factor

Bio-layer interferometry (biolayer-interferometry)

Surface forms. "bio-layer interferometry"

Publications. The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Cellular cholesterol quantification (metabolite-quantification)

Surface forms. "cholesterol quantification"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Chimeric minigene splicing reporters (splicing-reporter)

Surface forms. "chimeric minigene reporters"

Publications. Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Combinatorial peptide substrate specificity profiling (kinase-substrate-profiling)

Surface forms. "combinatorial peptide substrate specificity profiling"

Publications. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Kinase activity inference (kinase-activity-inference)

Surface forms. "kinase activity inference"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Phos-tag gel electrophoresis (phos-tag-electrophoresis)

Surface forms. "Phos-tag gel electrophoresis"

Publications. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Single-molecule FRET (single-molecule-fret)

Surface forms. "single-molecule FRET"

Publications. The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Size-exclusion chromatography (size-exclusion-chromatography)

Surface forms. "size-exclusion chromatography"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

Transcription and translation inhibitor blocks (metabolic-inhibitor-blocks)

Surface forms. "cycloheximide and actinomycin D blocks"

Publications. The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Sequence and population analysis

Deep sequencing of viral populations (viral-population-deep-sequencing)

Surface forms. "deep sequencing", "deep sequencing of barcodes", "deep sequencing of virus populations", "escape mutant sequencing", "whole-genome consensus sequencing"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Synthetic Virology: Building Viruses to Better Understand Them, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Phylogenetic and coalescent analysis (phylogenetics)

Surface forms. "dated coalescent analysis", "maximum likelihood phylogenetics", "phylogenetic analysis", "phylogenetic inference"

Publications. The Evolution of Antiviral Defense Systems, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Amplicon sequencing (amplicon-sequencing)

Surface forms. "amplicon sequencing", "unique molecular identifier amplicon sequencing"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Mouse genome rewriting and tailoring of three important disease loci

Short-read sequencing platforms (short-read-sequencing-platform)

Surface forms. "Illumina deep sequencing", "Illumina MiSeq", "SOLiD sequencing"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

Comparative genomics and conservation analysis (comparative-sequence-analysis)

Surface forms. "comparative genomics", "comparative sequence conservation analysis", "evolutionary parsimony analysis"

Publications. The Evolution of Antiviral Defense Systems, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Population diversity statistics and simulation (population-diversity-statistics)

Surface forms. "Monte Carlo simulation", "Shannon diversity analysis"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Targeted in-solution hybridisation capture (targeted-capture)

Surface forms. "capture sequencing", "targeted in-solution hybridisation capture"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade, Mouse genome rewriting and tailoring of three important disease loci

Ancient DNA extraction (ancient-dna)

Surface forms. "ancient DNA extraction"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Deamination damage authentication (ancient-dna-authentication)

Surface forms. "deamination damage analysis"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Host genetic ancestry analysis (host-ancestry-analysis)

Surface forms. "ADMIXTURE ancestry analysis", "principal component analysis of ancient genomes"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Radiocarbon dating and strontium isotope analysis (archaeometric-dating)

Surface forms. "radiocarbon dating", "strontium isotope analysis"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Shotgun metagenomic sequencing (metagenomic-sequencing)

Surface forms. "shotgun metagenomic sequencing"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Small RNA methods

Small interfering RNA and short hairpin knockdown (sirna-knockdown)

Surface forms. "RNA interference", "RNA interference knockdown", "short hairpin RNAs", "siRNA knockdown", "siRNA transfection", "small interfering RNA knockdown", "small interfering RNA silencing", "small interfering RNA transfection"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Small RNA deep sequencing (small-rna-seq)

Surface forms. "small RNA cloning and sequencing", "small RNA deep sequencing", "small RNA sequencing"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Drosha as an interferon-independent antiviral factor, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Small RNA northern blot (small-rna-northern-blot)

Surface forms. "small RNA Northern blot", "small RNA northern blot", "small RNA Northern blotting"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Drosha as an interferon-independent antiviral factor, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Northern blot (northern-blot)

Surface forms. "northern blot", "Northern blot", "Northern blotting"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, A Small-RNA Enhancer of Viral Polymerase Activity, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Post-transcriptional silencing reporter assay (silencing-reporter-assay)

Surface forms. "luciferase 3-prime UTR reporter assay", "luciferase reporter silencing assay", "reporter silencing assay", "reporter-based post-transcriptional silencing assay"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Evidence for a cytoplasmic microprocessor of pri-miRNAs, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Argonaute immunoprecipitation (argonaute-ip)

Surface forms. "Argonaute 2 immunoprecipitation", "argonaute immunoprecipitation", "Argonaute immunoprecipitation"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs

Locked nucleic acid antisense inhibition (lna-antisense-inhibition)

Surface forms. "locked nucleic acid antagomir inhibition", "locked nucleic acid antimiR inhibition", "locked nucleic acid antisense inhibition"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Primer extension (primer-extension)

Surface forms. "primer extension"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, A Small-RNA Enhancer of Viral Polymerase Activity, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

RNA immunoprecipitation (rna-immunoprecipitation)

Surface forms. "RNA immunoprecipitation"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Stem-loop quantitative RT-PCR for small RNAs (small-rna-rt-qpcr)

Surface forms. "small RNA RT-qPCR", "stem-loop quantitative RT-PCR"

Publications. Engineered RNA viral synthesis of microRNAs, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Synthetic and chemically modified RNA mimetics (synthetic-rna-mimetics)

Surface forms. "synthetic 5-prime triphosphate RNA chemistry", "synthetic modified RNA mimetics"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, A Small-RNA Enhancer of Viral Polymerase Activity

5 prime RACE (five-prime-race)

Surface forms. "5' RACE"

Publications. Engineered RNA viral synthesis of microRNAs

Genetic panels lacking small RNA machinery (rnai-machinery-knockout-cells)

Surface forms. "Argonaute knockout cells", "Dicer deficient cells"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Morpholino knockdown (morpholino-knockdown)

Surface forms. "morpholino knockdown"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

SELEX selection of bound RNA (selex)

Surface forms. "SELEX"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

UV crosslinking immunoprecipitation sequencing (clip-seq)

Surface forms. "UV crosslinking immunoprecipitation sequencing"

Publications. Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Transcriptomics and epigenomics

Bulk RNA sequencing (bulk-rna-seq)

Surface forms. "bulk mRNA sequencing", "bulk RNA sequencing", "messenger RNA sequencing", "mRNA deep sequencing", "mRNA sequencing", "ribosomal RNA-depleted total RNA sequencing", "RNA sequencing"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Type I interferon response impairs differentiation potential of pluripotent stem cells, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Mouse genome rewriting and tailoring of three important disease loci, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Gene ontology and gene set enrichment analysis (pathway-enrichment-analysis)

Surface forms. "gene ontology and gene set enrichment analysis", "gene ontology enrichment", "gene ontology enrichment analysis", "gene set enrichment analysis", "gene set enrichment with Enrichr", "Ingenuity Pathway Analysis"

Publications. microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Single-cell RNA sequencing (single-cell-rna-seq)

Surface forms. "single-cell RNA sequencing"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

ATAC sequencing (atac-seq)

Surface forms. "ATAC sequencing", "ATAC-seq"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, Mouse genome rewriting and tailoring of three important disease loci, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Chromatin immunoprecipitation and CUT&RUN (chip)

Surface forms. "ChIP sequencing", "chromatin immunoprecipitation", "CUT&RUN"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Mouse genome rewriting and tailoring of three important disease loci

Dimensionality reduction and clustering (dimensionality-reduction)

Surface forms. "multidimensional scaling", "network and medoid clustering analysis", "principal component analysis", "sparse principal component analysis"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Cell type deconvolution of bulk transcriptomes (deconvolution)

Surface forms. "cell type deconvolution", "RNA sequencing deconvolution"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Differential expression analysis (differential-expression-analysis)

Surface forms. "differential expression analysis with DESeq2", "differential gene expression analysis"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

Expression microarray (microarray)

Surface forms. "Affymetrix microarray"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State

Promoter motif discovery and enrichment (motif-analysis)

Surface forms. "motif discovery", "motif enrichment analysis"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Transcription factor activity and motif accessibility inference (tf-activity-inference)

Surface forms. "transcription factor activity inference", "transcription factor motif accessibility analysis"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Cross-dataset meta-analysis (meta-analysis)

Surface forms. "cross-dataset meta-analysis"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

De novo transcriptome assembly (de-novo-transcriptome-assembly)

Surface forms. "de novo transcriptome assembly"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity

In situ Hi-C and compartment analysis (in-situ-hi-c)

Surface forms. "hidden Markov model compartment analysis", "in situ Hi-C"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Noncanonical splice junction read analysis (splice-junction-analysis)

Surface forms. "noncanonical junction read analysis"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Viral engineering

Reverse genetics and virus rescue (reverse-genetics)

Surface forms. "alphavirus reverse genetics", "bidirectional plasmid reverse genetics", "flavivirus infectious cDNA clone and virus rescue", "in vitro transcription and electroporation", "influenza A virus reverse genetics", "influenza reverse genetics", "paramyxovirus reverse genetics", "recombinant alphavirus engineering", "recombinant poxvirus engineering", "recombinant Sindbis virus", "recombinant viral vectors", "recombinant VSV reverse genetics", "reverse genetics"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Homologous recombination is an intrinsic defense against antiviral RNA interference, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

MicroRNA target site insertion into viral genomes (mirna-target-site-insertion)

Surface forms. "microRNA target cassette engineering", "microRNA target site attenuation", "microRNA target site engineering", "microRNA target site insertion", "microRNA target site insertion into viral genomes", "microRNA-mediated attenuation"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Homologous recombination is an intrinsic defense against antiviral RNA interference, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Barcoded virus libraries (barcoded-virus-library)

Surface forms. "barcoded virus libraries", "barcoded virus library", "genetic barcoding", "RNA barcoding"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Virus-encoded artificial microRNAs (artificial-mirna)

Surface forms. "artificial microRNA expression", "artificial microRNAs", "virus-encoded artificial microRNA"

Publications. RNA viruses and the host microRNA machinery, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Synthetic Virology: Building Viruses to Better Understand Them

Serial passage and selection (serial-passage)

Surface forms. "in vivo serial passage selection", "serial passage", "serial passage selection"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Homologous recombination is an intrinsic defense against antiviral RNA interference, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

2A peptide recoding of viral segments (2a-recoding)

Surface forms. "2A peptide polycistronic design", "2A ribosome recoding"

Publications. Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Synthetic Virology: Building Viruses to Better Understand Them

Bacterial artificial chromosome recombineering (bac-recombineering)

Surface forms. "bacterial artificial chromosomes", "galK one-step BAC recombineering"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Mouse genome rewriting and tailoring of three important disease loci

Replication-incompetent influenza vector (single-cycle-influenza-vector)

Surface forms. "replication-incompetent virus-like vectors"

Publications. Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs

Deep mutational scanning (deep-mutational-scanning)

Surface forms. "deep mutational scanning"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Fluorescent and luciferase reporter viruses (reporter-virus)

