{ "technologies": [ { "id": "rt-qpcr", "label": "Quantitative RT-PCR", "family": "virology assays", "aliases": [ "quantitative PCR", "quantitative RT-PCR", "real-time quantitative RT-PCR", "RT-PCR", "RT-qPCR" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2013-langlois-microrna-based-strategy-to-mitigat", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-schmid-mitogen-activated-protein-kinase-m", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-han-genome-wide-crispr-cas9-screen-ide", "2018-m-ller-mirna-mediated-targeting-of-human-", "2019-eggenberger-type-i-interferon-response-impairs", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-", "2023-carrau-delayed-engagement-of-host-defense", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2023-serafini-sars-cov-2-airway-infection-result", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "bulk-rna-seq", "label": "Bulk RNA sequencing", "family": "transcriptomics and epigenomics", "aliases": [ "bulk mRNA sequencing", "bulk RNA sequencing", "messenger RNA sequencing", "mRNA deep sequencing", "mRNA sequencing", "ribosomal RNA-depleted total RNA sequencing", "RNA sequencing" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-m-ller-mirna-mediated-targeting-of-human-", "2019-eggenberger-type-i-interferon-response-impairs", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-carrau-delayed-engagement-of-host-defense", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2023-serafini-sars-cov-2-airway-infection-result", "2023-uhl-adar1-biology-can-hinder-effective", "2023-zhang-mouse-genome-rewriting-and-tailori", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "plaque-assay", "label": "Plaque assay and TCID50 titration", "family": "virology assays", "aliases": [ "plaque and TCID50 titration", "plaque assay", "TCID50 titration" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2007-tenoever-multiple-functions-of-the-ikk-rela", "2009-perez-microrna-mediated-species-specific", "2012-langlois-hematopoietic-specific-targeting-o", "2012-pham-replication-in-cells-of-hematopoie", "2013-langlois-microrna-based-strategy-to-mitigat", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-aguado-homologous-recombination-is-an-int", "2018-m-ller-mirna-mediated-targeting-of-human-", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-mccune-rapid-dissemination-and-monopoliza", "2021-daniloski-identification-of-required-host-fa", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-", "2023-carrau-delayed-engagement-of-host-defense", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-serafini-sars-cov-2-airway-infection-result", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "reverse-genetics", "label": "Reverse genetics and virus rescue", "family": "viral engineering", "aliases": [ "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": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-aguado-homologous-recombination-is-an-int", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "immunofluorescence-microscopy", "label": "Immunofluorescence and confocal microscopy", "family": "imaging and histology", "aliases": [ "confocal immunofluorescence", "immunofluorescence", "immunofluorescence confocal microscopy", "immunofluorescence microscopy", "immunofluorescence microscopy and colocalization analysis" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2018-aguado-homologous-recombination-is-an-int", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-yaron-host-protein-kinases-required-for-", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-carrau-delayed-engagement-of-host-defense", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "sirna-knockdown", "label": "Small interfering RNA and short hairpin knockdown", "family": "small RNA methods", "aliases": [ "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": [ "2003-sharma-triggering-the-interferon-antivira", "2010-schmid-transcription-factor-redundancy-en", "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2015-benitez-in-vivo-rnai-screening-identifies-", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-yaron-host-protein-kinases-required-for-", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "small-rna-seq", "label": "Small RNA deep sequencing", "family": "small RNA methods", "aliases": [ "small RNA cloning and sequencing", "small RNA deep sequencing", "small RNA sequencing" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-cullen-is-rna-interference-a-physiologica", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-shapiro-drosha-as-an-interferon-independen", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "flow-cytometry", "label": "Flow cytometry", "family": "immunology assays", "aliases": [ "flow cytometry", "flow cytometry DNA content analysis", "flow cytometry immune profiling", "flow cytometry with cross-reactive antibodies", "imaging cytometry" ], "publications": [ "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-oishi-a-diminished-immune-response-under", "2023-carrau-delayed-engagement-of-host-defense", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "small-rna-northern-blot", "label": "Small RNA northern blot", "family": "small RNA methods", "aliases": [ "small RNA Northern blot", "small RNA northern blot", "small RNA Northern blotting" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-shapiro-drosha-as-an-interferon-independen", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "mirna-target-site-insertion", "label": "MicroRNA target site insertion into viral genomes", "family": "viral engineering", "aliases": [ "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": [ "2012-langlois-hematopoietic-specific-targeting-o", "2012-pham-replication-in-cells-of-hematopoie", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-aguado-homologous-recombination-is-an-int", "2018-m-ller-mirna-mediated-targeting-of-human-", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "pathway-enrichment-analysis", "label": "Gene ontology and gene set enrichment analysis", "family": "transcriptomics and epigenomics", "aliases": [ "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": [ "2015-aguado-microrna-function-is-limited-to-cy", "2018-m-ller-mirna-mediated-targeting-of-human-", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-a-diminished-immune-response-under", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "luciferase-promoter-reporter", "label": "Luciferase promoter reporter assay", "family": "proteomics and biochemistry", "aliases": [ "interferon-stimulated response element luciferase reporter", "luciferase promoter reporter assay", "luciferase reporter assay", "luciferase reporter assays", "promoter reporter assays" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2009-perez-microrna-mediated-species-specific", "2010-schmid-transcription-factor-redundancy-en", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2014-schmid-mitogen-activated-protein-kinase-m", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-han-genome-wide-crispr-cas9-screen-ide", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "immunoblotting", "label": "Immunoblotting", "family": "proteomics and biochemistry", "aliases": [ "immunoblotting", "western blot", "western blotting" ], "publications": [ "2014-schmid-a-versatile-rna-vector-for-deliver", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2019-eggenberger-type-i-interferon-response-impairs", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "site-directed-mutagenesis", "label": "Site-directed and alanine scanning mutagenesis", "family": "functional genomics and screening", "aliases": [ "alanine scanning mutagenesis", "site-directed mutagenesis", "site-directed promoter mutagenesis", "site-directed splice site mutagenesis" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2009-perez-microrna-mediated-species-specific", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-schmid-mitogen-activated-protein-kinase-m", "2021-daniloski-the-spike-d614g-mutation-increases", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-yaron-host-protein-kinases-required-for-", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "in-vivo-infection-route", "label": "Route-controlled in vivo infection and delivery", "family": "animal, organoid and tissue models", "aliases": [ "intranasal and intravenous infection of mice", "intranasal delivery", "intranasal infection of hamsters", "intranasal interferon administration", "intranasal mouse infection", "intravenous infection" ], "publications": [ "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-schmid-a-versatile-rna-vector-for-deliver", "2017-morales-sars-cov-encoded-small-rnas-contri", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "histopathology", "label": "Histopathology", "family": "imaging and histology", "aliases": [ "haematoxylin and eosin histology", "histology and immunohistochemistry", "histopathology", "lung histology", "lung histopathology scoring" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi", "2015-benitez-engineered-mammalian-rnai-can-elic", "2017-morales-sars-cov-encoded-small-rnas-contri", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-the-host-response-to-influenza-a-v", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "northern-blot", "label": "Northern blot", "family": "small RNA methods", "aliases": [ "northern blot", "Northern blot", "Northern blotting" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2013-cullen-is-rna-interference-a-physiologica", "2013-langlois-microrna-based-strategy-to-mitigat", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "viral-population-deep-sequencing", "label": "Deep sequencing of viral populations", "family": "sequence and population analysis", "aliases": [ "deep sequencing", "deep sequencing of barcodes", "deep sequencing of virus populations", "escape mutant sequencing", "whole-genome consensus sequencing" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie", "2014-varble-influenza-a-virus-transmission-bot", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-tenoever-synthetic-virology-building-viruse", "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "emsa", "label": "Electrophoretic mobility shift assay", "family": "proteomics and biochemistry", "aliases": [ "electrophoretic mobility shift assay" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2014-schmid-mitogen-activated-protein-kinase-m", "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "elisa", "label": "ELISA", "family": "immunology assays", "aliases": [ "anti-RBD ELISA", "ELISA" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-oishi-a-diminished-immune-response-under", "2023-paget-stress-granules-are-shock-absorber", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "immunohistochemistry", "label": "Immunohistochemistry", "family": "imaging and histology", "aliases": [ "immunohistochemistry" ], "publications": [ "2017-morales-sars-cov-encoded-small-rnas-contri", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2022-oishi-a-diminished-immune-response-under", "2023-carrau-delayed-engagement-of-host-defense", "2023-serafini-sars-cov-2-airway-infection-result", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "growth-curve", "label": "Multicycle growth curves", "family": "virology assays", "aliases": [ "multicycle growth curve", "multicycle growth curves" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-varble-an-in-vivo-rnai-screening-approach", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "multiplex-cytokine-assay", "label": "Multiplexed cytokine measurement", "family": "immunology assays", "aliases": [ "cytokine multiplex assay", "ELISA cytokine profiling", "Luminex cytokine panel", "multiplex bead cytokine array", "multiplexed ELISA" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi", "2015-aguado-microrna-function-is-limited-to-cy", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "small-molecule-inhibitor-profiling", "label": "Small molecule inhibitor profiling", "family": "virology assays", "aliases": [ "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": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "barcoded-virus-library", "label": "Barcoded virus libraries", "family": "viral engineering", "aliases": [ "barcoded virus libraries", "barcoded virus library", "genetic barcoding", "RNA barcoding" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach", "2014-varble-influenza-a-virus-transmission-bot", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "in-vitro-reconstitution", "label": "In vitro reconstitution with purified components", "family": "proteomics and biochemistry", "aliases": [ "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": [ "2012-perez-a-small-rna-enhancer-of-viral-poly", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "adenoviral-vector", "label": "Adenoviral vector delivery", "family": "functional genomics and screening", "aliases": [ "adenoviral overexpression", "adenoviral reconstitution", "adenoviral vector delivery", "adenoviral vector transduction" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2015-aguado-microrna-function-is-limited-to-cy", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "animal-transmission-model", "label": "Animal transmission models", "family": "animal, organoid and tissue models", "aliases": [ "cohousing transmission model", "ferret transmission study", "hamster challenge and transmission models", "nebulized aerosol exposure" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat", "2014-varble-influenza-a-virus-transmission-bot", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "co-ip", "label": "Coimmunoprecipitation", "family": "proteomics and biochemistry", "aliases": [ "coimmunoprecipitation", "immunoprecipitation" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2014-schmid-mitogen-activated-protein-kinase-m", "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "crispr-knockout", "label": "CRISPR-Cas9 knockout cell lines", "family": "functional genomics and screening", "aliases": [ "CRISPR Cas9 gene disruption", "CRISPR knockout", "CRISPR knockout cell lines", "CRISPR-Cas9 knockout" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2023-paget-stress-granules-are-shock-absorber", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "in-vitro-kinase-assay", "label": "In vitro kinase assay", "family": "proteomics and biochemistry", "aliases": [ "in vitro kinase assay", "in vitro kinase assays", "radiolabeled ATP incorporation", "recombinant kinase