Surface forms. "fluorescent and luciferase reporter viruses"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Neutral red light-sensitive virus labeling (neutral-red-labeling)

Surface forms. "neutral red light-sensitive virus labeling"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

NS1-deleted influenza A virus (delns1-virus)

Surface forms. "influenza A virus lacking NS1"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells

RNA affinity tagging of viral genomes (rna-affinity-tagging)

Surface forms. "RNA affinity tagging"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Small molecule-assisted shutoff of viral proteins (degron-shutoff)

Surface forms. "small molecule-assisted shutoff"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Split NS segment 8 design (split-ns-segment)

Surface forms. "split NS segment design"

Publications. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

Suppressor-deficient virus mutants (vsr-mutant-viruses)

Surface forms. "viral suppressor mutant viruses"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Transposon insertional mutagenesis of viral genomes (transposon-mutagenesis)

Surface forms. "transposon insertional mutagenesis"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

VP55-mediated ablation of the cellular microRNA pool (vp55-mirna-ablation)

Surface forms. "VP55 poly(A) polymerase microRNA degradation"

Publications. microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Virology assays

Quantitative RT-PCR (rt-qpcr)

Surface forms. "quantitative PCR", "quantitative RT-PCR", "real-time quantitative RT-PCR", "RT-PCR", "RT-qPCR"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Type I interferon response impairs differentiation potential of pluripotent stem cells, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Plaque assay and TCID50 titration (plaque-assay)

Surface forms. "plaque and TCID50 titration", "plaque assay", "TCID50 titration"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, MicroRNA-mediated species-specific attenuation of influenza A virus, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Homologous recombination is an intrinsic defense against antiviral RNA interference, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, Mouse genome rewriting and tailoring of three important disease loci

Multicycle growth curves (growth-curve)

Surface forms. "multicycle growth curve", "multicycle growth curves"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Small molecule inhibitor profiling (small-molecule-inhibitor-profiling)

Surface forms. "JAK inhibitor treatment", "pharmacological dose response profiling", "protease inhibition with TPCK", "small molecule kinase inhibition", "small-molecule inhibitor dose response", "small-molecule inhibitor panels"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Pseudotyped entry reporters (pseudotyped-entry-reporter)

Surface forms. "beta-lactamase virus-like particle entry assay", "lentiviral pseudotyping", "pseudotyped virus entry assay", "vesicular stomatitis virus pseudo-entry virus"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Amplification on permissive cells to detect low-level infectious virus (virus-amplification-assay)

Surface forms. "virus amplification on permissive cells"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Pathogens

43 canonical terms from 59 surface forms. Grouped by family, then ordered by number of publications.

Adenoviridae

Adenovirus (adenovirus)

Surface forms. "adenovirus", "adenovirus type 5"

Publications. RNA viruses and the host microRNA machinery, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Arenaviridae

Lassa virus (lassa-virus)

Surface forms. "Lassa virus"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Bornaviridae

Borna disease virus (borna-disease-virus)

Surface forms. "Borna disease virus"

Publications. The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

Coronaviridae

SARS-CoV-2 (sars-cov-2)

Surface forms. "SARS-CoV-2", "SARS-CoV-2 B.1.351 beta variant", "SARS-CoV-2 USA-WA1/2020"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, Mouse genome rewriting and tailoring of three important disease loci

SARS-CoV (sars-cov)

Surface forms. "SARS-CoV", "SARS-CoV-1", "severe acute respiratory syndrome coronavirus"

Publications. SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Human coronavirus 229E (hcov-229e)

Surface forms. "human coronavirus 229E"

Publications. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Human coronavirus OC43 (hcov-oc43)

Surface forms. "human coronavirus OC43"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

MERS-CoV (mers-cov)

Surface forms. "MERS-CoV"

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

Dicistroviridae

Drosophila C virus (drosophila-c-virus)

Surface forms. "Drosophila C virus"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Filoviridae

Ebola virus (ebola-virus)

Surface forms. "Ebola virus"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Flaviviridae

Dengue virus (dengue-virus)

Surface forms. "dengue virus", "dengue virus serotype 2"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, RNA viruses and the host microRNA machinery

Zika virus (zika-virus)

Surface forms. "Zika virus"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Hepatitis C virus (hcv)

Surface forms. "hepatitis C virus"

Publications. RNA viruses and the host microRNA machinery

Langat virus (langat-virus)

Surface forms. "Langat virus"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

West Nile virus (west-nile-virus)

Surface forms. "West Nile virus"

Publications. RNA viruses and the host microRNA machinery

Hepadnaviridae

Hepatitis B virus (hbv)

Surface forms. "hepatitis B virus"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Herpesviridae

Herpesviruses as a group (herpesviruses)

Surface forms. "herpesviruses"

Publications. RNA viruses and the host microRNA machinery

Human cytomegalovirus (hcmv)

Surface forms. "human cytomegalovirus"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Nodaviridae

Nodamura virus (nodamura-virus)

Surface forms. "nodamura virus"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Orthomyxoviridae

Influenza A virus (influenza-a-virus)

Surface forms. "influenza A virus", "influenza A virus H1N1 A/Puerto Rico/8/34", "influenza A virus H1N1 A/Puerto Rico/8/34 NS1 R38A K41A", "influenza A virus H3N2", "influenza A virus H5N1", "influenza A virus H5N1 A/Vietnam/1203/04", "influenza A/California/04/2009", "influenza A/California/04/2009 (H1N1pdm09)", "influenza A/WSN/33"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Engineered RNA viral synthesis of microRNAs, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Type I interferon response impairs differentiation potential of pluripotent stem cells, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Infectious salmon anemia virus (infectious-salmon-anemia-virus)

Surface forms. "infectious salmon anemia virus"

Publications. Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Influenza B virus (influenza-b-virus)

Surface forms. "influenza B virus"

Publications. Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Paramyxoviridae

Sendai virus (sendai-virus)

Surface forms. "Sendai virus"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Human parainfluenza virus 3 (hpiv3)

Surface forms. "human parainfluenza virus 3", "human parainfluenza virus type 3"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Measles virus (measles-virus)

Surface forms. "measles virus"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Parvoviridae

Human parvovirus B19 (parvovirus-b19)

Surface forms. "human parvovirus B19"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Picornaviridae

Encephalomyocarditis virus (emcv)

Surface forms. "encephalomyocarditis virus"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Poliovirus (poliovirus)

Surface forms. "poliovirus"

Publications. RNA viruses and the host microRNA machinery, Homologous recombination is an intrinsic defense against antiviral RNA interference, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Coxsackievirus B3 (coxsackievirus-b3)

Surface forms. "coxsackievirus B3"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Pneumoviridae

Respiratory syncytial virus (rsv)

Surface forms. "human respiratory syncytial virus", "respiratory syncytial virus"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Poxviridae

Vaccinia virus (vaccinia-virus)

Surface forms. "vaccinia virus"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Amsacta moorei entomopoxvirus (amsacta-entomopoxvirus)

Surface forms. "Amsacta moorei entomopoxvirus"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism

Poxviruses as a group (poxviruses)

Surface forms. "poxviruses"

Publications. RNA viruses and the host microRNA machinery

Retroviridae

Bovine leukaemia virus (blv)

Surface forms. "bovine leukaemia virus"

Publications. RNA viruses and the host microRNA machinery

Human immunodeficiency virus 1 (hiv-1)

Surface forms. "human immunodeficiency virus 1"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Rhabdoviridae

Vesicular stomatitis virus (vsv)

Surface forms. "vesicular stomatitis virus"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Togaviridae

Sindbis virus (sindbis-virus)

Surface forms. "Sindbis virus"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference

Ross River virus (ross-river-virus)

Surface forms. "Ross River virus"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Semliki Forest virus (semliki-forest-virus)

Surface forms. "Semliki Forest virus"

Publications. Homologous recombination is an intrinsic defense against antiviral RNA interference

Tombusviridae

Turnip crinkle virus (turnip-crinkle-virus)

Surface forms. "turnip crinkle virus"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Group

DNA viruses as a group (dna-viruses)

Surface forms. "DNA viruses"

Publications. The Evolution of Antiviral Defense Systems

RNA viruses as a group (rna-viruses)

Surface forms. "RNA viruses"

Publications. The Evolution of Antiviral Defense Systems

Phage

Bacteriophage (bacteriophage)

Surface forms. "bacteriophage"

Publications. The Evolution of Antiviral Defense Systems

Viral families

20 canonical terms from 20 surface forms. Grouped by family, then ordered by number of publications.

Double-stranded DNA

Poxviridae (poxviridae)

Surface forms. "Poxviridae"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Adenoviridae (adenoviridae)

Surface forms. "Adenoviridae"

Publications. RNA viruses and the host microRNA machinery, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Herpesviridae (herpesviridae)

Surface forms. "Herpesviridae"

Publications. RNA viruses and the host microRNA machinery, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Negative-sense nonsegmented RNA

Rhabdoviridae (rhabdoviridae)

Surface forms. "Rhabdoviridae"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Paramyxoviridae (paramyxoviridae)

Surface forms. "Paramyxoviridae"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Pneumoviridae (pneumoviridae)

Surface forms. "Pneumoviridae"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Filoviridae (filoviridae)

Surface forms. "Filoviridae"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Bornaviridae (bornaviridae)

Surface forms. "Bornaviridae"

Publications. The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

Negative-sense segmented RNA

Orthomyxoviridae (orthomyxoviridae)

Surface forms. "Orthomyxoviridae"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Engineered RNA viral synthesis of microRNAs, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Type I interferon response impairs differentiation potential of pluripotent stem cells, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Arenaviridae (arenaviridae)

Surface forms. "Arenaviridae"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Positive-sense RNA

Coronaviridae (coronaviridae)

Surface forms. "Coronaviridae"

Publications. SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, Mouse genome rewriting and tailoring of three important disease loci

Togaviridae (togaviridae)

Surface forms. "Togaviridae"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference

Picornaviridae (picornaviridae)

Surface forms. "Picornaviridae"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, RNA viruses and the host microRNA machinery, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Flaviviridae (flaviviridae)

Surface forms. "Flaviviridae"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, RNA viruses and the host microRNA machinery, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Dicistroviridae (dicistroviridae)

Surface forms. "Dicistroviridae"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Nodaviridae (nodaviridae)

Surface forms. "Nodaviridae"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Tombusviridae (tombusviridae)

Surface forms. "Tombusviridae"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Reverse-transcribing

Retroviridae (retroviridae)

Surface forms. "Retroviridae"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, RNA viruses and the host microRNA machinery

Hepadnaviridae (hepadnaviridae)

Surface forms. "Hepadnaviridae"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Single-stranded DNA

Parvoviridae (parvoviridae)

Surface forms. "Parvoviridae"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Host species

21 canonical terms from 30 surface forms. Grouped by family, then ordered by number of publications.

Archaeon

Archaea (archaea)

Surface forms. "archaea"

Publications. The Evolution of Antiviral Defense Systems

Bird

Chicken (chicken)

Surface forms. "chicken", "chicken embryo"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Engineered RNA viral synthesis of microRNAs, RNA viruses and the host microRNA machinery, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Fish

Zebrafish (zebrafish)

Surface forms. "zebrafish"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Fungus

Yeast (yeast)

Surface forms. "yeast"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Group

Chordates as a group (chordates)

Surface forms. "chordates"

Publications. The Evolution of Antiviral Defense Systems

Invertebrate

Drosophila melanogaster (drosophila)

Surface forms. "Drosophila", "Drosophila melanogaster"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Drosha as an interferon-independent antiviral factor, The Evolution of Antiviral Defense Systems, RNase III nucleases from diverse kingdoms serve as antiviral effectors

Amsacta moorei (amsacta-moorei)

Surface forms. "Amsacta moorei"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism

Insects as a group (insect)

Surface forms. "insect"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Mosquito (mosquito)

Surface forms. "mosquito"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination

Nematode (nematode)

Surface forms. "nematode"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Mammal

Human (human)

Surface forms. "human", "human cells"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, The Evolution of Antiviral Defense Systems, RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Type I interferon response impairs differentiation potential of pluripotent stem cells, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Mouse genome rewriting and tailoring of three important disease loci, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Mouse (mouse)

Surface forms. "mouse"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, The Evolution of Antiviral Defense Systems, RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Homologous recombination is an intrinsic defense against antiviral RNA interference, Type I interferon response impairs differentiation potential of pluripotent stem cells, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Mouse genome rewriting and tailoring of three important disease loci, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Golden hamster (golden-hamster)

Surface forms. "golden hamster", "hamster", "hamster cells"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Mouse genome rewriting and tailoring of three important disease loci

Dog (dog)

Surface forms. "canine", "canine cells", "dog"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Engineered RNA viral synthesis of microRNAs, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

African green monkey (african-green-monkey)

Surface forms. "African green monkey", "African green monkey cells"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Ferret (ferret)

Surface forms. "ferret"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Synthetic Virology: Building Viruses to Better Understand Them, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Guinea pig (guinea-pig)

Surface forms. "guinea pig"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host

Plant

Plants as a group (plants)

Surface forms. "plant", "plants"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, The Evolution of Antiviral Defense Systems

Arabidopsis thaliana (arabidopsis)

Surface forms. "Arabidopsis thaliana"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Nicotiana benthamiana (nicotiana-benthamiana)

Surface forms. "Nicotiana benthamiana"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Prokaryote

Bacteria (bacteria)

Surface forms. "bacteria"

Publications. The Evolution of Antiviral Defense Systems

Biological systems

197 canonical terms from 240 surface forms. Grouped by family, then ordered by number of publications.

Animal or egg system

Embryonated chicken eggs (embryonated-eggs)

Surface forms. "embryonated chicken eggs"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Engineered RNA viral synthesis of microRNAs, RNA viruses and the host microRNA machinery, Long-term survival of influenza virus infected club cells drives immunopathology, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Synthetic Virology: Building Viruses to Better Understand Them

Golden hamster (golden-hamster-animal)

Surface forms. "golden hamster"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Mouse genome rewriting and tailoring of three important disease loci

Laboratory mice (mouse-animal)

Surface forms. "BALB/c mice", "C57BL/6 mice", "C57BL/6 mouse", "mouse", "mouse models", "suckling mice"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Synthetic Virology: Building Viruses to Better Understand Them

Ferret (ferret-animal)

Surface forms. "ferret"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Synthetic Virology: Building Viruses to Better Understand Them

Guinea pig (guinea-pig)

Surface forms. "guinea pig"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host

LoxP reporter mice (loxp-reporter-mice)

Surface forms. "LoxP reporter mice"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

SCID-beige mouse xenograft (scid-beige-mouse-xenograft)

Surface forms. "SCID-beige mouse xenograft"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Zebrafish embryos (zebrafish-embryos)

Surface forms. "zebrafish embryos"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Cell-free or reconstituted

Cell-free in vitro polymerase reactions (cell-free-in-vitro-polymerase-reactions)

Surface forms. "cell-free in vitro polymerase reactions"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity

Cell-free mitochondrial fraction assay (cell-free-mitochondrial-fraction-assay)

Surface forms. "cell-free mitochondrial fraction assay"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

In vitro replicase assays (in-vitro-replicase-assays)

Surface forms. "in vitro replicase assays"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Purified recombinant influenza A virus polymerase (purified-recombinant-influenza-a-virus-polymerase)

Surface forms. "purified recombinant influenza A virus polymerase"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity

Recombinant protein in vitro kinase reactions (recombinant-protein-in-vitro-kinase-reactions)

Surface forms. "recombinant protein in vitro kinase reactions"

Publications. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Recombinant purified influenza RNA polymerase (recombinant-purified-influenza-rna-polymerase)

Surface forms. "recombinant purified influenza RNA polymerase"

Publications. The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Engineered cell line

ACE2-expressing A549 cells (a549-ace2)

Surface forms. "A549 cells expressing ACE2", "A549-ACE2 cells", "ACE2-expressing A549 cells"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Huh7.5-ACE2 cells (huh7-5-ace2-cells)

Surface forms. "Huh7.5-ACE2 cells"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

A549-Dual reporter cells (a549-dual-reporter-cells)

Surface forms. "A549-Dual reporter cells"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Cas9-expressing A549 clonal line (cas9-expressing-a549-clonal-line)

Surface forms. "Cas9-expressing A549 clonal line"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

Complementing MDCK cells (mdck-complementing)

Surface forms. "HA and NP complementing MDCK cells", "HA-complementing MDCK cells"

Publications. A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs

DBT-mACE2 cells (dbt-mace2-cells)

Surface forms. "DBT-mACE2 cells"

Publications. SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

HEK293T cells stably expressing IRF7 (hek293t-cells-stably-expressing-irf7)

Surface forms. "HEK293T cells stably expressing IRF7"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

HeLa cells expressing E1A (hela-cells-expressing-e1a)

Surface forms. "HeLa cells expressing E1A"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

HeLa-ACE2 cells (hela-ace2-cells)

Surface forms. "HeLa-ACE2 cells"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

K18-hACE2 mouse (k18-hace2-mouse)

Surface forms. "K18-hACE2 mouse"

Publications. Mouse genome rewriting and tailoring of three important disease loci

MDCK cells expressing miR-124 (mdck-cells-expressing-mir-124)

Surface forms. "MDCK cells expressing miR-124"

Publications. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response

MiR-122-expressing MRC-5 fibroblasts (mir-122-expressing-mrc-5-fibroblasts)

Surface forms. "miR-122-expressing MRC-5 fibroblasts"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

MiR-142-expressing MDCK cells (mir-142-expressing-mdck-cells)

Surface forms. "miR-142-expressing MDCK cells"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

MiR-142-expressing MRC-5 fibroblasts (mir-142-expressing-mrc-5-fibroblasts)

Surface forms. "miR-142-expressing MRC-5 fibroblasts"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Engineered knockout line

Dicer-deficient fibroblasts (dicer-deficient-fibroblasts)

Surface forms. "Dicer conditional knockout fibroblasts", "Dicer knockout fibroblasts", "Dicer-deficient fibroblasts", "Dicer-deficient murine fibroblasts", "Dicer1-deficient fibroblasts"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Homologous recombination is an intrinsic defense against antiviral RNA interference

NoDice Dicer-deficient HEK293T cells (nodice-cells)

Surface forms. "HEK-293T NoDice cells", "NoDice 293T cells", "NoDice Dicer-deficient cells", "NoDice Dicer-deficient HEK293T cells", "NoDice HEK293T cells"

Publications. microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Drosha and Dicer double knockout HEK293T cells (drosha-dicer-dko-293t)

Surface forms. "Drosha and Dicer deficient 293T cells", "Drosha and Dicer double knockout HEK293T cells"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Ifnar1 and Il28r double knockout mice (ifnar1-and-il28r-double-knockout-mice)

Surface forms. "Ifnar1 and Il28r double knockout mice"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

ADAR1 knockout A549 cells (adar1-knockout-a549-cells)

Surface forms. "ADAR1 knockout A549 cells"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Argonaute knockout fibroblasts (argonaute-knockout-fibroblasts)

Surface forms. "Argonaute knockout fibroblasts"

Publications. Homologous recombination is an intrinsic defense against antiviral RNA interference

Conditional knockout fibroblast lines (conditional-knockout-fibroblast-lines)

Surface forms. "conditional knockout fibroblast lines"

Publications. Evidence for a cytoplasmic microprocessor of pri-miRNAs

CRISPR knockout clonal lines (crispr-knockout-clonal-lines)

Surface forms. "CRISPR knockout clonal lines"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

DGCR8-deficient fibroblasts (dgcr8-deficient-fibroblasts)

Surface forms. "DGCR8-deficient fibroblasts"

Publications. Noncanonical cytoplasmic processing of viral microRNAs

G3BP1 and G3BP2 knockout cells (g3bp1-and-g3bp2-knockout-cells)

Surface forms. "G3BP1 and G3BP2 knockout cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Ifnar1 knockout mice (ifnar1-knockout-mice)

Surface forms. "Ifnar1 knockout mice"

Publications. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response

Ifnar1-deficient fibroblasts (ifnar1-deficient-fibroblasts)

Surface forms. "Ifnar1-deficient fibroblasts"

Publications. Noncanonical cytoplasmic processing of viral microRNAs

Ikbke knockout mice (ikbke-knockout-mice)

Surface forms. "Ikbke knockout mice"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

Ikbke-deficient mice (ikbke-deficient-mice)

Surface forms. "Ikbke-deficient mice"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity

Irf3 and Irf7 double knockout fibroblasts (irf3-and-irf7-double-knockout-fibroblasts)

Surface forms. "Irf3 and Irf7 double knockout fibroblasts"

Publications. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response

Map3k8 knockout fibroblasts (map3k8-knockout-fibroblasts)

Surface forms. "Map3k8 knockout fibroblasts"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

MAVS knockout cells (mavs-knockout-cells)

Surface forms. "MAVS knockout cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

MAVS-deficient A549 cells (mavs-deficient-a549-cells)

Surface forms. "MAVS-deficient A549 cells"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

MDA5-deficient A549 cells (mda5-deficient-a549-cells)

Surface forms. "MDA5-deficient A549 cells"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

PKR knockout cells (pkr-knockout-cells)

Surface forms. "PKR knockout cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Rag1 deficient mice (rag1-deficient-mice)

Surface forms. "Rag1 deficient mice"

Publications. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

RELA knockout HeLa-ACE2 cells (rela-knockout-hela-ace2-cells)

Surface forms. "RELA knockout HeLa-ACE2 cells"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

RIG-I-deficient A549 cells (rig-i-deficient-a549-cells)

Surface forms. "RIG-I-deficient A549 cells"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

RNase III deficient fibroblasts (rnase-iii-deficient-fibroblasts)

Surface forms. "RNase III deficient fibroblasts"

Publications. Homologous recombination is an intrinsic defense against antiviral RNA interference

RNase L knockout cells (rnase-l-knockout-cells)