assay" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2007-tenoever-multiple-functions-of-the-ikk-rela", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "lentiviral-transduction", "label": "Lentiviral transduction", "family": "functional genomics and screening", "aliases": [ "lentiviral microRNA transduction", "lentiviral transduction", "lentiviral vectors" ], "publications": [ "2010-schmid-transcription-factor-redundancy-en", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2018-han-genome-wide-crispr-cas9-screen-ide", "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "mass-spectrometry-proteomics", "label": "Mass spectrometry proteomics", "family": "proteomics and biochemistry", "aliases": [ "mass spectrometry", "mass spectrometry proteomics", "quantitative mass spectrometry", "quantitative mass spectrometry proteomics" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-si-a-human-airway-on-a-chip-for-the-r", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "phylogenetics", "label": "Phylogenetic and coalescent analysis", "family": "sequence and population analysis", "aliases": [ "dated coalescent analysis", "maximum likelihood phylogenetics", "phylogenetic analysis", "phylogenetic inference" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2021-guzman-solis-ancient-viral-genomes-reveal-intro", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "silencing-reporter-assay", "label": "Post-transcriptional silencing reporter assay", "family": "small RNA methods", "aliases": [ "luciferase 3-prime UTR reporter assay", "luciferase reporter silencing assay", "reporter silencing assay", "reporter-based post-transcriptional silencing assay" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "pseudotyped-entry-reporter", "label": "Pseudotyped entry reporters", "family": "virology assays", "aliases": [ "beta-lactamase virus-like particle entry assay", "lentiviral pseudotyping", "pseudotyped virus entry assay", "vesicular stomatitis virus pseudo-entry virus" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "rna-in-situ-hybridization", "label": "RNA in situ hybridisation", "family": "imaging and histology", "aliases": [ "RNA in situ hybridization", "RNAscope in situ hybridization" ], "publications": [ "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "single-cell-rna-seq", "label": "Single-cell RNA sequencing", "family": "transcriptomics and epigenomics", "aliases": [ "single-cell RNA sequencing" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "artificial-mirna", "label": "Virus-encoded artificial microRNAs", "family": "viral engineering", "aliases": [ "artificial microRNA expression", "artificial microRNAs", "virus-encoded artificial microRNA" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-benitez-engineered-mammalian-rnai-can-elic", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "amplicon-sequencing", "label": "Amplicon sequencing", "family": "sequence and population analysis", "aliases": [ "amplicon sequencing", "unique molecular identifier amplicon sequencing" ], "publications": [ "2021-daniloski-identification-of-required-host-fa", "2023-uhl-adar1-biology-can-hinder-effective", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "argonaute-ip", "label": "Argonaute immunoprecipitation", "family": "small RNA methods", "aliases": [ "Argonaute 2 immunoprecipitation", "argonaute immunoprecipitation", "Argonaute immunoprecipitation" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr" ] }, { "id": "atac-seq", "label": "ATAC sequencing", "family": "transcriptomics and epigenomics", "aliases": [ "ATAC sequencing", "ATAC-seq" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2023-zhang-mouse-genome-rewriting-and-tailori", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "cell-sorting", "label": "Cell and nuclei sorting", "family": "immunology assays", "aliases": [ "fluorescence-activated cell sorting", "fluorescence-activated nuclei sorting", "magnetic-activated cell sorting" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie", "2014-heaton-long-term-survival-of-influenza-vi", "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "cell-death-assays", "label": "Cell viability and cell death assays", "family": "imaging and histology", "aliases": [ "cell viability assay", "Sytox and caspase activity cell death assays", "TUNEL staining" ], "publications": [ "2014-schmid-a-versatile-rna-vector-for-deliver", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "chip", "label": "Chromatin immunoprecipitation and CUT&RUN", "family": "transcriptomics and epigenomics", "aliases": [ "ChIP sequencing", "chromatin immunoprecipitation", "CUT&RUN" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "conditional-knockout", "label": "Conditional and inducible gene knockout", "family": "functional genomics and screening", "aliases": [ "conditional gene knockout", "conditional knockout with Cre-expressing adenoviral vectors", "tamoxifen-inducible conditional knockout mouse" ], "publications": [ "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2014-shapiro-drosha-as-an-interferon-independen", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "dimensionality-reduction", "label": "Dimensionality reduction and clustering", "family": "transcriptomics and epigenomics", "aliases": [ "multidimensional scaling", "network and medoid clustering analysis", "principal component analysis", "sparse principal component analysis" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "genome-wide-crispr-screen", "label": "Genome-wide CRISPR-Cas9 knockout screening", "family": "functional genomics and screening", "aliases": [ "GeCKO library", "GeCKOv2 library", "genome-scale CRISPR-Cas9 knockout screening", "genome-wide CRISPR knockout screening", "MAGeCK analysis", "robust rank aggregation" ], "publications": [ "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "in-vivo-rnai-screen", "label": "In vivo RNAi screening through viral fitness", "family": "functional genomics and screening", "aliases": [ "artificial microRNA libraries", "artificial microRNA library", "in vivo RNAi screening" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach", "2015-benitez-in-vivo-rnai-screening-identifies-", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "knockout-mice", "label": "Knockout mouse infection", "family": "functional genomics and screening", "aliases": [ "gene knockout mice", "knockout mouse infection" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2015-benitez-in-vivo-rnai-screening-identifies-" ] }, { "id": "lna-antisense-inhibition", "label": "Locked nucleic acid antisense inhibition", "family": "small RNA methods", "aliases": [ "locked nucleic acid antagomir inhibition", "locked nucleic acid antimiR inhibition", "locked nucleic acid antisense inhibition" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "minigenome-assay", "label": "Minigenome, minireplicon and replicon reporters", "family": "proteomics and biochemistry", "aliases": [ "minigenome assay", "minireplicon systems", "Sindbis replicon and luciferase reporters" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2019-tenoever-synthetic-virology-building-viruse", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "primer-extension", "label": "Primer extension", "family": "small RNA methods", "aliases": [ "primer extension" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "translation-measurement", "label": "Radiolabelling and translation measurement", "family": "proteomics and biochemistry", "aliases": [ "in vivo radiolabeling", "puromycin incorporation translation assay", "radiolabeled amino acid tracing" ], "publications": [ "2014-schmid-mitogen-activated-protein-kinase-m", "2020-mccune-rapid-dissemination-and-monopoliza", "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "serial-passage", "label": "Serial passage and selection", "family": "viral engineering", "aliases": [ "in vivo serial passage selection", "serial passage", "serial passage selection" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach", "2018-aguado-homologous-recombination-is-an-int", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "short-read-sequencing-platform", "label": "Short-read sequencing platforms", "family": "sequence and population analysis", "aliases": [ "Illumina deep sequencing", "Illumina MiSeq", "SOLiD sequencing" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2014-varble-influenza-a-virus-transmission-bot", "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "2a-recoding", "label": "2A peptide recoding of viral segments", "family": "viral engineering", "aliases": [ "2A peptide polycistronic design", "2A ribosome recoding" ], "publications": [ "2013-chua-influenza-a-virus-utilizes-subopti", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "antigen-specific-b-cell-detection", "label": "Antigen-specific B cell detection", "family": "immunology assays", "aliases": [ "antigen-specific B cell staining", "biotinylated antigen B cell probe" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "bac-recombineering", "label": "Bacterial artificial chromosome recombineering", "family": "viral engineering", "aliases": [ "bacterial artificial chromosomes", "galK one-step BAC recombineering" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "behavioural-and-sensory-testing", "label": "Behavioural and sensory testing", "family": "animal, organoid and tissue models", "aliases": [ "buried food finding test", "Hargreaves thermal testing", "locomotor beam break assay", "marble burying assay", "von Frey monofilament testing" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "deconvolution", "label": "Cell type deconvolution of bulk transcriptomes", "family": "transcriptomics and epigenomics", "aliases": [ "cell type deconvolution", "RNA sequencing deconvolution" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "comparative-sequence-analysis", "label": "Comparative genomics and conservation analysis", "family": "sequence and population analysis", "aliases": [ "comparative genomics", "comparative sequence conservation analysis", "evolutionary parsimony analysis" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "cre-lox-lineage-tracing", "label": "Cre-LoxP lineage tracing of infected cells", "family": "animal, organoid and tissue models", "aliases": [ "Cre-lox lineage tracing", "Cre-LoxP lineage tracing", "tdTomato reporter mice" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "differential-expression-analysis", "label": "Differential expression analysis", "family": "transcriptomics and epigenomics", "aliases": [ "differential expression analysis with DESeq2", "differential gene expression analysis" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-", "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "hpsc-directed-differentiation", "label": "Directed differentiation of human pluripotent stem cells", "family": "animal, organoid and tissue models", "aliases": [ "directed differentiation of human pluripotent stem cells", "directed trilineage differentiation", "embryoid body cardiomyocyte differentiation", "hPSC ScoreCard assay" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs", "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "inducible-expression", "label": "Doxycycline-inducible lentiviral expression", "family": "functional genomics and screening", "aliases": [ "doxycycline-inducible lentiviral expression", "lentiviral doxycycline-inducible expression" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "cell-division-tracking", "label": "Dye dilution cell division tracking", "family": "immunology assays", "aliases": [ "CellTrace Violet labeling", "CFSE cell division tracking" ], "publications": [ "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2021-horiuchi-immune-memory-from-sars-cov-2-infe" ] }, { "id": "engineered-tf-constructs", "label": "Engineered transcription factor constructs", "family": "functional genomics and screening", "aliases": [ "chimeric VPR transcriptional activators", "constitutively active IRF7 truncation" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs", "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "microarray", "label": "Expression microarray", "family": "transcriptomics and epigenomics", "aliases": [ "Affymetrix microarray" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en" ] }, { "id": "phosphoproteomics", "label": "Phosphoproteomics", "family": "proteomics and biochemistry", "aliases": [ "data-independent acquisition phosphoproteomics", "phosphoproteomics by liquid chromatography mass spectrometry" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "phospho-immunoblotting", "label": "Phosphospecific immunoblotting and phosphatase treatment", "family": "proteomics and biochemistry", "aliases": [ "phosphatase treatment", "phosphospecific immunoblotting" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "neutralization-assay", "label": "Plaque reduction neutralisation test", "family": "immunology assays", "aliases": [ "plaque reduction neutralization test" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "population-diversity-statistics", "label": "Population diversity statistics and simulation", "family": "sequence and population analysis", "aliases": [ "Monte Carlo simulation", "Shannon diversity analysis" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot", "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "motif-analysis", "label": "Promoter motif discovery and enrichment", "family": "transcriptomics and epigenomics", "aliases": [ "motif discovery", "motif enrichment analysis" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "single-cycle-influenza-vector", "label": "Replication-incompetent influenza vector", "family": "viral engineering", "aliases": [ "replication-incompetent virus-like vectors" ], "publications": [ "2013-chua-influenza-a-virus-utilizes-subopti", "2014-schmid-a-versatile-rna-vector-for-deliver" ] }, { "id": "rna-immunoprecipitation", "label": "RNA immunoprecipitation", "family": "small RNA methods", "aliases": [ "RNA immunoprecipitation" ], "publications": [ "2012-perez-a-small-rna-enhancer-of-viral-poly", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "small-rna-rt-qpcr", "label": "Stem-loop quantitative RT-PCR for small RNAs", "family": "small RNA methods", "aliases": [ "small RNA RT-qPCR", "stem-loop quantitative RT-PCR" ], "publications": [ "2010-varble-engineered-rna-viral-synthesis-of-", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "subcellular-fractionation", "label": "Subcellular fractionation", "family": "proteomics and