Surface forms. "RNase L knockout cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Stat1 deficient mice (stat1-deficient-mice)

Surface forms. "Stat1 deficient mice"

Publications. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

STAT1 knockout A549 cells (stat1-knockout-a549-cells)

Surface forms. "STAT1 knockout A549 cells"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Stat1-deficient embryonic fibroblasts (stat1-deficient-embryonic-fibroblasts)

Surface forms. "Stat1-deficient embryonic fibroblasts"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity

U3A STAT1-deficient cells (u3a-stat1-deficient-cells)

Surface forms. "U3A STAT1-deficient cells"

Publications. Transcription Factor Redundancy Ensures Induction of the Antiviral State

UBAP2L knockout cells (ubap2l-knockout-cells)

Surface forms. "UBAP2L knockout cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Zfx conditional knockout primary fibroblasts (zfx-conditional-knockout-primary-fibroblasts)

Surface forms. "Zfx conditional knockout primary fibroblasts"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication

General

Mammalian cell culture in general (mammalian-cell-culture)

Surface forms. "mammalian cell culture", "mammalian somatic cells"

Publications. RNA viruses and the host microRNA machinery, The Evolution of Antiviral Defense Systems, Synthetic Virology: Building Viruses to Better Understand Them

Human clinical or post-mortem material

Archaeological human dental remains (archaeological-human-dental-remains)

Surface forms. "archaeological human dental remains"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

COVID-19 lung autopsy tissue (covid-19-lung-autopsy-tissue)

Surface forms. "COVID-19 lung autopsy tissue"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Ferret nasal wash and trachea (ferret-nasal-wash-and-trachea)

Surface forms. "ferret nasal wash and trachea"

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

Human COVID-19 cadaver lung tissue (human-covid-19-cadaver-lung-tissue)

Surface forms. "human COVID-19 cadaver lung tissue"

Publications. A diminished immune response underlies age-related SARS-CoV-2 pathologies

Human olfactory epithelium autopsy tissue (human-olfactory-epithelium-autopsy-tissue)

Surface forms. "human olfactory epithelium autopsy tissue"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Human serum (human-serum)

Surface forms. "human serum"

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

Nasal wash (nasal-wash)

Surface forms. "nasal wash"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host

Parietal bone (parietal-bone)

Surface forms. "parietal bone"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Peripheral blood mononuclear cells (peripheral-blood-mononuclear-cells)

Surface forms. "peripheral blood mononuclear cells"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission

Phalanx (phalanx)

Surface forms. "phalanx"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Post-mortem human lung (post-mortem-human-lung)

Surface forms. "post-mortem human lung"

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

Post-mortem human ocular surface tissue (post-mortem-human-ocular-surface-tissue)

Surface forms. "post-mortem human ocular surface tissue"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium

Post-mortem human olfactory bulb and olfactory epithelium (post-mortem-human-olfactory-bulb-and-olfactory-epithelium)

Surface forms. "post-mortem human olfactory bulb and olfactory epithelium"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery

Stool (stool)

Surface forms. "stool"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Tooth enamel (tooth-enamel)

Surface forms. "tooth enamel"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Whole blood (whole-blood)

Surface forms. "whole blood"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Immortalised cell line

HEK293 and HEK293T cells (hek293)

Surface forms. "293T cells", "HEK-293T cells", "HEK293 and 293T cells", "HEK293 cells", "HEK293FT cells", "HEK293T cells"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Type I interferon response impairs differentiation potential of pluripotent stem cells, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

A549 cells (a549)

Surface forms. "A549 cells"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, A Small-RNA Enhancer of Viral Polymerase Activity, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Homologous recombination is an intrinsic defense against antiviral RNA interference, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

MDCK cells (mdck)

Surface forms. "MDCK cells"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Engineered RNA viral synthesis of microRNAs, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

BHK-21 baby hamster kidney cells (bhk)

Surface forms. "baby hamster kidney cells", "BHK cells", "BHK-21 cells", "BHK21 cells"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Drosha as an interferon-independent antiviral factor, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Vero E6 cells (vero-e6)

Surface forms. "Vero E6 cells"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Calu-3 cells (calu-3)

Surface forms. "Calu-3 2B4 cells", "Calu-3 cells", "Calu3 cells"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Vero cells (vero)

Surface forms. "Vero cells"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Noncanonical cytoplasmic processing of viral microRNAs, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Caco-2 cells (caco-2)

Surface forms. "Caco-2 cells"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

HeLa cells (hela)

Surface forms. "HeLa cells"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

2FTGH fibrosarcoma cells (2ftgh)

Surface forms. "2FTGH cells", "2FTGH fibrosarcoma cells"

Publications. Transcription Factor Redundancy Ensures Induction of the Antiviral State, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

Huh7 cells (huh7)

Surface forms. "Huh-7 cells", "Huh7 cells"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

BSC-1 cells (bsc-1-cells)

Surface forms. "BSC-1 cells"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism

BSRT7 cells (bsrt7-cells)

Surface forms. "BSRT7 cells"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

C6 glial cells (c6-glial-cells)

Surface forms. "C6 glial cells"

Publications. The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

CAD neuronal precursor cells (cad-neuronal-precursor-cells)

Surface forms. "CAD neuronal precursor cells"

Publications. Engineered RNA viral synthesis of microRNAs

COS-7 cells (cos-7-cells)

Surface forms. "COS-7 cells"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway

DF-1 chicken embryonic fibroblasts (df-1-chicken-embryonic-fibroblasts)

Surface forms. "DF-1 chicken embryonic fibroblasts"

Publications. The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Endothelial cells (endothelial-cells)

Surface forms. "endothelial cells"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Genetically engineered mouse models (genetically-engineered-mouse-models)

Surface forms. "genetically engineered mouse models"

Publications. Mouse genome rewriting and tailoring of three important disease loci

H441 human club cell line (h441-human-club-cell-line)

Surface forms. "H441 human club cell line"

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

Hepa 1.6 cells (hepa-1-6-cells)

Surface forms. "Hepa 1.6 cells"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication

Human bronchial epithelial cells (human-bronchial-epithelial-cells)

Surface forms. "human bronchial epithelial cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

JAWS II dendritic cell line (jaws-ii-dendritic-cell-line)

Surface forms. "JAWS II dendritic cell line"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

Jurkat T cells (jurkat-t-cells)

Surface forms. "Jurkat T cells"

Publications. Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection

Mouse hindpaw inflammatory pain model (mouse-hindpaw-inflammatory-pain-model)

Surface forms. "mouse hindpaw inflammatory pain model"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Mouse oocytes (mouse-oocytes)

Surface forms. "mouse oocytes"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Mouse paw incision model (mouse-paw-incision-model)

Surface forms. "mouse paw incision model"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Mouse spared nerve injury comparison dataset (mouse-spared-nerve-injury-comparison-dataset)

Surface forms. "mouse spared nerve injury comparison dataset"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

MRC-5 fibroblasts (mrc-5)

Surface forms. "MRC-5 fibroblasts"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

MtCC10-1 murine club cell line (mtcc10-1-murine-club-cell-line)

Surface forms. "mtCC10-1 murine club cell line"

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

Pancreatic endocrine cells (pancreatic-endocrine-cells)

Surface forms. "pancreatic endocrine cells"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Raji B cells (raji-b-cells)

Surface forms. "Raji B cells"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination

RAW macrophage cells (raw-macrophage-cells)

Surface forms. "RAW macrophage cells"

Publications. The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

Rederived fibroblasts (rederived-fibroblasts)

Surface forms. "rederived fibroblasts"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells

U2OS cells (u2os-cells)

Surface forms. "U2OS cells"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Invertebrate cell system

Drosophila DL1 cells (drosophila-dl1)

Surface forms. "Drosophila DL1 cells"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors

Non-vertebrate or plant system

Arthropods (arthropods)

Surface forms. "arthropods"

Publications. RNA viruses and the host microRNA machinery, The Evolution of Antiviral Defense Systems

Plants (plants)

Surface forms. "plants"

Publications. RNA viruses and the host microRNA machinery, The Evolution of Antiviral Defense Systems

Amsacta moorei Ld652 cells (amsacta-moorei-ld652-cells)

Surface forms. "Amsacta moorei Ld652 cells"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism

Arabidopsis protoplasts (arabidopsis-protoplasts)

Surface forms. "Arabidopsis protoplasts"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Archaea (archaea)

Surface forms. "archaea"

Publications. The Evolution of Antiviral Defense Systems

Bacteria (bacteria)

Surface forms. "bacteria"

Publications. The Evolution of Antiviral Defense Systems

C6/36 Aedes albopictus cells (c6-36-aedes-albopictus-cells)

Surface forms. "C6/36 Aedes albopictus cells"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination

Chordates (chordates)

Surface forms. "chordates"

Publications. The Evolution of Antiviral Defense Systems

Eukaryotes (eukaryotes)

Surface forms. "eukaryotes"

Publications. The Evolution of Antiviral Defense Systems

Nematodes (nematodes)

Surface forms. "nematodes"

Publications. RNA viruses and the host microRNA machinery

Nicotiana benthamiana (nicotiana-benthamiana)

Surface forms. "Nicotiana benthamiana"

Publications. ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

TB40/E bacterial artificial chromosome (tb40-e-bacterial-artificial-chromosome)

Surface forms. "TB40/E bacterial artificial chromosome"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Yeast assembly vector (yeast-assembly-vector)

Surface forms. "yeast assembly vector"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Organoid, chip or stem cell system

Adult cholangiocyte organoids (adult-cholangiocyte-organoids)

Surface forms. "adult cholangiocyte organoids"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Adult hepatocyte organoids (adult-hepatocyte-organoids)

Surface forms. "adult hepatocyte organoids"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Adult primary human islets (adult-primary-human-islets)

Surface forms. "adult primary human islets"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Cardiomyocytes (cardiomyocytes)

Surface forms. "cardiomyocytes"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Human embryonic stem cell derived SEAM whole-eye cultures (human-embryonic-stem-cell-derived-seam-whole-eye-cultures)

Surface forms. "human embryonic stem cell derived SEAM whole-eye cultures"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium

Human induced pluripotent stem cells (human-induced-pluripotent-stem-cells)

Surface forms. "human induced pluripotent stem cells"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells

Human pluripotent stem cell derivatives (human-pluripotent-stem-cell-derivatives)

Surface forms. "human pluripotent stem cell derivatives"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

IPSC-derived cardiomyocytes (ipsc-derived-cardiomyocytes)

Surface forms. "iPSC-derived cardiomyocytes"

Publications. Type I interferon response impairs differentiation potential of pluripotent stem cells

Liver organoids (liver-organoids)

Surface forms. "liver organoids"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Microfluidic human bronchial airway chip (microfluidic-human-bronchial-airway-chip)

Surface forms. "microfluidic human bronchial airway chip"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Primary human bronchial airway basal stem cells (primary-human-bronchial-airway-basal-stem-cells)

Surface forms. "primary human bronchial airway basal stem cells"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Stem cells (stem-cells)

Surface forms. "stem cells"

Publications. The Evolution of Antiviral Defense Systems

Primary or early-passage cell

Mouse embryonic fibroblasts (mef)

Surface forms. "mouse embryonic fibroblasts", "murine embryonic fibroblasts", "murine fibroblasts", "primary mouse embryonic fibroblasts"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Drosha as an interferon-independent antiviral factor, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Homologous recombination is an intrinsic defense against antiviral RNA interference, Type I interferon response impairs differentiation potential of pluripotent stem cells, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Bone marrow derived macrophages (bmdm)

Surface forms. "bone marrow derived macrophages", "bone marrow-derived macrophages", "murine bone marrow derived macrophages"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Primary human fibroblasts (human-fibroblasts)

Surface forms. "BJ human foreskin fibroblasts", "human fibroblasts", "human primary foreskin fibroblasts", "normal human dermal fibroblasts"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Noncanonical cytoplasmic processing of viral microRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Type I interferon response impairs differentiation potential of pluripotent stem cells

Primary mouse lung fibroblasts (mouse-lung-fibroblasts)

Surface forms. "murine lung fibroblasts", "primary lung fibroblasts", "primary mouse lung fibroblasts"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Long-term survival of influenza virus infected club cells drives immunopathology, Drosha as an interferon-independent antiviral factor

Bone marrow derived dendritic cells (bone-marrow-derived-dendritic-cells)

Surface forms. "bone marrow derived dendritic cells"

Publications. Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

FACS-sorted olfactory sensory neuron nuclei (facs-sorted-olfactory-sensory-neuron-nuclei)

Surface forms. "FACS-sorted olfactory sensory neuron nuclei"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Olfactory sensory neurons (olfactory-sensory-neurons)

Surface forms. "olfactory sensory neurons"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Primary adult human cornea limbus sclera iris retinal pigment epithelium and choroid cultures (primary-adult-human-cornea-limbus-sclera-iris-retinal-pigment-epithelium-and-choroid-cultures)

Surface forms. "primary adult human cornea limbus sclera iris retinal pigment epithelium and choroid cultures"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium

Primary conditional Drosha mouse lung fibroblasts (primary-conditional-drosha-mouse-lung-fibroblasts)

Surface forms. "primary conditional Drosha mouse lung fibroblasts"

Publications. RNase III nucleases from diverse kingdoms serve as antiviral effectors

Primary ferret lung (primary-ferret-lung)

Surface forms. "primary ferret lung"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies

Primary human airway basal cells (primary-human-airway-basal-cells)

Surface forms. "primary human airway basal cells"

Publications. Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Primary human bronchial epithelial cells (primary-human-bronchial-epithelial-cells)

Surface forms. "primary human bronchial epithelial cells"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Primary human nasal epithelial cells (primary-human-nasal-epithelial-cells)

Surface forms. "primary human nasal epithelial cells"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies

Primary human neutrophils (primary-human-neutrophils)

Surface forms. "primary human neutrophils"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Primary human pulmonary microvascular endothelium (primary-human-pulmonary-microvascular-endothelium)

Surface forms. "primary human pulmonary microvascular endothelium"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

Primary human type II pneumocytes (primary-human-type-ii-pneumocytes)

Surface forms. "primary human type II pneumocytes"

Publications. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Primary mouse lung cultures from GFP transgenic mice (primary-mouse-lung-cultures-from-gfp-transgenic-mice)

Surface forms. "primary mouse lung cultures from GFP transgenic mice"

Publications. A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs

Primary normal human bronchial epithelial cells (primary-normal-human-bronchial-epithelial-cells)

Surface forms. "primary normal human bronchial epithelial cells"

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

Stem cell system

Mouse embryonic stem cells (mouse-esc)

Surface forms. "mouse embryonic stem cells"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, Type I interferon response impairs differentiation potential of pluripotent stem cells, Mouse genome rewriting and tailoring of three important disease loci

Embryoid bodies (embryoid-bodies)

Surface forms. "embryoid bodies"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, Type I interferon response impairs differentiation potential of pluripotent stem cells

Tissue or organ

Mouse lung (mouse-lung)

Surface forms. "BALB/c mouse lung", "C57BL/6 mouse lung", "mouse lung", "mouse lung tissue"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Mouse genome rewriting and tailoring of three important disease loci, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Hamster lung (hamster-lung)

Surface forms. "hamster lung"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Mouse spleen (mouse-spleen)

Surface forms. "mouse spleen"

Publications. In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

Brain (brain)

Surface forms. "brain"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Liver (liver)

Surface forms. "liver"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Mediastinal lymph node (mediastinal-lymph-node)

Surface forms. "mediastinal lymph node"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A diminished immune response underlies age-related SARS-CoV-2 pathologies

Mouse liver (mouse-liver)

Surface forms. "mouse liver"

Publications. In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination

Olfactory bulb (olfactory-bulb)

Surface forms. "olfactory bulb"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Pancreas (pancreas)

Surface forms. "pancreas"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Spleen (spleen)

Surface forms. "spleen"

Publications. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Alveolar epithelium (alveolar-epithelium)

Surface forms. "alveolar epithelium"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Bronchus tissue (bronchus-tissue)

Surface forms. "bronchus tissue"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host

Club cells (club-cells)

Surface forms. "club cells"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Cortical neurons (cortical-neurons)

Surface forms. "cortical neurons"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Dopaminergic neurons (dopaminergic-neurons)

Surface forms. "dopaminergic neurons"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Gastrointestinal tract (gastrointestinal-tract)

Surface forms. "gastrointestinal tract"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Golden hamster dorsal root ganglia (golden-hamster-dorsal-root-ganglia)

Surface forms. "golden hamster dorsal root ganglia"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Golden hamster lung heart and kidney (golden-hamster-lung-heart-and-kidney)

Surface forms. "golden hamster lung heart and kidney"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery

Golden hamster olfactory epithelium (golden-hamster-olfactory-epithelium)

Surface forms. "golden hamster olfactory epithelium"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Hamster olfactory bulb and olfactory epithelium (hamster-olfactory-bulb-and-olfactory-epithelium)

Surface forms. "hamster olfactory bulb and olfactory epithelium"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery

Hamster spinal cord (hamster-spinal-cord)

Surface forms. "hamster spinal cord"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Hamster spleen (hamster-spleen)

Surface forms. "hamster spleen"

Publications. A diminished immune response underlies age-related SARS-CoV-2 pathologies

Hamster striatum thalamus cerebellum medial prefrontal cortex and trigeminal ganglion (hamster-striatum-thalamus-cerebellum-medial-prefrontal-cortex-and-trigeminal-ganglion)

Surface forms. "hamster striatum thalamus cerebellum medial prefrontal cortex and trigeminal ganglion"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery

Hamster trachea (hamster-trachea)

Surface forms. "hamster trachea"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity

Heart (heart)

Surface forms. "heart"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Kidney (kidney)

Surface forms. "kidney"

Publications. Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Lung draining lymph node (lung-draining-lymph-node)

Surface forms. "lung draining lymph node"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

Macrophages (macrophages)

Surface forms. "macrophages"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Mesenteric lymph nodes (mesenteric-lymph-nodes)

Surface forms. "mesenteric lymph nodes"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Microglia (microglia)

Surface forms. "microglia"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

MLE-15 murine lung epithelial cell line (mle-15-murine-lung-epithelial-cell-line)

Surface forms. "MLE-15 murine lung epithelial cell line"

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

Mouse gastrointestinal tract (mouse-gastrointestinal-tract)

Surface forms. "mouse gastrointestinal tract"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Mouse heart (mouse-heart)

Surface forms. "mouse heart"

Publications. In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs

Mouse kidney (mouse-kidney)

Surface forms. "mouse kidney"

Publications. In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs

Mouse small intestine (mouse-small-intestine)

Surface forms. "mouse small intestine"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Mouse testis (mouse-testis)

Surface forms. "mouse testis"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Mouse trachea (mouse-trachea)

Surface forms. "mouse trachea"

Publications. Mouse genome rewriting and tailoring of three important disease loci

Small intestine (small-intestine)

Surface forms. "small intestine"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity

Sustentacular cells (sustentacular-cells)

Surface forms. "sustentacular cells"

Publications. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

THP-1-derived macrophages (thp-1-derived-macrophages)

Surface forms. "THP-1-derived macrophages"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Key concepts

154 canonical terms from 542 surface forms. Grouped by family, then ordered by number of publications.

Cell identity and development

Lineage tracing of infected cells (lineage-tracing)

Surface forms. "bronchiolar epithelium", "cell survival of lytic infection", "club cells", "lineage tracing of infected cells", "peribronchiolar metaplasia", "tissue repair", "virulence independent of replication"

Publications. Long-term survival of influenza virus infected club cells drives immunopathology, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Synthetic Virology: Building Viruses to Better Understand Them, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, A diminished immune response underlies age-related SARS-CoV-2 pathologies

Interferon and cell identity (interferon-and-cell-identity)

Surface forms. "cellular reprogramming", "differentiation potential", "germ layer specification", "piRNA pathway", "pluripotency", "pluripotency and RNAi competence"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, The Evolution of Antiviral Defense Systems, Type I interferon response impairs differentiation potential of pluripotent stem cells

Cell cycle arrest (cell-cycle-arrest)

Surface forms. "cell cycle arrest"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Limbal stem cell niche (limbal-stem-cell-niche)

Surface forms. "limbal stem cell niche"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium

General virology

Airway host response (airway-host-response)

Surface forms. "airway host response"

Publications. The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

Bystander versus infected cell responses (bystander-versus-infected-cell-responses)

Surface forms. "bystander versus infected cell responses"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium

Coinfection (coinfection)

Surface forms. "coinfection"

Publications. The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

Dorsal root ganglia (dorsal-root-ganglia)

Surface forms. "dorsal root ganglia"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Filopodial protrusions (filopodial-protrusions)

Surface forms. "filopodial protrusions"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Gastrointestinal barrier (gastrointestinal-barrier)

Surface forms. "gastrointestinal barrier"

Publications. Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Hepatocyte and cholangiocyte infection (hepatocyte-and-cholangiocyte-infection)

Surface forms. "hepatocyte and cholangiocyte infection"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Host transcriptome modulation (host-transcriptome-modulation)

Surface forms. "host transcriptome modulation"

Publications. Drosha as an interferon-independent antiviral factor

Host transcriptome remodelling (host-transcriptome-remodelling)

Surface forms. "host transcriptome remodelling"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

IE2 autorepression through the cis-repression sequence (ie2-autorepression-through-the-cis-repression-sequence)

Surface forms. "IE2 autorepression through the cis-repression sequence"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

IL-6 (il-6)

Surface forms. "IL-6"

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

Immediate early gene circuitry (immediate-early-gene-circuitry)

Surface forms. "immediate early gene circuitry"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

In vivo RNA interference screening (in-vivo-rna-interference-screening)

Surface forms. "in vivo RNA interference screening"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication

Infected versus bystander cells (infected-versus-bystander-cells)

Surface forms. "infected versus bystander cells"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Microglial and myeloid activation (microglial-and-myeloid-activation)