biochemistry", "aliases": [ "subcellular fractionation" ], "publications": [ "2012-perez-a-small-rna-enhancer-of-viral-poly", "2014-shapiro-drosha-as-an-interferon-independen" ] }, { "id": "synthetic-rna-mimetics", "label": "Synthetic and chemically modified RNA mimetics", "family": "small RNA methods", "aliases": [ "synthetic 5-prime triphosphate RNA chemistry", "synthetic modified RNA mimetics" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2012-perez-a-small-rna-enhancer-of-viral-poly" ] }, { "id": "targeted-capture", "label": "Targeted in-solution hybridisation capture", "family": "sequence and population analysis", "aliases": [ "capture sequencing", "targeted in-solution hybridisation capture" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "tf-activity-inference", "label": "Transcription factor activity and motif accessibility inference", "family": "transcriptomics and epigenomics", "aliases": [ "transcription factor activity inference", "transcription factor motif accessibility analysis" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "five-prime-race", "label": "5 prime RACE", "family": "small RNA methods", "aliases": [ "5' RACE" ], "publications": [ "2010-varble-engineered-rna-viral-synthesis-of-" ] }, { "id": "aav-vector", "label": "Adeno-associated virus vectors", "family": "functional genomics and screening", "aliases": [ "adeno-associated virus vectors" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "adoptive-transfer", "label": "Adoptive cell transfer", "family": "immunology assays", "aliases": [ "adoptive cell transfer" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe" ] }, { "id": "agroinfiltration", "label": "Agroinfiltration of plant tissue", "family": "functional genomics and screening", "aliases": [ "agroinfiltration" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "ali-culture", "label": "Air-liquid interface culture", "family": "animal, organoid and tissue models", "aliases": [ "air-liquid interface culture" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "virus-amplification-assay", "label": "Amplification on permissive cells to detect low-level infectious virus", "family": "virology assays", "aliases": [ "virus amplification on permissive cells" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "ancient-dna", "label": "Ancient DNA extraction", "family": "sequence and population analysis", "aliases": [ "ancient DNA extraction" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "biolayer-interferometry", "label": "Bio-layer interferometry", "family": "proteomics and biochemistry", "aliases": [ "bio-layer interferometry" ], "publications": [ "2021-daniloski-the-spike-d614g-mutation-increases" ] }, { "id": "genetic-complementation", "label": "cDNA complementation of knockouts", "family": "functional genomics and screening", "aliases": [ "cDNA complementation" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "metabolite-quantification", "label": "Cellular cholesterol quantification", "family": "proteomics and biochemistry", "aliases": [ "cholesterol quantification" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "cellular-reprogramming", "label": "Cellular reprogramming to pluripotency", "family": "genome engineering", "aliases": [ "cellular reprogramming with OCT4 SOX2 KLF4 and c-MYC" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "splicing-reporter", "label": "Chimeric minigene splicing reporters", "family": "proteomics and biochemistry", "aliases": [ "chimeric minigene reporters" ], "publications": [ "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "kinase-substrate-profiling", "label": "Combinatorial peptide substrate specificity profiling", "family": "proteomics and biochemistry", "aliases": [ "combinatorial peptide substrate specificity profiling" ], "publications": [ "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "meta-analysis", "label": "Cross-dataset meta-analysis", "family": "transcriptomics and epigenomics", "aliases": [ "cross-dataset meta-analysis" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "de-novo-transcriptome-assembly", "label": "De novo transcriptome assembly", "family": "transcriptomics and epigenomics", "aliases": [ "de novo transcriptome assembly" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in" ] }, { "id": "ancient-dna-authentication", "label": "Deamination damage authentication", "family": "sequence and population analysis", "aliases": [ "deamination damage analysis" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "deep-mutational-scanning", "label": "Deep mutational scanning", "family": "viral engineering", "aliases": [ "deep mutational scanning" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "electron-microscopy", "label": "Electron microscopy", "family": "imaging and histology", "aliases": [ "scanning electron microscopy", "transmission electron microscopy" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca" ] }, { "id": "barrier-permeability", "label": "Epithelial barrier permeability measurement", "family": "animal, organoid and tissue models", "aliases": [ "barrier permeability measurement" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "heterologous-protein-expression-screen", "label": "Expression screening of codon-optimised heterologous proteins", "family": "functional genomics and screening", "aliases": [ "expression screening of codon-optimized proteins" ], "publications": [ "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "reporter-virus", "label": "Fluorescent and luciferase reporter viruses", "family": "viral engineering", "aliases": [ "fluorescent and luciferase reporter viruses" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "fluorescent-fusion-localization", "label": "Fluorescent fusion protein localisation", "family": "imaging and histology", "aliases": [ "GFP fusion localization" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira" ] }, { "id": "rnai-machinery-knockout-cells", "label": "Genetic panels lacking small RNA machinery", "family": "small RNA methods", "aliases": [ "Argonaute knockout cells", "Dicer deficient cells" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "competition-assay", "label": "Head-to-head competition assay", "family": "functional genomics and screening", "aliases": [ "in vitro competition assay" ], "publications": [ "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "hemagglutination-inhibition", "label": "Hemagglutination inhibition assay", "family": "immunology assays", "aliases": [ "hemagglutination inhibition assay" ], "publications": [ "2009-perez-microrna-mediated-species-specific" ] }, { "id": "high-content-imaging", "label": "High-content microscopy", "family": "imaging and histology", "aliases": [ "high-content microscopy" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "host-ancestry-analysis", "label": "Host genetic ancestry analysis", "family": "sequence and population analysis", "aliases": [ "ADMIXTURE ancestry analysis", "principal component analysis of ancient genomes" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "in-situ-hi-c", "label": "In situ Hi-C and compartment analysis", "family": "transcriptomics and epigenomics", "aliases": [ "hidden Markov model compartment analysis", "in situ Hi-C" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "interferon-bioassay", "label": "Interferon bioassay", "family": "immunology assays", "aliases": [ "interferon bioassay" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "xenotransplantation", "label": "Kidney capsule xenotransplantation", "family": "animal, organoid and tissue models", "aliases": [ "kidney capsule xenotransplantation" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "kinase-activity-inference", "label": "Kinase activity inference", "family": "proteomics and biochemistry", "aliases": [ "kinase activity inference" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca" ] }, { "id": "lectin-staining", "label": "Lectin staining of surface glycans", "family": "imaging and histology", "aliases": [ "lectin staining" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "tetramer-staining", "label": "MHC class I tetramer staining", "family": "immunology assays", "aliases": [ "MHC class I tetramer staining" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o" ] }, { "id": "epitope-prediction", "label": "MHC epitope prediction", "family": "immunology assays", "aliases": [ "MHC epitope prediction" ], "publications": [ "2021-daniloski-the-spike-d614g-mutation-increases" ] }, { "id": "morpholino-knockdown", "label": "Morpholino knockdown", "family": "small RNA methods", "aliases": [ "morpholino knockdown" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "mswap-in-genome-writing", "label": "mSwAP-In iterative genome writing", "family": "genome engineering", "aliases": [ "CRISPR-Cas9 assisted homologous recombination", "mSwAP-In genome writing", "yeast assembly of large DNA" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "neutral-red-labeling", "label": "Neutral red light-sensitive virus labeling", "family": "viral engineering", "aliases": [ "neutral red light-sensitive virus labeling" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "splice-junction-analysis", "label": "Noncanonical splice junction read analysis", "family": "transcriptomics and epigenomics", "aliases": [ "noncanonical junction read analysis" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "delns1-virus", "label": "NS1-deleted influenza A virus", "family": "viral engineering", "aliases": [ "influenza A virus lacking NS1" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "organ-on-chip", "label": "Organ-on-a-chip microfluidics", "family": "animal, organoid and tissue models", "aliases": [ "organ-on-a-chip microfluidics" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "organoid-culture", "label": "Organoid culture", "family": "animal, organoid and tissue models", "aliases": [ "organoid culture" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "t-cell-restimulation", "label": "Peptide restimulation of T cells", "family": "immunology assays", "aliases": [ "peptide restimulation assay" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe" ] }, { "id": "pharmacokinetics", "label": "Pharmacokinetic analysis", "family": "animal, organoid and tissue models", "aliases": [ "pharmacokinetic analysis" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "immunosuppression-treatment", "label": "Pharmacological immunosuppression", "family": "animal, organoid and tissue models", "aliases": [ "dexamethasone immunosuppression" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "phos-tag-electrophoresis", "label": "Phos-tag gel electrophoresis", "family": "proteomics and biochemistry", "aliases": [ "Phos-tag gel electrophoresis" ], "publications": [ "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "archaeometric-dating", "label": "Radiocarbon dating and strontium isotope analysis", "family": "sequence and population analysis", "aliases": [ "radiocarbon dating", "strontium isotope analysis" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "rna-affinity-tagging", "label": "RNA affinity tagging of viral genomes", "family": "viral engineering", "aliases": [ "RNA affinity tagging" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "selex", "label": "SELEX selection of bound RNA", "family": "small RNA methods", "aliases": [ "SELEX" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "serum-transfer", "label": "Serum transfer with ultraviolet inactivation", "family": "animal, organoid and tissue models", "aliases": [ "serum transfer with ultraviolet inactivation" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "metagenomic-sequencing", "label": "Shotgun metagenomic sequencing", "family": "sequence and population analysis", "aliases": [ "shotgun metagenomic sequencing" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "single-cell-crispr-screen", "label": "Single-cell CRISPR screening with ECCITE-seq", "family": "functional genomics and screening", "aliases": [ "ECCITE-seq single-cell CRISPR screening" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "single-molecule-fret", "label": "Single-molecule FRET", "family": "proteomics and biochemistry", "aliases": [ "single-molecule FRET" ], "publications": [ "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "size-exclusion-chromatography", "label": "Size-exclusion chromatography", "family": "proteomics and biochemistry", "aliases": [ "size-exclusion chromatography" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "degron-shutoff", "label": "Small molecule-assisted shutoff of viral proteins", "family": "viral engineering", "aliases": [ "small molecule-assisted shutoff" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "split-ns-segment", "label": "Split NS segment 8 design", "family": "viral engineering", "aliases": [ "split NS segment design" ], "publications": [ "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "vsr-mutant-viruses", "label": "Suppressor-deficient virus mutants", "family": "viral engineering", "aliases": [ "viral suppressor mutant viruses" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "antigen-presentation-assay", "label": "T cell hybridoma antigen presentation assay", "family": "immunology assays", "aliases": [ "CD8 T cell hybridoma antigen presentation assay" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o" ] }, { "id": "cell-ablation", "label": "Targeted cell ablation", "family": "animal, organoid and tissue models", "aliases": [ "diphtheria toxin receptor depletion" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi" ] }, { "id": "tetraploid-complementation", "label": "Tetraploid blastocyst complementation", "family": "genome engineering", "aliases": [ "tetraploid blastocyst complementation" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "trans-complementation-assay", "label": "Trans-complementation infection assay", "family": "functional genomics and screening", "aliases": [ "trans-complementation infection assay" ], "publications": [ "2021-daniloski-the-spike-d614g-mutation-increases" ] }, { "id": "metabolic-inhibitor-blocks", "label": "Transcription and translation inhibitor blocks", "family": "proteomics and biochemistry", "aliases": [ "cycloheximide and actinomycin D blocks" ], "publications": [ "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "transposon-mutagenesis", "label": "Transposon insertional mutagenesis of viral genomes", "family": "viral engineering", "aliases": [ "transposon insertional mutagenesis" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "clip-seq", "label": "UV crosslinking immunoprecipitation sequencing", "family": "small RNA methods", "aliases": [ "UV crosslinking immunoprecipitation sequencing" ], "publications": [ "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "vp55-mirna-ablation", "label": "VP55-mediated ablation of the cellular microRNA pool", "family": "viral engineering", "aliases": [ "VP55 poly(A) polymerase microRNA degradation" ], "publications": [ "2015-aguado-microrna-function-is-limited-to-cy" ] } ], "pathogens": [ { "id": "influenza-a-virus", "label": "Influenza A virus", "family": "Orthomyxoviridae", "aliases": [ "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": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2010-varble-engineered-rna-viral-synthesis-of-", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-cullen-is-rna-interference-a-physiologica", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-eggenberger-type-i-interferon-response-impairs", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-oishi-the-host-response-to-influenza-a-v", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2023-serafini-sars-cov-2-airway-infection-result", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "sars-cov-2", "label": "SARS-CoV-2", "family": "Coronaviridae", "aliases": [ "SARS-CoV-2", "SARS-CoV-2 B.1.351 beta variant", "SARS-CoV-2 USA-WA1/2020" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-carrau-delayed-engagement-of-host-defense", "2023-serafini-sars-cov-2-airway-infection-result", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "vsv", "label": "Vesicular stomatitis virus", "family": "Rhabdoviridae", "aliases": [ "vesicular stomatitis virus" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2010-perez-influenza-a-virus-generated-small-", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-si-a-human-airway-on-a-chip-for-the-r", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "sindbis-virus", "label": "Sindbis virus", "family": "Togaviridae", "aliases": [ "Sindbis virus" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "sendai-virus", "label": "Sendai virus", "family": "Paramyxoviridae", "aliases": [ "Sendai virus" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-paget-stress-granules-are-shock-absorber", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "emcv", "label": "Encephalomyocarditis virus", "family": "Picornaviridae", "aliases": [ "encephalomyocarditis virus" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2018-han-genome-wide-crispr-cas9-screen-ide", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "hpiv3", "label": "Human parainfluenza virus 3", "family": "Paramyxoviridae", "aliases": [ "human parainfluenza virus 3", "human parainfluenza virus type 3" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "poliovirus", "label": "Poliovirus", "family": "Picornaviridae", "aliases": [ "poliovirus" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2018-aguado-homologous-recombination-is-an-int", "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "rsv", "label": "Respiratory syncytial virus", "family": "Pneumoviridae", "aliases": [ "human respiratory syncytial virus", "respiratory syncytial virus" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "vaccinia-virus", "label": "Vaccinia virus", "family": "Poxviridae", "aliases": [ "vaccinia virus" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2014-backes-the-mammalian-response-to-virus-in", "2015-aguado-microrna-function-is-limited-to-cy" ] }, { "id": "adenovirus", "label": "Adenovirus", "family": "Adenoviridae", "aliases": [ "adenovirus", "adenovirus type 5" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2015-aguado-microrna-function-is-limited-to-cy" ] }, { "id": "dengue-virus", "label": "Dengue virus", "family": "Flaviviridae", "aliases": [ "dengue virus", "dengue virus serotype 2" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie", "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "ebola-virus", "label": "Ebola virus", "family": "Filoviridae", "aliases": [ "Ebola virus" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "sars-cov", "label": "SARS-CoV", "family": "Coronaviridae", "aliases": [ "SARS-CoV", "SARS-CoV-1", "severe acute respiratory syndrome coronavirus" ], "publications": [ "2017-morales-sars-cov-encoded-small-rnas-contri", "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "zika-virus", "label": "Zika virus", "family": "Flaviviridae", "aliases": [ "Zika virus" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "amsacta-entomopoxvirus", "label": "Amsacta moorei entomopoxvirus", "family": "Poxviridae", "aliases": [ "Amsacta moorei entomopoxvirus" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p" ] }, { "id": "bacteriophage", "label": "Bacteriophage", "family": "phage", "aliases": [ "bacteriophage" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "borna-disease-virus", "label": "Borna disease virus", "family": "Bornaviridae", "aliases": [ "Borna disease virus" ], "publications": [ "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "blv", "label": "Bovine leukaemia virus", "family": "Retroviridae", "aliases": [ "bovine leukaemia virus" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "coxsackievirus-b3", "label": "Coxsackievirus B3", "family": "Picornaviridae", "aliases": [ "coxsackievirus B3" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "dna-viruses", "label": "DNA viruses as a group", "family": "group", "aliases": [ "DNA viruses" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "drosophila-c-virus", "label": "Drosophila C virus", "family": "Dicistroviridae", "aliases": [ "Drosophila C virus" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "hbv", "label": "Hepatitis B virus", "family": "Hepadnaviridae", "aliases": [ "hepatitis B virus" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "hcv", "label": "Hepatitis C virus", "family": "Flaviviridae", "aliases": [ "hepatitis C virus" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "herpesviruses", "label": "Herpesviruses as a group", "family": "Herpesviridae", "aliases": [ "herpesviruses" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "hcov-229e", "label": "Human coronavirus 229E", "family": "Coronaviridae", "aliases": [ "human coronavirus 229E" ], "publications": [ "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "hcov-oc43", "label": "Human coronavirus OC43", "family": "Coronaviridae", "aliases": [ "human coronavirus OC43" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "hcmv", "label": "Human cytomegalovirus", "family": "Herpesviridae", "aliases": [ "human cytomegalovirus" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "hiv-1", "label": "Human immunodeficiency virus 1", "family": "Retroviridae", "aliases": [ "human immunodeficiency virus 1" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "parvovirus-b19", "label": "Human parvovirus B19", "family": "Parvoviridae", "aliases": [ "human parvovirus B19" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "infectious-salmon-anemia-virus", "label": "Infectious salmon anemia virus", "family": "Orthomyxoviridae", "aliases": [ "infectious salmon anemia virus" ], "publications": [ "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "influenza-b-virus", "label": "Influenza B virus", "family": "Orthomyxoviridae", "aliases": [ "influenza B virus" ], "publications": [ "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "langat-virus", "label": "Langat virus", "family": "Flaviviridae", "aliases": [ "Langat virus" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "lassa-virus", "label": "Lassa virus", "family": "Arenaviridae", "aliases": [ "Lassa virus" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "measles-virus", "label": "Measles virus", "family": "Paramyxoviridae", "aliases": [ "measles virus" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "mers-cov", "label": "MERS-CoV", "family": "Coronaviridae", "aliases": [ "MERS-CoV" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "nodamura-virus", "label": "Nodamura virus", "family": "Nodaviridae", "aliases": [ "nodamura virus" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "poxviruses", "label": "Poxviruses as a group", "family": "Poxviridae", "aliases": [ "poxviruses" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "rna-viruses", "label": "RNA viruses as a group", "family": "group", "aliases": [ "RNA viruses" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "ross-river-virus", "label": "Ross River virus", "family": "Togaviridae", "aliases": [ "Ross River virus" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "semliki-forest-virus", "label": "Semliki Forest virus", "family": "Togaviridae", "aliases": [ "Semliki Forest virus" ], "publications": [ "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "turnip-crinkle-virus", "label": "Turnip crinkle virus", "family": "Tombusviridae", "aliases": [ "turnip crinkle virus" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "west-nile-virus", "label": "West Nile virus", "family": "Flaviviridae", "aliases": [ "West Nile virus" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] } ], "viral_families": [ { "id": "orthomyxoviridae", "label": "Orthomyxoviridae", "family": "negative-sense segmented RNA", "aliases": [ "Orthomyxoviridae" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2010-varble-engineered-rna-viral-synthesis-of-", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-cullen-is-rna-interference-a-physiologica", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-eggenberger-type-i-interferon-response-impairs", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-oishi-the-host-response-to-influenza-a-v", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2023-serafini-sars-cov-2-airway-infection-result", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "coronaviridae", "label": "Coronaviridae", "family": "positive-sense RNA", "aliases": [ "Coronaviridae" ], "publications": [ "2017-morales-sars-cov-encoded-small-rnas-contri", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-carrau-delayed-engagement-of-host-defense", "2023-serafini-sars-cov-2-airway-infection-result", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "rhabdoviridae", "label": "Rhabdoviridae", "family": "negative-sense nonsegmented RNA", "aliases": [ "Rhabdoviridae" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2010-perez-influenza-a-virus-generated-small-", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2018-han-genome-wide-crispr-cas9-screen-ide", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-si-a-human-airway-on-a-chip-for-the-r", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "togaviridae", "label": "Togaviridae", "family": "positive-sense RNA", "aliases": [ "Togaviridae" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "paramyxoviridae", "label": "Paramyxoviridae", "family": "negative-sense nonsegmented RNA", "aliases": [ "Paramyxoviridae" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-paget-stress-granules-are-shock-absorber", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "picornaviridae", "label": "Picornaviridae", "family": "positive-sense RNA", "aliases": [ "Picornaviridae" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2020-mccune-rapid-dissemination-and-monopoliza", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "flaviviridae", "label": "Flaviviridae", "family": "positive-sense RNA", "aliases": [ "Flaviviridae" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-han-genome-wide-crispr-cas9-screen-ide", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "poxviridae", "label": "Poxviridae", "family": "double-stranded DNA", "aliases": [ "Poxviridae" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2015-aguado-microrna-function-is-limited-to-cy" ] }, { "id": "pneumoviridae", "label": "Pneumoviridae", "family": "negative-sense nonsegmented RNA", "aliases": [ "Pneumoviridae" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "adenoviridae", "label": "Adenoviridae", "family": "double-stranded DNA", "aliases": [ "Adenoviridae" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2015-aguado-microrna-function-is-limited-to-cy" ] }, { "id": "filoviridae", "label": "Filoviridae", "family": "negative-sense nonsegmented RNA", "aliases": [ "Filoviridae" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "herpesviridae", "label": "Herpesviridae", "family": "double-stranded DNA", "aliases": [ "Herpesviridae" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "retroviridae", "label": "Retroviridae", "family": "reverse-transcribing", "aliases": [ "Retroviridae" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "arenaviridae", "label": "Arenaviridae", "family": "negative-sense segmented RNA", "aliases": [ "Arenaviridae" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "bornaviridae", "label": "Bornaviridae", "family": "negative-sense nonsegmented RNA", "aliases": [ "Bornaviridae" ], "publications": [ "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "dicistroviridae", "label": "Dicistroviridae", "family": "positive-sense RNA", "aliases": [ "Dicistroviridae" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "hepadnaviridae", "label": "Hepadnaviridae", "family": "reverse-transcribing", "aliases": [ "Hepadnaviridae" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "nodaviridae", "label": "Nodaviridae", "family": "positive-sense RNA", "aliases": [ "Nodaviridae" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "parvoviridae", "label": "Parvoviridae", "family": "single-stranded DNA", "aliases": [ "Parvoviridae" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "tombusviridae", "label": "Tombusviridae", "family": "positive-sense RNA", "aliases": [ "Tombusviridae" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] } ], "host_species": [ { "id": "human", "label": "Human", 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"2014-schmid-a-versatile-rna-vector-for-deliver", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2014-varble-influenza-a-virus-transmission-bot", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2016-tenoever-the-evolution-of-antiviral-defense", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2018-m-ller-mirna-mediated-targeting-of-human-", "2019-eggenberger-type-i-interferon-response-impairs", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-mccune-rapid-dissemination-and-monopoliza", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-guzman-solis-ancient-viral-genomes-reveal-intro", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2023-uhl-adar1-biology-can-hinder-effective", "2023-zhang-mouse-genome-rewriting-and-tailori", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "mouse", "label": "Mouse", "family": "mammal", "aliases": [ "mouse" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-cullen-is-rna-interference-a-physiologica", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2014-varble-influenza-a-virus-transmission-bot", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2016-tenoever-the-evolution-of-antiviral-defense", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri", "2018-aguado-homologous-recombination-is-an-int", "2019-eggenberger-type-i-interferon-response-impairs", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2020-mccune-rapid-dissemination-and-monopoliza", "2020-yang-a-human-pluripotent-stem-cell-base", "2023-serafini-sars-cov-2-airway-infection-result", "2023-uhl-adar1-biology-can-hinder-effective", "2023-zhang-mouse-genome-rewriting-and-tailori", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "golden-hamster", "label": "Golden hamster", "family": "mammal", "aliases": [ "golden hamster", "hamster", "hamster cells" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-cullen-is-rna-interference-a-physiologica", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-carrau-delayed-engagement-of-host-defense", "2023-serafini-sars-cov-2-airway-infection-result", "2023-uhl-adar1-biology-can-hinder-effective", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "dog", "label": "Dog", "family": "mammal", "aliases": [ "canine", "canine cells", "dog" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-hematopoietic-specific-targeting-o", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-langlois-microrna-based-strategy-to-mitigat", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "chicken", "label": "Chicken", "family": "bird", "aliases": [ "chicken", "chicken embryo" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-varble-engineered-rna-viral-synthesis-of-", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "african-green-monkey", "label": "African green monkey", "family": "mammal", "aliases": [ "African green monkey", "African green monkey cells" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2020-bouhaddou-the-global-phosphorylation-landsca", "2022-yaron-host-protein-kinases-required-for-", "2023-carrau-delayed-engagement-of-host-defense", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "drosophila", "label": "Drosophila melanogaster", "family": "invertebrate", "aliases": [ "Drosophila", "Drosophila melanogaster" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2014-shapiro-drosha-as-an-interferon-independen", "2016-tenoever-the-evolution-of-antiviral-defense", "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "ferret", "label": "Ferret", "family": "mammal", "aliases": [ "ferret" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat", "2014-varble-influenza-a-virus-transmission-bot", "2019-tenoever-synthetic-virology-building-viruse", "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "plants", "label": "Plants as a group", "family": "plant", "aliases": [ "plant", "plants" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "amsacta-moorei", "label": "Amsacta moorei", "family": "invertebrate", "aliases": [ "Amsacta moorei" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p" ] }, { "id": "arabidopsis", "label": "Arabidopsis thaliana", "family": "plant", "aliases": [ "Arabidopsis thaliana" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "archaea", "label": "Archaea", "family": "archaeon", "aliases": [ "archaea" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "bacteria", "label": "Bacteria", "family": "prokaryote", "aliases": [ "bacteria" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "chordates", "label": "Chordates as a group", "family": "group", "aliases": [ "chordates" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "guinea-pig", "label": "Guinea pig", "family": "mammal", "aliases": [ "guinea pig" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot" ] }, { "id": "insect", "label": "Insects as a group", "family": "invertebrate", "aliases": [ "insect" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "mosquito", "label": "Mosquito", "family": "invertebrate", "aliases": [ "mosquito" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie" ] }, { "id": "nematode", "label": "Nematode", "family": "invertebrate", "aliases": [ "nematode" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "nicotiana-benthamiana", "label": "Nicotiana benthamiana", "family": "plant", "aliases": [ "Nicotiana benthamiana" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "yeast", "label": "Yeast", "family": "fungus", "aliases": [ "yeast" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "zebrafish", "label": "Zebrafish", "family": "fish", "aliases": [ "zebrafish" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] } ], "biological_systems": [ { "id": "hek293", "label": "HEK293 and HEK293T cells", "family": "immortalised cell line", "aliases": [ "293T cells", "HEK-293T cells", "HEK293 and 293T cells", "HEK293 cells", "HEK293FT cells", "HEK293T cells" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2012-pham-replication-in-cells-of-hematopoie", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri", "2019-eggenberger-type-i-interferon-response-impairs", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-mccune-rapid-dissemination-and-monopoliza", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2023-oishi-archaeal-kink-turn-binding-protein", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "mef", "label": "Mouse embryonic fibroblasts", "family": "primary or early-passage cell", "aliases": [ "mouse embryonic fibroblasts", "murine embryonic fibroblasts", "murine fibroblasts", "primary mouse embryonic fibroblasts" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-cullen-is-rna-interference-a-physiologica", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-mitogen-activated-protein-kinase-m", "2014-shapiro-drosha-as-an-interferon-independen", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-aguado-homologous-recombination-is-an-int", "2019-eggenberger-type-i-interferon-response-impairs", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "a549", "label": "A549 cells", "family": "immortalised cell line", "aliases": [ "A549 cells" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-schmid-transcription-factor-redundancy-en", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-aguado-homologous-recombination-is-an-int", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-paget-stress-granules-are-shock-absorber", "2023-uhl-adar1-biology-can-hinder-effective", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "mdck", "label": "MDCK cells", "family": "immortalised cell line", "aliases": [ "MDCK cells" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-hematopoietic-specific-targeting-o", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-langlois-microrna-based-strategy-to-mitigat", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2022-oishi-the-host-response-to-influenza-a-v", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "mouse-lung", "label": "Mouse lung", "family": "tissue or organ", "aliases": [ "BALB/c mouse lung", "C57BL/6 mouse lung", "mouse lung", "mouse lung tissue" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-morales-sars-cov-encoded-small-rnas-contri", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2023-zhang-mouse-genome-rewriting-and-tailori", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "bhk", "label": "BHK-21 baby hamster kidney cells", "family": "immortalised cell line", "aliases": [ "baby hamster kidney cells", "BHK cells", "BHK-21 cells", "BHK21 cells" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-cullen-is-rna-interference-a-physiologica", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-shapiro-drosha-as-an-interferon-independen", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "vero-e6", "label": "Vero E6 cells", "family": "immortalised cell line", "aliases": [ "Vero E6 cells" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-", "2023-carrau-delayed-engagement-of-host-defense", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "a549-ace2", "label": "ACE2-expressing A549 cells", "family": "engineered cell line", "aliases": [ "A549 cells expressing ACE2", "A549-ACE2 cells", "ACE2-expressing A549 cells" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-oishi-the-host-response-to-influenza-a-v", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "embryonated-eggs", "label": "Embryonated chicken eggs", "family": "animal or egg system", "aliases": [ "embryonated chicken eggs" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2010-varble-engineered-rna-viral-synthesis-of-", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-heaton-long-term-survival-of-influenza-vi", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "bmdm", "label": "Bone marrow derived macrophages", "family": "primary or early-passage cell", "aliases": [ "bone marrow derived macrophages", "bone marrow-derived macrophages", "murine bone marrow derived macrophages" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2012-langlois-hematopoietic-specific-targeting-o", "2012-pham-replication-in-cells-of-hematopoie", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-a-versatile-rna-vector-for-deliver", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "dicer-deficient-fibroblasts", "label": "Dicer-deficient fibroblasts", "family": "engineered knockout line", "aliases": [ "Dicer conditional knockout fibroblasts", "Dicer knockout fibroblasts", "Dicer-deficient fibroblasts", "Dicer-deficient murine fibroblasts", "Dicer1-deficient fibroblasts" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "calu-3", "label": "Calu-3 cells", "family": "immortalised cell line", "aliases": [ "Calu-3 2B4 cells", "Calu-3 cells", "Calu3 cells" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat", "2017-morales-sars-cov-encoded-small-rnas-contri", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "golden-hamster-animal", "label": "Golden hamster", "family": "animal or egg system", "aliases": [ "golden hamster" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2023-carrau-delayed-engagement-of-host-defense", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "mouse-animal", "label": "Laboratory mice", "family": "animal or egg system", "aliases": [ "BALB/c mice", "C57BL/6 mice", "C57BL/6 mouse", "mouse", "mouse models", "suckling mice" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2013-cullen-is-rna-interference-a-physiologica", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "nodice-cells", "label": "NoDice Dicer-deficient HEK293T cells", "family": "engineered knockout line", "aliases": [ "HEK-293T NoDice cells", "NoDice 293T cells", "NoDice Dicer-deficient cells", "NoDice Dicer-deficient HEK293T cells", "NoDice HEK293T cells" ], "publications": [ "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "human-fibroblasts", "label": "Primary human fibroblasts", "family": "primary or early-passage cell", "aliases": [ "BJ human foreskin fibroblasts", "human fibroblasts", "human primary foreskin fibroblasts", "normal human dermal fibroblasts" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-pham-replication-in-cells-of-hematopoie", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-aguado-microrna-function-is-limited-to-cy", "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "hamster-lung", "label": "Hamster lung", "family": "tissue or organ", "aliases": [ "hamster lung" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-oishi-a-diminished-immune-response-under", "2023-carrau-delayed-engagement-of-host-defense", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "mouse-lung-fibroblasts", "label": "Primary mouse lung fibroblasts", "family": "primary or early-passage cell", "aliases": [ "murine lung fibroblasts", "primary lung fibroblasts", "primary mouse lung fibroblasts" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2012-langlois-hematopoietic-specific-targeting-o", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-heaton-long-term-survival-of-influenza-vi", "2014-shapiro-drosha-as-an-interferon-independen" ] }, { "id": "mouse-spleen", "label": "Mouse spleen", "family": "tissue or organ", "aliases": [ "mouse spleen" ], "publications": [ "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "vero", "label": "Vero cells", "family": "immortalised cell line", "aliases": [ "Vero cells" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2010-shapiro-noncanonical-cytoplasmic-processin", "2013-varble-an-in-vivo-rnai-screening-approach", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "caco-2", "label": "Caco-2 cells", "family": "immortalised cell line", "aliases": [ "Caco-2 cells" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases" ] }, { "id": "drosophila-dl1", "label": "Drosophila DL1 cells", "family": "invertebrate cell system", "aliases": [ "Drosophila DL1 cells" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "ferret-animal", "label": "Ferret", "family": "animal or egg system", "aliases": [ "ferret" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat", "2014-varble-influenza-a-virus-transmission-bot", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "hela", "label": "HeLa cells", "family": "immortalised cell line", "aliases": [ "HeLa cells" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "mammalian-cell-culture", "label": "Mammalian cell culture in general", "family": "general", "aliases": [ "mammalian cell culture", "mammalian somatic cells" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2016-tenoever-the-evolution-of-antiviral-defense", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "mouse-esc", "label": "Mouse embryonic stem cells", "family": "stem cell system", "aliases": [ "mouse embryonic stem cells" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2019-eggenberger-type-i-interferon-response-impairs", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "2ftgh", "label": "2FTGH fibrosarcoma cells", "family": "immortalised cell line", "aliases": [ "2FTGH cells", "2FTGH fibrosarcoma cells" ], "publications": [ "2010-schmid-transcription-factor-redundancy-en", "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "arthropods", "label": "Arthropods", "family": "non-vertebrate or plant system", "aliases": [ "arthropods" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "brain", "label": "Brain", "family": "tissue or organ", "aliases": [ "brain" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "drosha-dicer-dko-293t", "label": "Drosha and Dicer double knockout HEK293T cells", "family": "engineered knockout line", "aliases": [ "Drosha and Dicer deficient 293T cells", "Drosha and Dicer double knockout HEK293T cells" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "embryoid-bodies", "label": "Embryoid bodies", "family": "stem cell system", "aliases": [ "embryoid bodies" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "huh7", "label": "Huh7 cells", "family": "immortalised cell line", "aliases": [ "Huh-7 cells", "Huh7 cells" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "huh7-5-ace2-cells", "label": "Huh7.5-ACE2 cells", "family": "engineered cell line", "aliases": [ "Huh7.5-ACE2 cells" ], "publications": [ "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases" ] }, { "id": "ifnar1-and-il28r-double-knockout-mice", "label": "Ifnar1 and Il28r double knockout mice", "family": "engineered knockout line", "aliases": [ "Ifnar1 and Il28r double knockout mice" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie", "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "liver", "label": "Liver", "family": "tissue or organ", "aliases": [ "liver" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "mediastinal-lymph-node", "label": "Mediastinal lymph node", "family": "tissue or organ", "aliases": [ "mediastinal lymph node" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "mouse-liver", "label": "Mouse liver", "family": "tissue or organ", "aliases": [ "mouse liver" ], "publications": [ "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie" ] }, { "id": "olfactory-bulb", "label": "Olfactory bulb", "family": "tissue or organ", "aliases": [ "olfactory bulb" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "pancreas", "label": "Pancreas", "family": "tissue or organ", "aliases": [ "pancreas" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "plants", "label": "Plants", "family": "non-vertebrate or plant system", "aliases": [ "plants" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-", "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "spleen", "label": "Spleen", "family": "tissue or organ", "aliases": [ "spleen" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "a549-dual-reporter-cells", "label": "A549-Dual reporter cells", "family": "engineered cell line", "aliases": [ "A549-Dual reporter cells" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "adar1-knockout-a549-cells", "label": "ADAR1 knockout A549 cells", "family": "engineered knockout line", "aliases": [ "ADAR1 knockout A549 cells" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "adult-cholangiocyte-organoids", "label": "Adult cholangiocyte organoids", "family": "organoid, chip or stem cell system", "aliases": [ "adult cholangiocyte organoids" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "adult-hepatocyte-organoids", "label": "Adult hepatocyte organoids", "family": "organoid, chip or stem cell system", "aliases": [ "adult hepatocyte organoids" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "adult-primary-human-islets", "label": "Adult primary human islets", "family": "organoid, chip or stem cell system", "aliases": [ "adult primary human islets" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "alveolar-epithelium", "label": "Alveolar epithelium", "family": "tissue or organ", "aliases": [ "alveolar epithelium" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "amsacta-moorei-ld652-cells", "label": "Amsacta moorei Ld652 cells", "family": "non-vertebrate or plant system", "aliases": [ "Amsacta moorei Ld652 cells" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p" ] }, { "id": "arabidopsis-protoplasts", "label": "Arabidopsis protoplasts", "family": "non-vertebrate or plant system", "aliases": [ "Arabidopsis protoplasts" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "archaea", "label": "Archaea", "family": "non-vertebrate or plant system", "aliases": [ "archaea" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "archaeological-human-dental-remains", "label": "Archaeological human dental remains", "family": "human clinical or post-mortem material", "aliases": [ "archaeological human dental remains" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "argonaute-knockout-fibroblasts", "label": "Argonaute knockout fibroblasts", "family": "engineered knockout line", "aliases": [ "Argonaute knockout fibroblasts" ], "publications": [ "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "bacteria", "label": "Bacteria", "family": "non-vertebrate or plant system", "aliases": [ "bacteria" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "bone-marrow-derived-dendritic-cells", "label": "Bone marrow derived dendritic cells", "family": "primary or early-passage cell", "aliases": [ "bone marrow derived dendritic cells" ], "publications": [ "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "bronchus-tissue", "label": "Bronchus tissue", "family": "tissue or organ", "aliases": [ "bronchus tissue" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot" ] }, { "id": "bsc-1-cells", "label": "BSC-1 cells", "family": "immortalised cell line", "aliases": [ "BSC-1 cells" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p" ] }, { "id": "bsrt7-cells", "label": "BSRT7 cells", "family": "immortalised cell line", "aliases": [ "BSRT7 cells" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "c6-glial-cells", "label": "C6 glial cells", "family": "immortalised cell line", "aliases": [ "C6 glial cells" ], "publications": [ "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "c6-36-aedes-albopictus-cells", "label": "C6/36 Aedes albopictus cells", "family": "non-vertebrate or plant system", "aliases": [ "C6/36 Aedes albopictus cells" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie" ] }, { "id": "cad-neuronal-precursor-cells", "label": "CAD neuronal precursor cells", "family": "immortalised cell line", "aliases": [ "CAD neuronal precursor cells" ], "publications": [ "2010-varble-engineered-rna-viral-synthesis-of-" ] }, { "id": "cardiomyocytes", "label": "Cardiomyocytes", "family": "organoid, chip or stem cell system", "aliases": [ "cardiomyocytes" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "cas9-expressing-a549-clonal-line", "label": "Cas9-expressing A549 clonal line", "family": "engineered cell line", "aliases": [ "Cas9-expressing A549 clonal line" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "cell-free-in-vitro-polymerase-reactions", "label": "Cell-free in vitro polymerase reactions", "family": "cell-free or reconstituted", "aliases": [ "cell-free in vitro polymerase reactions" ], "publications": [ "2012-perez-a-small-rna-enhancer-of-viral-poly" ] }, { "id": "cell-free-mitochondrial-fraction-assay", "label": "Cell-free mitochondrial fraction assay", "family": "cell-free or reconstituted", "aliases": [ "cell-free mitochondrial fraction assay" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "chordates", "label": "Chordates", "family": "non-vertebrate or plant system", "aliases": [ "chordates" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "club-cells", "label": "Club cells", "family": "tissue or organ", "aliases": [ "club cells" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "mdck-complementing", "label": "Complementing MDCK cells", "family": "engineered cell line", "aliases": [ "HA and NP complementing MDCK cells", "HA-complementing MDCK cells" ], "publications": [ "2014-schmid-a-versatile-rna-vector-for-deliver" ] }, { "id": "conditional-knockout-fibroblast-lines", "label": "Conditional knockout fibroblast lines", "family": "engineered knockout line", "aliases": [ "conditional knockout fibroblast lines" ], "publications": [ "2012-shapiro-evidence-for-a-cytoplasmic-micropr" ] }, { "id": "cortical-neurons", "label": "Cortical neurons", "family": "tissue or organ", "aliases": [ "cortical neurons" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "cos-7-cells", "label": "COS-7 cells", "family": "immortalised cell line", "aliases": [ "COS-7 cells" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira" ] }, { "id": "covid-19-lung-autopsy-tissue", "label": "COVID-19 lung autopsy tissue", "family": "human clinical or post-mortem material", "aliases": [ "COVID-19 lung autopsy tissue" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "crispr-knockout-clonal-lines", "label": "CRISPR knockout clonal lines", "family": "engineered knockout line", "aliases": [ "CRISPR knockout clonal lines" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "dbt-mace2-cells", "label": "DBT-mACE2 cells", "family": "engineered cell line", "aliases": [ "DBT-mACE2 cells" ], "publications": [ "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "df-1-chicken-embryonic-fibroblasts", "label": "DF-1 chicken embryonic fibroblasts", "family": "immortalised cell line", "aliases": [ "DF-1 chicken embryonic fibroblasts" ], "publications": [ "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "dgcr8-deficient-fibroblasts", "label": "DGCR8-deficient fibroblasts", "family": "engineered knockout line", "aliases": [ "DGCR8-deficient fibroblasts" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin" ] }, { "id": "dopaminergic-neurons", "label": "Dopaminergic neurons", "family": "tissue or organ", "aliases": [ "dopaminergic neurons" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "endothelial-cells", "label": "Endothelial cells", "family": "immortalised cell line", "aliases": [ "endothelial cells" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "eukaryotes", "label": "Eukaryotes", "family": "non-vertebrate or plant system", "aliases": [ "eukaryotes" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "facs-sorted-olfactory-sensory-neuron-nuclei", "label": "FACS-sorted olfactory sensory neuron nuclei", "family": "primary or early-passage cell", "aliases": [ "FACS-sorted olfactory sensory neuron nuclei" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "ferret-nasal-wash-and-trachea", "label": "Ferret nasal wash and trachea", "family": "human clinical or post-mortem material", "aliases": [ "ferret nasal wash and trachea" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "g3bp1-and-g3bp2-knockout-cells", "label": "G3BP1 and G3BP2 knockout cells", "family": "engineered knockout line", "aliases": [ "G3BP1 and G3BP2 knockout cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "gastrointestinal-tract", "label": "Gastrointestinal tract", "family": "tissue or organ", "aliases": [ "gastrointestinal tract" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "genetically-engineered-mouse-models", "label": "Genetically engineered mouse models", "family": "immortalised cell line", "aliases": [ "genetically engineered mouse models" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "golden-hamster-dorsal-root-ganglia", "label": "Golden hamster dorsal root ganglia", "family": "tissue or organ", "aliases": [ "golden hamster dorsal root ganglia" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "golden-hamster-lung-heart-and-kidney", "label": "Golden hamster lung heart and kidney", "family": "tissue or organ", "aliases": [ "golden hamster lung heart and kidney" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a" ] }, { "id": "golden-hamster-olfactory-epithelium", "label": "Golden hamster olfactory epithelium", "family": "tissue or organ", "aliases": [ "golden hamster olfactory epithelium" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "guinea-pig", "label": "Guinea pig", "family": "animal or egg system", "aliases": [ "guinea pig" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot" ] }, { "id": "h441-human-club-cell-line", "label": "H441 human club cell line", "family": "immortalised cell line", "aliases": [ "H441 human club cell line" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi" ] }, { "id": "hamster-olfactory-bulb-and-olfactory-epithelium", "label": "Hamster olfactory bulb and olfactory epithelium", "family": "tissue or organ", "aliases": [ "hamster olfactory bulb and olfactory epithelium" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a" ] }, { "id": "hamster-spinal-cord", "label": "Hamster spinal cord", "family": "tissue or organ", "aliases": [ "hamster spinal cord" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "hamster-spleen", "label": "Hamster spleen", "family": "tissue or organ", "aliases": [ "hamster spleen" ], "publications": [ "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "hamster-striatum-thalamus-cerebellum-medial-prefrontal-cortex-and-trigeminal-ganglion", "label": "Hamster striatum thalamus cerebellum medial prefrontal cortex and trigeminal ganglion", "family": "tissue or organ", "aliases": [ "hamster striatum thalamus cerebellum medial prefrontal cortex and trigeminal ganglion" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a" ] }, { "id": "hamster-trachea", "label": "Hamster trachea", "family": "tissue or organ", "aliases": [ "hamster trachea" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in" ] }, { "id": "heart", "label": "Heart", "family": "tissue or organ", "aliases": [ "heart" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "hek293t-cells-stably-expressing-irf7", "label": "HEK293T cells stably expressing IRF7", "family": "engineered cell line", "aliases": [ "HEK293T cells stably expressing IRF7" ], "publications": [ "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "hela-cells-expressing-e1a", "label": "HeLa cells expressing E1A", "family": "engineered cell line", "aliases": [ "HeLa cells expressing E1A" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "hela-ace2-cells", "label": "HeLa-ACE2 cells", "family": "engineered cell line", "aliases": [ "HeLa-ACE2 cells" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "hepa-1-6-cells", "label": "Hepa 1.6 cells", "family": "immortalised cell line", "aliases": [ "Hepa 1.6 cells" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach" ] }, { "id": "human-bronchial-epithelial-cells", "label": "Human bronchial epithelial cells", "family": "immortalised cell line", "aliases": [ "human bronchial epithelial cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "human-covid-19-cadaver-lung-tissue", "label": "Human COVID-19 cadaver lung tissue", "family": "human clinical or post-mortem material", "aliases": [ "human COVID-19 cadaver lung tissue" ], "publications": [ "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "human-embryonic-stem-cell-derived-seam-whole-eye-cultures", "label": "Human embryonic stem cell derived SEAM whole-eye cultures", "family": "organoid, chip or stem cell system", "aliases": [ "human embryonic stem cell derived SEAM whole-eye cultures" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don" ] }, { "id": "human-induced-pluripotent-stem-cells", "label": "Human induced pluripotent stem cells", "family": "organoid, chip or stem cell system", "aliases": [ "human induced pluripotent stem cells" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "human-olfactory-epithelium-autopsy-tissue", "label": "Human olfactory epithelium autopsy tissue", "family": "human clinical or post-mortem material", "aliases": [ "human olfactory epithelium autopsy tissue" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "human-pluripotent-stem-cell-derivatives", "label": "Human pluripotent stem cell derivatives", "family": "organoid, chip or stem cell system", "aliases": [ "human pluripotent stem cell derivatives" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "human-serum", "label": "Human serum", "family": "human clinical or post-mortem material", "aliases": [ "human serum" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "ifnar1-knockout-mice", "label": "Ifnar1 knockout mice", "family": "engineered knockout line", "aliases": [ "Ifnar1 knockout mice" ], "publications": [ "2015-benitez-engineered-mammalian-rnai-can-elic" ] }, { "id": "ifnar1-deficient-fibroblasts", "label": "Ifnar1-deficient fibroblasts", "family": "engineered knockout line", "aliases": [ "Ifnar1-deficient fibroblasts" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin" ] }, { "id": "ikbke-knockout-mice", "label": "Ikbke knockout mice", "family": "engineered knockout line", "aliases": [ "Ikbke knockout mice" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "ikbke-deficient-mice", "label": "Ikbke-deficient mice", "family": "engineered knockout line", "aliases": [ "Ikbke-deficient mice" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela" ] }, { "id": "in-vitro-replicase-assays", "label": "In vitro replicase assays", "family": "cell-free or reconstituted", "aliases": [ "in vitro replicase assays" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "ipsc-derived-cardiomyocytes", "label": "IPSC-derived cardiomyocytes", "family": "organoid, chip or stem cell system", "aliases": [ "iPSC-derived cardiomyocytes" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "irf3-and-irf7-double-knockout-fibroblasts", "label": "Irf3 and Irf7 double knockout fibroblasts", "family": "engineered knockout line", "aliases": [ "Irf3 and Irf7 double knockout fibroblasts" ], "publications": [ "2015-benitez-engineered-mammalian-rnai-can-elic" ] }, { "id": "jaws-ii-dendritic-cell-line", "label": "JAWS II dendritic cell line", "family": "immortalised cell line", "aliases": [ "JAWS II dendritic cell line" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o" ] }, { "id": "jurkat-t-cells", "label": "Jurkat T cells", "family": "immortalised cell line", "aliases": [ "Jurkat T cells" ], "publications": [ "2013-chua-influenza-a-virus-utilizes-subopti" ] }, { "id": "k18-hace2-mouse", "label": "K18-hACE2 mouse", "family": "engineered cell line", "aliases": [ "K18-hACE2 mouse" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "kidney", "label": "Kidney", "family": "tissue or organ", "aliases": [ "kidney" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "liver-organoids", "label": "Liver organoids", "family": "organoid, chip or stem cell system", "aliases": [ "liver organoids" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "loxp-reporter-mice", "label": "LoxP reporter mice", "family": "animal or egg system", "aliases": [ "LoxP reporter mice" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "lung-draining-lymph-node", "label": "Lung draining lymph node", "family": "tissue or organ", "aliases": [ "lung draining lymph node" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o" ] }, { "id": "macrophages", "label": "Macrophages", "family": "tissue or organ", "aliases": [ "macrophages" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "map3k8-knockout-fibroblasts", "label": "Map3k8 knockout fibroblasts", "family": "engineered knockout line", "aliases": [ "Map3k8 knockout fibroblasts" ], "publications": [ "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "mavs-knockout-cells", "label": "MAVS knockout cells", "family": "engineered knockout line", "aliases": [ "MAVS knockout cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "mavs-deficient-a549-cells", "label": "MAVS-deficient A549 cells", "family": "engineered knockout line", "aliases": [ "MAVS-deficient A549 cells" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "mda5-deficient-a549-cells", "label": "MDA5-deficient A549 cells", "family": "engineered knockout line", "aliases": [ "MDA5-deficient A549 cells" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "mdck-cells-expressing-mir-124", "label": "MDCK cells expressing miR-124", "family": "engineered cell line", "aliases": [ "MDCK cells expressing miR-124" ], "publications": [ "2015-benitez-engineered-mammalian-rnai-can-elic" ] }, { "id": "mesenteric-lymph-nodes", "label": "Mesenteric lymph nodes", "family": "tissue or organ", "aliases": [ "mesenteric lymph nodes" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "microfluidic-human-bronchial-airway-chip", "label": "Microfluidic human bronchial airway chip", "family": "organoid, chip or stem cell system", "aliases": [ "microfluidic human bronchial airway chip" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "microglia", "label": "Microglia", "family": "tissue or organ", "aliases": [ "microglia" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "mir-122-expressing-mrc-5-fibroblasts", "label": "MiR-122-expressing MRC-5 fibroblasts", "family": "engineered cell line", "aliases": [ "miR-122-expressing MRC-5 fibroblasts" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "mir-142-expressing-mdck-cells", "label": "MiR-142-expressing MDCK cells", "family": "engineered cell line", "aliases": [ "miR-142-expressing MDCK cells" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o" ] }, { "id": "mir-142-expressing-mrc-5-fibroblasts", "label": "MiR-142-expressing MRC-5 fibroblasts", "family": "engineered cell line", "aliases": [ "miR-142-expressing MRC-5 fibroblasts" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "mle-15-murine-lung-epithelial-cell-line", "label": "MLE-15 murine lung epithelial cell line", "family": "tissue or organ", "aliases": [ "MLE-15 murine lung epithelial cell line" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi" ] }, { "id": "mouse-gastrointestinal-tract", "label": "Mouse gastrointestinal tract", "family": "tissue or organ", "aliases": [ "mouse gastrointestinal tract" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "mouse-heart", "label": "Mouse heart", "family": "tissue or organ", "aliases": [ "mouse heart" ], "publications": [ "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn" ] }, { "id": "mouse-hindpaw-inflammatory-pain-model", "label": "Mouse hindpaw inflammatory pain model", "family": "immortalised cell line", "aliases": [ "mouse hindpaw inflammatory pain model" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "mouse-kidney", "label": "Mouse kidney", "family": "tissue or organ", "aliases": [ "mouse kidney" ], "publications": [ "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn" ] }, { "id": "mouse-oocytes", "label": "Mouse oocytes", "family": "immortalised cell line", "aliases": [ "mouse oocytes" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "mouse-paw-incision-model", "label": "Mouse paw incision model", "family": "immortalised cell line", "aliases": [ "mouse paw incision model" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "mouse-small-intestine", "label": "Mouse small intestine", "family": "tissue or organ", "aliases": [ "mouse small intestine" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "mouse-spared-nerve-injury-comparison-dataset", "label": "Mouse spared nerve injury comparison dataset", "family": "immortalised cell line", "aliases": [ "mouse spared nerve injury comparison dataset" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "mouse-testis", "label": "Mouse testis", "family": "tissue or organ", "aliases": [ "mouse testis" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "mouse-trachea", "label": "Mouse trachea", "family": "tissue or organ", "aliases": [ "mouse trachea" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "mrc-5", "label": "MRC-5 fibroblasts", "family": "immortalised cell line", "aliases": [ "MRC-5 fibroblasts" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "mtcc10-1-murine-club-cell-line", "label": "MtCC10-1 murine club cell line", "family": "immortalised cell line", "aliases": [ "mtCC10-1 murine club cell line" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi" ] }, { "id": "nasal-wash", "label": "Nasal wash", "family": "human clinical or post-mortem material", "aliases": [ "nasal wash" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot" ] }, { "id": "nematodes", "label": "Nematodes", "family": "non-vertebrate or plant system", "aliases": [ "nematodes" ], "publications": [ "2013-tenoever-rna-viruses-and-the-host-microrna-" ] }, { "id": "nicotiana-benthamiana", "label": "Nicotiana benthamiana", "family": "non-vertebrate or plant system", "aliases": [ "Nicotiana benthamiana" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "olfactory-sensory-neurons", "label": "Olfactory sensory neurons", "family": "primary or early-passage cell", "aliases": [ "olfactory sensory neurons" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "pancreatic-endocrine-cells", "label": "Pancreatic endocrine cells", "family": "immortalised cell line", "aliases": [ "pancreatic endocrine cells" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "parietal-bone", "label": "Parietal bone", "family": "human clinical or post-mortem material", "aliases": [ "parietal bone" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "peripheral-blood-mononuclear-cells", "label": "Peripheral blood mononuclear cells", "family": "human clinical or post-mortem material", "aliases": [ "peripheral blood mononuclear cells" ], "publications": [ "2021-horiuchi-immune-memory-from-sars-cov-2-infe" ] }, { "id": "phalanx", "label": "Phalanx", "family": "human clinical or post-mortem material", "aliases": [ "phalanx" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "pkr-knockout-cells", "label": "PKR knockout cells", "family": "engineered knockout line", "aliases": [ "PKR knockout cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "post-mortem-human-lung", "label": "Post-mortem human lung", "family": "human clinical or post-mortem material", "aliases": [ "post-mortem human lung" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "post-mortem-human-ocular-surface-tissue", "label": "Post-mortem human ocular surface tissue", "family": "human clinical or post-mortem material", "aliases": [ "post-mortem human ocular surface tissue" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don" ] }, { "id": "post-mortem-human-olfactory-bulb-and-olfactory-epithelium", "label": "Post-mortem human olfactory bulb and olfactory epithelium", "family": "human clinical or post-mortem material", "aliases": [ "post-mortem human olfactory bulb and olfactory epithelium" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a" ] }, { "id": "primary-adult-human-cornea-limbus-sclera-iris-retinal-pigment-epithelium-and-choroid-cultures", "label": "Primary adult human cornea limbus sclera iris retinal pigment epithelium and choroid cultures", "family": "primary or early-passage cell", "aliases": [ "primary adult human cornea limbus sclera iris retinal pigment epithelium and choroid cultures" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don" ] }, { "id": "primary-conditional-drosha-mouse-lung-fibroblasts", "label": "Primary conditional Drosha mouse lung fibroblasts", "family": "primary or early-passage cell", "aliases": [ "primary conditional Drosha mouse lung fibroblasts" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "primary-ferret-lung", "label": "Primary ferret lung", "family": "primary or early-passage cell", "aliases": [ "primary ferret lung" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat" ] }, { "id": "primary-human-airway-basal-cells", "label": "Primary human airway basal cells", "family": "primary or early-passage cell", "aliases": [ "primary human airway basal cells" ], "publications": [ "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "primary-human-bronchial-airway-basal-stem-cells", "label": "Primary human bronchial airway basal stem cells", "family": "organoid, chip or stem cell system", "aliases": [ "primary human bronchial airway basal stem cells" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "primary-human-bronchial-epithelial-cells", "label": "Primary human bronchial epithelial cells", "family": "primary or early-passage cell", "aliases": [ "primary human bronchial epithelial cells" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca" ] }, { "id": "primary-human-nasal-epithelial-cells", "label": "Primary human nasal epithelial cells", "family": "primary or early-passage cell", "aliases": [ "primary human nasal epithelial cells" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat" ] }, { "id": "primary-human-neutrophils", "label": "Primary human neutrophils", "family": "primary or early-passage cell", "aliases": [ "primary human neutrophils" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "primary-human-pulmonary-microvascular-endothelium", "label": "Primary human pulmonary microvascular endothelium", "family": "primary or early-passage cell", "aliases": [ "primary human pulmonary microvascular endothelium" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "primary-human-type-ii-pneumocytes", "label": "Primary human type II pneumocytes", "family": "primary or early-passage cell", "aliases": [ "primary human type II pneumocytes" ], "publications": [ "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "primary-mouse-lung-cultures-from-gfp-transgenic-mice", "label": "Primary mouse lung cultures from GFP transgenic mice", "family": "primary or early-passage cell", "aliases": [ "primary mouse lung cultures from GFP transgenic mice" ], "publications": [ "2014-schmid-a-versatile-rna-vector-for-deliver" ] }, { "id": "primary-normal-human-bronchial-epithelial-cells", "label": "Primary normal human bronchial