Surface forms. "microglial and myeloid activation"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery

Negative feedback by apoptotic caspases (negative-feedback-by-apoptotic-caspases)

Surface forms. "negative feedback by apoptotic caspases"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

PA RNA binding cleft (pa-rna-binding-cleft)

Surface forms. "PA RNA binding cleft"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity

Pancreatic beta cell infection (pancreatic-beta-cell-infection)

Surface forms. "pancreatic beta cell infection"

Publications. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids

Promyelocytic leukemia nuclear bodies (promyelocytic-leukemia-nuclear-bodies)

Surface forms. "promyelocytic leukemia nuclear bodies"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

Sequential infection (sequential-infection)

Surface forms. "sequential infection"

Publications. The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

SP100 family (sp100-family)

Surface forms. "SP100 family"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

Strain-dependent virulence (strain-dependent-virulence)

Surface forms. "strain-dependent virulence"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics

TGF-beta signalling (tgf-beta-signalling)

Surface forms. "TGF-beta signalling"

Publications. A diminished immune response underlies age-related SARS-CoV-2 pathologies

Transcriptional maintenance of antiviral capacity (transcriptional-maintenance-of-antiviral-capacity)

Surface forms. "transcriptional maintenance of antiviral capacity"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication

Upstream regulator prediction (upstream-regulator-prediction)

Surface forms. "upstream regulator prediction"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Viral genomic RNA cleavage (viral-genomic-rna-cleavage)

Surface forms. "viral genomic RNA cleavage"

Publications. Drosha as an interferon-independent antiviral factor

Viral interference (viral-interference)

Surface forms. "viral interference"

Publications. The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

Viral transcriptional cascade (viral-transcriptional-cascade)

Surface forms. "viral transcriptional cascade"

Publications. miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Virus clearance (virus-clearance)

Surface forms. "virus clearance"

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

Host factors

SARS-CoV-2 entry and receptor use (sars-cov-2-entry)

Surface forms. "ACE2 and TMPRSS2 expression", "ACE2 binding kinetics", "ACE2 expression", "ACE2 receptor", "ACE2 surface availability", "hemagglutinin receptor specificity", "proteolytic processing of Spike", "pseudotyped entry virus", "pseudotyped particle systems", "serine protease priming of hemagglutinin", "Spike D614G", "TMPRSS2", "TMPRSS4 as an alternative protease", "viral entry efficiency", "viral entry inhibition", "viral receptor expression"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Mouse genome rewriting and tailoring of three important disease loci

Host dependency factors (host-dependency-factors)

Surface forms. "druggable target identification", "essential gene function in myeloid cells", "host dependency factors", "host factor discovery", "host restriction factors", "pan-proviral versus virus-specific factors", "proviral host dependency"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Viral tropism and cell-type permissiveness (viral-tropism)

Surface forms. "cell-type permissiveness", "cell-type restriction of replication", "cell-type-specific conditional knockdown", "hematopoietic cells", "hematopoietic-specific microRNA targeting", "SARS-CoV-2 tropism", "upper respiratory tract replication", "viral tropism"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Host-directed antiviral strategies (host-directed-antivirals)

Surface forms. "alectinib repurposing", "antiviral drug target selection", "drug repurposing", "host-directed antiviral strategy", "host-directed antiviral therapy", "kinase inhibitor repurposing"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

ANP32A (anp32a)

Surface forms. "ANP32A"

Publications. The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

ARP2 and ARP3 complex (arp2-and-arp3-complex)

Surface forms. "ARP2 and ARP3 complex"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Cholesterol biosynthesis (cholesterol-biosynthesis)

Surface forms. "cholesterol biosynthesis"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Class 3 PI3K (class-3-pi3k)

Surface forms. "class 3 PI3K"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

CMP-sialic acid transport (cmp-sialic-acid-transport)

Surface forms. "CMP-sialic acid transport"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

Commander complex (commander-complex)

Surface forms. "Commander complex"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Endosomal trafficking (endosomal-trafficking)

Surface forms. "endosomal trafficking"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Retromer complex (retromer-complex)

Surface forms. "Retromer complex"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Sialic acid biosynthesis (sialic-acid-biosynthesis)

Surface forms. "sialic acid biosynthesis"

Publications. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

Vacuolar ATPase (vacuolar-atpase)

Surface forms. "vacuolar ATPase"

Publications. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Immunology

Immune memory and reinfection (immune-memory)

Surface forms. "adaptive immune response", "adoptive transfer", "affinity maturation", "antigen presenting cells", "antigen-specific B cells", "antigen-specific T cells", "bystander priming", "CD8 T cell priming", "cross-presentation", "germinal centre B cells", "immune memory", "immune priming", "neutralizing antibody", "neutralizing antibody potency", "regulatory T cells", "systemic antiviral priming", "transmission despite immunity", "V(D)J recombination"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, The Evolution of Antiviral Defense Systems, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Age and immunosenescence (age-and-immunosenescence)

Surface forms. "IL-17 and neutrophil recruitment", "immunosenescence", "immunosuppression", "neutrophil recruitment and transmigration"

Publications. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Interferon and innate signalling

Interferon-stimulated genes (interferon-stimulated-genes)

Surface forms. "interferon-stimulated gene amplification", "interferon-stimulated gene selectivity", "interferon-stimulated gene subsets", "interferon-stimulated genes"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Long-term survival of influenza virus infected club cells drives immunopathology, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Type I interferon response impairs differentiation potential of pluripotent stem cells, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, A diminished immune response underlies age-related SARS-CoV-2 pathologies, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Type I interferon (type-i-interferon)

Surface forms. "type I and type III interferon", "type I interferon", "type I interferon receptor", "type I interferon response", "type I interferon signaling", "type I interferon signalling", "type I interferon system"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, RNA viruses and the host microRNA machinery, Long-term survival of influenza virus infected club cells drives immunopathology, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, The Evolution of Antiviral Defense Systems, Type I interferon response impairs differentiation potential of pluripotent stem cells, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Chemokine induction (chemokine-induction)

Surface forms. "chemokine induction", "inflammatory cytokine production", "leukocyte recruitment", "proinflammatory chemokines", "proinflammatory cytokine induction"

Publications. Long-term survival of influenza virus infected club cells drives immunopathology, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Cell-intrinsic antiviral state (antiviral-state)

Surface forms. "antiviral immunity", "antiviral innate immunity", "antiviral state", "cell-intrinsic immunity", "innate antiviral state", "intrinsic antiviral response"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, RNA viruses and the host microRNA machinery, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication

Interferon-stimulated response element (isre)

Surface forms. "interferon regulatory factor binding element", "interferon-stimulated response element", "IRF7 as transactivator of interferon-stimulated response elements"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Type I interferon response impairs differentiation potential of pluripotent stem cells

Viral interferon antagonism (interferon-antagonism)

Surface forms. "interferon antagonism", "NS1 antagonist", "NS1 interferon antagonism", "type I interferon antagonism", "viral interferon antagonism"

Publications. Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Capicua and transcriptional gatekeeping (capicua)

Surface forms. "ATXN1L", "Capicua", "capicua and ATXN1 corepressor", "CIC binding site motif", "GAF complex", "low-complexity acidic region"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

MAPK signalling (mapk-signalling)

Surface forms. "casein kinase 1", "casein kinase II", "EGFR-MAPK signaling", "ERK activation", "GSK-3", "kinase activity rewiring", "kinase substrate motif prediction", "MAP3K8", "p38 MAPK signalling", "phospho-priming", "phosphoproteomics", "proline-rich hinge phosphorylation", "SRPK1 and SRPK2"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, The Global Phosphorylation Landscape of SARS-CoV-2 Infection, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Pattern recognition receptors (pattern-recognition-receptors)

Surface forms. "pathogen-associated molecular patterns", "pattern recognition receptor", "pattern recognition receptors"

Publications. In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, The Evolution of Antiviral Defense Systems, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

RIG-I-like receptors (rig-i-like-receptors)

Surface forms. "MDA5", "RIG-I", "RIG-I sensing of alphavirus", "RIG-I-like receptor", "RIG-I-like receptors"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Transcriptional repression of interferon-stimulated genes (isg-repression)

Surface forms. "cytokine derepression", "KLF4-mediated repression of antiviral induction", "transcriptional repression", "transcriptional repression of interferon-stimulated genes"

Publications. microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Type I interferon response impairs differentiation potential of pluripotent stem cells, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Type I interferon induction (type-i-interferon-induction)

Surface forms. "feed forward amplification of innate immunity", "interferon beta enhanceosome", "interferon induction", "type I interferon induction"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

IKK-related kinases (ikk-related-kinases)

Surface forms. "IKK-related kinases", "IKKepsilon", "IKKε", "TBK1", "virus-activated kinase"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

IRF3 activation (irf3-activation)

Surface forms. "C-terminal phosphorylation", "IRF-3 activation", "IRF3", "sequential multisite phosphorylation"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

IRF7 activation (irf7-activation)

Surface forms. "IRF-7 activation", "IRF3 and IRF7 heterodimer", "IRF7"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway, Transcription Factor Redundancy Ensures Induction of the Antiviral State, Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus

ISGF3 (isgf3)

Surface forms. "ISGF3", "ISGF3 assembly"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Transcription Factor Redundancy Ensures Induction of the Antiviral State, IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

MAVS signalling (mavs-signalling)

Surface forms. "MAVS signaling", "MDA5 and MAVS signaling", "RIG-I and MAVS signalling"

Publications. Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

NF-kappaB signalling (nf-kb-signalling)

Surface forms. "NF-kappaB signalling", "NF-kB-driven chemokine response", "NF-κB signalling"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, A diminished immune response underlies age-related SARS-CoV-2 pathologies

Chromatin accessibility (chromatin-accessibility)

Surface forms. "chromatin accessibility"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

OAS and RNase L system (oas-rnase-l)

Surface forms. "OAS and RNase L", "OAS and RNase L system"

Publications. In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Type III interferon (type-iii-interferon)

Surface forms. "type III interferon", "type III interferon signaling"

Publications. Transcription Factor Redundancy Ensures Induction of the Antiviral State, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Allosteric enhancer RNA (allosteric-enhancer-rna)

Surface forms. "allosteric enhancer RNA"

Publications. A Small-RNA Enhancer of Viral Polymerase Activity

Enhancer remodelling (enhancer-remodelling)

Surface forms. "enhancer remodelling"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Gamma-activated sequence (gamma-activated-sequence)

Surface forms. "gamma-activated sequence"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

ILF3 (ilf3)

Surface forms. "ILF3"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Innate sensing compartment (innate-sensing-compartment)

Surface forms. "innate sensing compartment"

Publications. Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

Interferon response (interferon-response)

Surface forms. "interferon response"

Publications. The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing

PKR (pkr)

Surface forms. "PKR"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Promoter motif specificity (promoter-motif-specificity)

Surface forms. "promoter motif specificity"

Publications. Transcription Factor Redundancy Ensures Induction of the Antiviral State

Promoter panhandle (promoter-panhandle)

Surface forms. "promoter panhandle"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication

Promoter selectivity (promoter-selectivity)

Surface forms. "promoter selectivity"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity

STAT1 dependent selection (stat1-dependent-selection)

Surface forms. "STAT1 dependent selection"

Publications. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

STAT1 homodimer interface (stat1-homodimer-interface)

Surface forms. "STAT1 homodimer interface"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

STAT1 serine 708 phosphorylation (stat1-serine-708-phosphorylation)

Surface forms. "STAT1 serine 708 phosphorylation"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

STAT1 serine phosphorylation (stat1-serine-phosphorylation)

Surface forms. "STAT1 serine phosphorylation"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity

Stress granules and biomolecular condensates (stress-granules)

Surface forms. "biomolecular condensates", "stress granules"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Transcription factor complex competition (transcription-factor-complex-competition)

Surface forms. "transcription factor complex competition"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

Transcription factor motif enrichment (transcription-factor-motif-enrichment)

Surface forms. "transcription factor motif enrichment"

Publications. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Transcription factor nuclear translocation (transcription-factor-nuclear-translocation)

Surface forms. "transcription factor nuclear translocation"

Publications. Triggering the Interferon Antiviral Response Through an IKK-Related Pathway

Transcription factor redundancy (transcription-factor-redundancy)

Surface forms. "transcription factor redundancy"

Publications. Transcription Factor Redundancy Ensures Induction of the Antiviral State

Type I interferon signalling in sensory tissue (type-i-interferon-signalling-in-sensory-tissue)

Surface forms. "type I interferon signalling in sensory tissue"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Type I versus type II interferon balance (type-i-versus-type-ii-interferon-balance)

Surface forms. "type I versus type II interferon balance"

Publications. IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses

Viral promoter mutation (viral-promoter-mutation)

Surface forms. "viral promoter mutation"

Publications. The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Models

Small animal models of respiratory infection (animal-models)

Surface forms. "aerosol transmission", "animal models of COVID-19", "benchmarking against influenza", "clinically relevant drug exposure under flow", "contact transmission", "dengue pathogenesis models", "ferret transmission model", "golden hamster model development", "herpesvirus latency models", "organoid disease modeling", "preclinical model fidelity", "route of inoculation", "SEAM whole-eye organoid model", "small animal model", "transmission blocking"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Mouse genome rewriting and tailoring of three important disease loci

Pandemic pathogenesis

COVID-19 pathogenesis (covid19-pathogenesis)

Surface forms. "circulating inflammatory signal", "COVID-19 heterogeneity", "COVID-19 pathogenesis", "immunopathology", "lung immunopathology", "sterile inflammation", "systemic inflammation"

Publications. Long-term survival of influenza virus infected club cells drives immunopathology, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Delayed engagement of host defences (delayed-innate-engagement)

Surface forms. "delayed innate immune engagement", "delayed innate response", "innate immune response kinetics", "prophylaxis", "prophylaxis versus treatment", "therapeutic time window", "threat-proportional antiviral response"

Publications. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics, A diminished immune response underlies age-related SARS-CoV-2 pathologies, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19

Extrapulmonary dissemination (extrapulmonary-dissemination)

Surface forms. "COVID-19 extrapulmonary involvement", "enteric virus dissemination", "extrapulmonary manifestations", "replication versus inoculum discrimination", "viral RNA dissemination without infectious virus", "viremia", "virus dissemination"

Publications. Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses, A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids, Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Imbalanced host response (imbalanced-host-response)

Surface forms. "attenuated type I and III interferon signaling", "imbalanced host response"

Publications. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19, SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium, Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity, The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication

Anosmia and olfactory disruption (anosmia)

Surface forms. "anosmia", "interchromosomal genomic compartments", "Lhx2 and Ebf transcription factors", "non-cell-autonomous transcriptional effect", "nuclear architecture disruption", "nuclear memory", "olfactory bulb inflammation", "olfactory receptor gene choice", "olfactory signal transduction genes", "sustentacular cell tropism"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Post-acute sequelae of SARS-CoV-2 infection (post-acute-sequelae)

Surface forms. "behavioral change after recovery", "long COVID", "persistent interferon signaling after viral clearance", "post-acute sequelae of COVID-19", "post-acute sequelae of SARS-CoV-2 infection"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery, SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Demyelination signature (demyelination-signature)

Surface forms. "demyelination signature"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Immune-mediated apoptosis (immune-mediated-apoptosis)

Surface forms. "immune-mediated apoptosis"

Publications. Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA

Mechanical hypersensitivity (mechanical-hypersensitivity)

Surface forms. "mechanical hypersensitivity"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Neuropathic transcriptome (neuropathic-transcriptome)

Surface forms. "neuropathic transcriptome"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Neuroplasticity (neuroplasticity)

Surface forms. "neuroplasticity"

Publications. SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model

Ocular route of SARS-CoV-2 entry (ocular-route-of-sars-cov-2-entry)

Surface forms. "ocular route of SARS-CoV-2 entry"

Publications. SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium

Renal tubular atrophy (renal-tubular-atrophy)

Surface forms. "renal tubular atrophy"

Publications. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery

Population genetics and evolution

Escape from small RNA targeting (escape-from-silencing)

Surface forms. "escape mutant fitness cost", "escape mutant resistance", "escape mutants", "escape variant selection", "mutational tolerance", "viral escape from silencing"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Homologous recombination is an intrinsic defense against antiviral RNA interference, Synthetic Virology: Building Viruses to Better Understand Them, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Host-pathogen arms race (host-pathogen-arms-race)

Surface forms. "conservation across coronaviruses", "convergent and divergent evolution", "host-pathogen arms race", "isogenic variant comparison", "linkage disequilibrium with ORF1b P314L", "vaccine antigen sequence choice", "variant of concern"

Publications. The Evolution of Antiviral Defense Systems, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types, Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission, Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Viral fitness landscapes (fitness-landscape)

Surface forms. "fitness-based genetic selection", "forward genetic screening", "natural selection as screen readout", "positive selection survival screen", "viral fitness landscape"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Homologous recombination in RNA viruses (homologous-recombination)

Surface forms. "genome polarity", "homologous recombination", "negative-sense RNA virus constraints", "no DNA intermediate", "positive-strand RNA virus specificity", "template switching"

Publications. A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Homologous recombination is an intrinsic defense against antiviral RNA interference, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Transmission bottlenecks (transmission-bottleneck)

Surface forms. "barcode control for drift", "founder effects", "founder population", "population bottlenecks", "stochastic transmission", "transmission bottleneck"

Publications. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Synthetic Virology: Building Viruses to Better Understand Them, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Viral population dynamics (viral-population-dynamics)

Surface forms. "barcoded library competition assay", "population monopolization", "viral population dynamics", "viral quasispecies", "virus population dynamics", "within-population competition"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Homologous recombination is an intrinsic defense against antiviral RNA interference, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

Host range restriction and adaptation (host-range-and-adaptation)

Surface forms. "host adaptation", "host range restriction", "host tropism", "pandemic emergence", "PB2 627 polymorphism"

Publications. Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host, Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Paleovirology and historical virus movement (paleovirology)

Surface forms. "ancient DNA authentication", "Cocoliztli", "Colonial epidemics", "cross-population transmission", "host genetic ancestry", "molecular tip calibration", "paleovirology", "transatlantic slave trade", "viral genotype geography"

Publications. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Small RNA biology

Quantitative limits of microRNA function (microrna-quantitative-limits)

Surface forms. "endogenous miRNA landscape stability", "Exportin-5 independence", "kinetics of microRNA action", "let-7 regulation of IL6", "microRNA", "microRNA targetome", "miR-124", "miR-142", "miR-192", "miR-23 regulation of IRF1", "miR-302/367 cluster", "miR-93 target site attenuation", "multiplicity of infection dependence", "RISC saturation", "small RNA copy number", "species-specific microRNA expression", "star strand accumulation", "strand selection", "target complementarity threshold"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Antiviral RNA interference (antiviral-rnai)

Surface forms. "antiviral RNA interference", "antiviral RNA interference in vertebrates", "engineered RNAi", "RNA interference", "small RNA-mediated antiviral restriction", "virus-delivered RNA interference", "virus-derived interfering RNA", "virus-derived small interfering RNAs", "virus-derived small RNAs", "virus-encoded small interfering RNA"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, RNA viruses and the host microRNA machinery, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Drosha as an interferon-independent antiviral factor, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus, The Evolution of Antiviral Defense Systems, Homologous recombination is an intrinsic defense against antiviral RNA interference, Synthetic Virology: Building Viruses to Better Understand Them, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Cytoplasmic microRNA biogenesis (cytoplasmic-microrna-biogenesis)

Surface forms. "cytoplasmic Drosha translocation", "cytoplasmic hairpin processing", "cytoplasmic microprocessor", "cytoplasmic microRNA biogenesis", "cytoplasmic pri-miRNA", "cytoplasmic translocation of Drosha", "Drosha relocalization", "intron-encoded microRNA", "mirtron-like processing", "noncanonical microRNA biogenesis", "noncanonical small RNA biogenesis", "noncanonical small RNA processing"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, RNA viruses and the host microRNA machinery, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

RNA-induced silencing complex (risc)

Surface forms. "Argonaute 2 slicing", "Argonaute and RISC", "RISC", "RISC loading", "RNA-induced silencing complex", "RNA-induced silencing complex inactivation", "RNA-induced silencing complex loading"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Homologous recombination is an intrinsic defense against antiviral RNA interference

Dicer (dicer)

Surface forms. "Dicer", "Dicer dependence", "Dicer independence"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors

Incompatibility of RNAi and interferon (rnai-interferon-incompatibility)

Surface forms. "developmental and defence system incompatibility", "evolution of antiviral strategies", "evolution of antiviral systems", "evolutionary divergence of antiviral strategies", "incompatibility of ADAR1 and RNAi", "incompatibility of RNAi and interferon", "type I interferon as an alternative antiviral system"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, The Evolution of Antiviral Defense Systems, RNase III nucleases from diverse kingdoms serve as antiviral effectors, Type I interferon response impairs differentiation potential of pluripotent stem cells, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Post-transcriptional gene silencing (post-transcriptional-silencing)

Surface forms. "microRNA-mediated gene silencing", "post-transcriptional gene silencing", "post-transcriptional silencing", "translational repression"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

The microprocessor and Drosha-DGCR8 processing (microprocessor)

Surface forms. "DGCR8 dependence", "Drosha", "Drosha and DGCR8 processing", "microprocessor", "microprocessor independence", "microRNA biogenesis machinery"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs, Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors

MicroRNA turnover and terminal modification (microrna-turnover)

Surface forms. "2-prime O-methylation", "microRNA depletion", "microRNA turnover", "nontemplated 3-prime adenylation", "poly(A) polymerase VP55", "proteasomal degradation", "small RNA tailing and degradation", "VP39 processivity factor", "VP55 poly(A) polymerase"

Publications. Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing, microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Virtrons (virtrons)

Surface forms. "viral microRNA synthesis", "virtron", "virtrons", "virus-encoded microRNA"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered RNA viral synthesis of microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, Evidence for a cytoplasmic microprocessor of pri-miRNAs

ADAR1 and RNA editing (adar1)

Surface forms. "ADAR1", "ADAR1 deficiency", "ADAR1 p110 and p150 isoforms", "adenosine to inosine RNA editing", "hypermutation"

Publications. Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

RNase III nucleases as antiviral effectors (rnase-iii-nucleases)

Surface forms. "interferon-independent antiviral defense", "interferon-independent defense", "microRNA-independent antiviral activity", "RNA stem loop recognition", "RNase III independence", "RNase III nucleases"

Publications. Drosha as an interferon-independent antiviral factor, RNase III nucleases from diverse kingdoms serve as antiviral effectors, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Viral suppressors of RNA silencing (viral-suppressors-of-rna-silencing)

Surface forms. "NS1 and small RNA silencing", "viral suppressor of RNA silencing", "viral suppressors of RNA silencing"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Prokaryotic and plant defence systems (prokaryotic-defence)

Surface forms. "antisense RNA defense", "CRISPR-Cas", "kink-turn RNA structure", "L30 protein family", "L7Ae", "prokaryotic Argonaute", "restriction modification systems"

Publications. The Evolution of Antiviral Defense Systems, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology

Criteria for demonstrating antiviral RNAi (criteria-for-demonstrating-antiviral-rnai)

Surface forms. "criteria for demonstrating antiviral RNAi"

Publications. Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?

Viral engineering and biocontainment

MicroRNA target site engineering (mirna-target-site-engineering)

Surface forms. "cell-type-restricted viral tropism", "microRNA response element", "microRNA target site engineering", "microRNA target site insertion", "microRNA-mediated attenuation", "microRNA-mediated species restriction", "microRNA-mediated targeting", "species-specific attenuation", "species-specific microRNA attenuation", "viral attenuation", "viral tropism control", "viral tropism restriction"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, RNA viruses and the host microRNA machinery, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, Homologous recombination is an intrinsic defense against antiviral RNA interference, Synthetic Virology: Building Viruses to Better Understand Them

Artificial microRNAs (artificial-microrna)

Surface forms. "artificial microRNA", "artificial microRNA delivery", "in vivo small RNA delivery", "RNA-based gene delivery", "small RNA delivery", "tunable small RNA dosing", "virus-delivered artificial microRNAs"

Publications. Engineered RNA viral synthesis of microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, RNA viruses and the host microRNA machinery, An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs

RNA virus vectors (rna-virus-vectors)

Surface forms. "engineered viral vectors", "replication-incompetent vector", "reporter virus design", "RNA virus vectors", "vector cytotoxicity", "vector tropism"

Publications. Engineered RNA viral synthesis of microRNAs, In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs, A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs, miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2, Synthetic Virology: Building Viruses to Better Understand Them

Live attenuated vaccine design (live-attenuated-vaccine-design)

Surface forms. "live attenuated influenza vaccine", "live attenuated vaccine design", "live-attenuated vaccine design"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, RNA viruses and the host microRNA machinery, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response

Self-targeting viruses (self-targeting-virus)

Surface forms. "self-targeting virus", "viral self-targeting"

Publications. Noncanonical cytoplasmic processing of viral microRNAs, Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response, In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus

Mammalian genome writing (mouse-genome-writing)

Surface forms. "biallelic engineering", "codon-level engineering of coding sequence", "genomic humanization", "iterative genome rewriting", "mammalian genome writing", "non-coding regulatory elements", "p53 mutational hotspots", "synonymous recoding"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Mouse genome rewriting and tailoring of three important disease loci

Molecular biocontainment (molecular-biocontainment)

Surface forms. "biocontainment kill switch", "gain-of-function research biosafety", "molecular biocontainment"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Synthetic Virology: Building Viruses to Better Understand Them

Antagomir antiviral strategy (antagomir-antiviral-strategy)

Surface forms. "antagomir antiviral strategy"

Publications. SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology

Synthetic virology (synthetic-virology)

Surface forms. "learning by building", "synthetic virology", "viral genetic circuitry"

Publications. Synthetic Virology: Building Viruses to Better Understand Them

Vaccine yield in ovo (vaccine-yield-in-ovo)

Surface forms. "vaccine yield in ovo"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus

Viral gene expression

Segment 8 splicing and the molecular timer (segment-8-splicing)

Surface forms. "3 prime splice acceptor site", "alternative splicing", "bicistronic segment 8", "M2 and NS2 splice products", "molecular timer", "molecular timer of infection", "NEP/NS2", "noncanonical splicing", "nuclear export protein NEP", "orthomyxovirus splicing", "segment 8 engineering", "splicing-independent virus", "suboptimal 5-prime splice site", "temporal coordination of the viral life cycle"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Engineered RNA viral synthesis of microRNAs, A Small-RNA Enhancer of Viral Polymerase Activity, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology, Mouse genome rewriting and tailoring of three important disease loci

Viral ribonucleoprotein complexes (viral-ribonucleoprotein)

Surface forms. "encapsidated genome", "exportin 1 CRM1-dependent nuclear export", "viral ribonucleoprotein", "viral ribonucleoprotein accessibility", "viral ribonucleoprotein complex", "viral ribonucleoprotein export"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Engineered RNA viral synthesis of microRNAs, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, Drosha as an interferon-independent antiviral factor, Homologous recombination is an intrinsic defense against antiviral RNA interference, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Defective viral genomes (defective-viral-genomes)

Surface forms. "5-prime triphosphate RNA", "copy-back defective genomes", "defective viral genomes", "endogenous double-stranded RNA", "self versus non-self RNA discrimination", "self-derived double-stranded RNA"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA, Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses

Genome segment stoichiometry (segment-stoichiometry)

Surface forms. "gene expression stoichiometry", "genome segment stoichiometry", "packaging signal duplication", "segment packaging signals", "segment-specific regulation"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, A Small-RNA Enhancer of Viral Polymerase Activity, Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection, MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies, Synthetic Virology: Building Viruses to Better Understand Them

Influenza nucleoprotein (nucleoprotein)

Surface forms. "influenza nucleoprotein", "nucleoprotein", "nucleoprotein scaffold", "ribonucleoprotein protection of genomes", "viral nucleoprotein"

Publications. MicroRNA-mediated species-specific attenuation of influenza A virus, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Small viral RNA (small-viral-rna)

Surface forms. "mini-viral RNA", "small viral RNA", "svRNA"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses, A Small-RNA Enhancer of Viral Polymerase Activity, SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition

Viral RNA-dependent RNA polymerase (viral-rna-polymerase)

Surface forms. "encapsidating polymerase", "RNA-dependent RNA polymerase", "steric hindrance of RNA-dependent RNA polymerase", "viral RNA-dependent RNA polymerase"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, A Small-RNA Enhancer of Viral Polymerase Activity, The Evolution of Antiviral Defense Systems, RNase III nucleases from diverse kingdoms serve as antiviral effectors, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Transcription to replication switch (transcription-to-replication-switch)

Surface forms. "cRNA intermediate", "cRNA synthesis", "polymerase processivity", "primary transcription", "replicase complex assembly", "transcription to replication switch", "vRNA synthesis"

Publications. Influenza A virus-generated small RNAs regulate the switch from transcription to replication, A Small-RNA Enhancer of Viral Polymerase Activity, Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition, The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis

Allele A and allele B NS segments (allele-a-and-allele-b-ns-segments)

Surface forms. "allele A and allele B NS segments"

Publications. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

Hemagglutinin segment engineering (hemagglutinin-segment-engineering)

Surface forms. "hemagglutinin segment engineering"

Publications. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies

NS1 protein (ns1-protein)

Surface forms. "NS1 protein"

Publications. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

Nucleocapsid SR-rich domain (nucleocapsid-sr-rich-domain)

Surface forms. "nucleocapsid SR-rich domain"

Publications. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication

Replication kinetics (replication-kinetics)

Surface forms. "replication kinetics"

Publications. The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection

Subgenomic RNA (subgenomic-rna)

Surface forms. "subgenomic RNA"

Publications. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity

Viral egress (viral-egress)

Surface forms. "viral egress"

Publications. The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Publications referenced

• Triggering the Interferon Antiviral Response Through an IKK-Related Pathway
• Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity
• MicroRNA-mediated species-specific attenuation of influenza A virus
• Influenza A virus-generated small RNAs regulate the switch from transcription to replication
• Transcription Factor Redundancy Ensures Induction of the Antiviral State
• Noncanonical cytoplasmic processing of viral microRNAs
• Engineered RNA viral synthesis of microRNAs
• IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses
• Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism
• Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses
• In Vivo Delivery of Cytoplasmic RNA Virus-derived miRNAs
• A Small-RNA Enhancer of Viral Polymerase Activity
• Replication in Cells of Hematopoietic Origin Is Necessary for Dengue Virus Dissemination
• Evidence for a cytoplasmic microprocessor of pri-miRNAs
• Influenza A Virus Utilizes Suboptimal Splicing to Coordinate the Timing of Infection
• Is RNA Interference a Physiologically Relevant Innate Antiviral Immune Response in Mammals?
• MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies
• RNA viruses and the host microRNA machinery
• An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication
• The Mammalian Response to Virus Infection Is Independent of Small RNA Silencing
• Long-term survival of influenza virus infected club cells drives immunopathology
• A Versatile RNA Vector for Delivery of Coding and Noncoding RNAs
• Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus
• Drosha as an interferon-independent antiviral factor
• Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host
• microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection
• Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response
• In Vivo RNAi Screening Identifies MDA5 as a Significant Contributor to the Cellular Defense against Influenza A Virus
• The Evolution of Antiviral Defense Systems
• RNase III nucleases from diverse kingdoms serve as antiviral effectors
• SARS-CoV-Encoded Small RNAs Contribute to Infection-Associated Lung Pathology
• Homologous recombination is an intrinsic defense against antiviral RNA interference
• Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication
• miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2
• Type I interferon response impairs differentiation potential of pluripotent stem cells
• Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses
• Synthetic Virology: Building Viruses to Better Understand Them
• Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19
• The Global Phosphorylation Landscape of SARS-CoV-2 Infection
• Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses
• A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids
• Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells
• The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types
• SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium
• Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade
• Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity
• Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission
• Reduced Nucleoprotein Availability Impairs Negative-Sense RNA Virus Replication and Promotes Host Recognition
• The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication
• A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics
• SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery
• The Host Factor ANP32A Is Required for Influenza A Virus vRNA and cRNA Synthesis
• A diminished immune response underlies age-related SARS-CoV-2 pathologies
• The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection
• Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication
• Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia
• Delayed engagement of host defenses enables SARS-CoV-2 viremia and productive infection of distal organs in the hamster model of COVID-19
• Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology
• Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA
• SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model
• ADAR1 Biology Can Hinder Effective Antiviral RNA Interference
• Mouse genome rewriting and tailoring of three important disease loci
• Transcriptional repressor Capicua is a gatekeeper of cell-intrinsic interferon responses