epithelial cells", "family": "primary or early-passage cell", "aliases": [ "primary normal human bronchial epithelial cells" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "purified-recombinant-influenza-a-virus-polymerase", "label": "Purified recombinant influenza A virus polymerase", "family": "cell-free or reconstituted", "aliases": [ "purified recombinant influenza A virus polymerase" ], "publications": [ "2012-perez-a-small-rna-enhancer-of-viral-poly" ] }, { "id": "rag1-deficient-mice", "label": "Rag1 deficient mice", "family": "engineered knockout line", "aliases": [ "Rag1 deficient mice" ], "publications": [ "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "raji-b-cells", "label": "Raji B cells", "family": "immortalised cell line", "aliases": [ "Raji B cells" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie" ] }, { "id": "raw-macrophage-cells", "label": "RAW macrophage cells", "family": "immortalised cell line", "aliases": [ "RAW macrophage cells" ], "publications": [ "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "recombinant-protein-in-vitro-kinase-reactions", "label": "Recombinant protein in vitro kinase reactions", "family": "cell-free or reconstituted", "aliases": [ "recombinant protein in vitro kinase reactions" ], "publications": [ "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "recombinant-purified-influenza-rna-polymerase", "label": "Recombinant purified influenza RNA polymerase", "family": "cell-free or reconstituted", "aliases": [ "recombinant purified influenza RNA polymerase" ], "publications": [ "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "rederived-fibroblasts", "label": "Rederived fibroblasts", "family": "immortalised cell line", "aliases": [ "rederived fibroblasts" ], "publications": [ "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "rela-knockout-hela-ace2-cells", "label": "RELA knockout HeLa-ACE2 cells", "family": "engineered knockout line", "aliases": [ "RELA knockout HeLa-ACE2 cells" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "rig-i-deficient-a549-cells", "label": "RIG-I-deficient A549 cells", "family": "engineered knockout line", "aliases": [ "RIG-I-deficient A549 cells" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "rnase-iii-deficient-fibroblasts", "label": "RNase III deficient fibroblasts", "family": "engineered knockout line", "aliases": [ "RNase III deficient fibroblasts" ], "publications": [ "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "rnase-l-knockout-cells", "label": "RNase L knockout cells", "family": "engineered knockout line", "aliases": [ "RNase L knockout cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "scid-beige-mouse-xenograft", "label": "SCID-beige mouse xenograft", "family": "animal or egg system", "aliases": [ "SCID-beige mouse xenograft" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "small-intestine", "label": "Small intestine", "family": "tissue or organ", "aliases": [ "small intestine" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in" ] }, { "id": "stat1-deficient-mice", "label": "Stat1 deficient mice", "family": "engineered knockout line", "aliases": [ "Stat1 deficient mice" ], "publications": [ "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "stat1-knockout-a549-cells", "label": "STAT1 knockout A549 cells", "family": "engineered knockout line", "aliases": [ "STAT1 knockout A549 cells" ], "publications": [ "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "stat1-deficient-embryonic-fibroblasts", "label": "Stat1-deficient embryonic fibroblasts", "family": "engineered knockout line", "aliases": [ "Stat1-deficient embryonic fibroblasts" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela" ] }, { "id": "stem-cells", "label": "Stem cells", "family": "organoid, chip or stem cell system", "aliases": [ "stem cells" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense" ] }, { "id": "stool", "label": "Stool", "family": "human clinical or post-mortem material", "aliases": [ "stool" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "sustentacular-cells", "label": "Sustentacular cells", "family": "tissue or organ", "aliases": [ "sustentacular cells" ], "publications": [ "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "tb40-e-bacterial-artificial-chromosome", "label": "TB40/E bacterial artificial chromosome", "family": "non-vertebrate or plant system", "aliases": [ "TB40/E bacterial artificial chromosome" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "thp-1-derived-macrophages", "label": "THP-1-derived macrophages", "family": "tissue or organ", "aliases": [ "THP-1-derived macrophages" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "tooth-enamel", "label": "Tooth enamel", "family": "human clinical or post-mortem material", "aliases": [ "tooth enamel" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "u2os-cells", "label": "U2OS cells", "family": "immortalised cell line", "aliases": [ "U2OS cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "u3a-stat1-deficient-cells", "label": "U3A STAT1-deficient cells", "family": "engineered knockout line", "aliases": [ "U3A STAT1-deficient cells" ], "publications": [ "2010-schmid-transcription-factor-redundancy-en" ] }, { "id": "ubap2l-knockout-cells", "label": "UBAP2L knockout cells", "family": "engineered knockout line", "aliases": [ "UBAP2L knockout cells" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "whole-blood", "label": "Whole blood", "family": "human clinical or post-mortem material", "aliases": [ "whole blood" ], "publications": [ "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "yeast-assembly-vector", "label": "Yeast assembly vector", "family": "non-vertebrate or plant system", "aliases": [ "yeast assembly vector" ], "publications": [ "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "zebrafish-embryos", "label": "Zebrafish embryos", "family": "animal or egg system", "aliases": [ "zebrafish embryos" ], "publications": [ "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "zfx-conditional-knockout-primary-fibroblasts", "label": "Zfx conditional knockout primary fibroblasts", "family": "engineered knockout line", "aliases": [ "Zfx conditional knockout primary fibroblasts" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach" ] } ], "key_concepts": [ { "id": "interferon-stimulated-genes", "label": "Interferon-stimulated genes", "family": "interferon and innate signalling", "aliases": [ "interferon-stimulated gene amplification", "interferon-stimulated gene selectivity", "interferon-stimulated gene subsets", "interferon-stimulated genes" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-backes-the-mammalian-response-to-virus-in", "2014-heaton-long-term-survival-of-influenza-vi", "2015-benitez-in-vivo-rnai-screening-identifies-", "2019-eggenberger-type-i-interferon-response-impairs", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2023-carrau-delayed-engagement-of-host-defense", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "microrna-quantitative-limits", "label": "Quantitative limits of microRNA function", "family": "small RNA biology", "aliases": [ "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": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-hematopoietic-specific-targeting-o", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "type-i-interferon", "label": "Type I interferon", "family": "interferon and innate signalling", "aliases": [ "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": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-heaton-long-term-survival-of-influenza-vi", "2015-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "2016-tenoever-the-evolution-of-antiviral-defense", "2019-eggenberger-type-i-interferon-response-impairs", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-mccune-rapid-dissemination-and-monopoliza", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2022-oishi-the-host-response-to-influenza-a-v", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "antiviral-rnai", "label": "Antiviral RNA interference", "family": "small RNA biology", "aliases": [ "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": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-backes-degradation-of-host-micrornas-by-p", "2013-cullen-is-rna-interference-a-physiologica", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-backes-the-mammalian-response-to-virus-in", "2014-shapiro-drosha-as-an-interferon-independen", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-", "2016-tenoever-the-evolution-of-antiviral-defense", "2018-aguado-homologous-recombination-is-an-int", "2019-tenoever-synthetic-virology-building-viruse", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "animal-models", "label": "Small animal models of respiratory infection", "family": "models", "aliases": [ "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": [ "2012-pham-replication-in-cells-of-hematopoie", "2013-langlois-microrna-based-strategy-to-mitigat", "2014-varble-influenza-a-virus-transmission-bot", "2018-m-ller-mirna-mediated-targeting-of-human-", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2023-carrau-delayed-engagement-of-host-defense", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "cytoplasmic-microrna-biogenesis", "label": "Cytoplasmic microRNA biogenesis", "family": "small RNA biology", "aliases": [ "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": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "mirna-target-site-engineering", "label": "MicroRNA target site engineering", "family": "viral engineering and biocontainment", "aliases": [ "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": [ "2009-perez-microrna-mediated-species-specific", "2012-langlois-hematopoietic-specific-targeting-o", "2012-pham-replication-in-cells-of-hematopoie", "2013-langlois-microrna-based-strategy-to-mitigat", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-aguado-homologous-recombination-is-an-int", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "risc", "label": "RNA-induced silencing complex", "family": "small RNA biology", "aliases": [ "Argonaute 2 slicing", "Argonaute and RISC", "RISC", "RISC loading", "RNA-induced silencing complex", "RNA-induced silencing complex inactivation", "RNA-induced silencing complex loading" ], "publications": [ "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-cullen-is-rna-interference-a-physiologica", "2014-backes-the-mammalian-response-to-virus-in", "2015-aguado-microrna-function-is-limited-to-cy", "2018-aguado-homologous-recombination-is-an-int" ] }, { "id": "sars-cov-2-entry", "label": "SARS-CoV-2 entry and receptor use", "family": "host factors", "aliases": [ "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": [ "2014-varble-influenza-a-virus-transmission-bot", "2018-han-genome-wide-crispr-cas9-screen-ide", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-daniloski-identification-of-required-host-fa", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-si-a-human-airway-on-a-chip-for-the-r", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "chemokine-induction", "label": "Chemokine induction", "family": "interferon and innate signalling", "aliases": [ "chemokine induction", "inflammatory cytokine production", "leukocyte recruitment", "proinflammatory chemokines", "proinflammatory cytokine induction" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi", "2017-morales-sars-cov-encoded-small-rnas-contri", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2020-bouhaddou-the-global-phosphorylation-landsca", "2020-yang-a-human-pluripotent-stem-cell-base", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "covid19-pathogenesis", "label": "COVID-19 pathogenesis", "family": "pandemic pathogenesis", "aliases": [ "circulating inflammatory signal", "COVID-19 heterogeneity", "COVID-19 pathogenesis", "immunopathology", "lung immunopathology", "sterile inflammation", "systemic inflammation" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi", "2017-morales-sars-cov-encoded-small-rnas-contri", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2022-zazhytska-non-cell-autonomous-disruption-of-", "2023-carrau-delayed-engagement-of-host-defense", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "dicer", "label": "Dicer", "family": "small RNA biology", "aliases": [ "Dicer", "Dicer dependence", "Dicer independence" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2013-cullen-is-rna-interference-a-physiologica", "2014-backes-the-mammalian-response-to-virus-in", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "escape-from-silencing", "label": "Escape from small RNA targeting", "family": "population genetics and evolution", "aliases": [ "escape mutant fitness cost", "escape mutant resistance", "escape mutants", "escape variant selection", "mutational tolerance", "viral escape from silencing" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2012-pham-replication-in-cells-of-hematopoie", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-aguado-homologous-recombination-is-an-int", "2019-tenoever-synthetic-virology-building-viruse", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "immune-memory", "label": "Immune memory and reinfection", "family": "immunology", "aliases": [ "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": [ "2012-langlois-hematopoietic-specific-targeting-o", "2016-tenoever-the-evolution-of-antiviral-defense", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-oishi-a-diminished-immune-response-under", "2022-oishi-the-host-response-to-influenza-a-v", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "rnai-interferon-incompatibility", "label": "Incompatibility of RNAi and interferon", "family": "small RNA biology", "aliases": [ "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": [ "2013-cullen-is-rna-interference-a-physiologica", "2014-backes-the-mammalian-response-to-virus-in", "2015-benitez-engineered-mammalian-rnai-can-elic", "2016-tenoever-the-evolution-of-antiviral-defense", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2019-eggenberger-type-i-interferon-response-impairs", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "post-transcriptional-silencing", "label": "Post-transcriptional gene silencing", "family": "small RNA biology", "aliases": [ "microRNA-mediated gene silencing", "post-transcriptional gene silencing", "post-transcriptional silencing", "translational repression" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-pham-replication-in-cells-of-hematopoie", "2015-aguado-microrna-function-is-limited-to-cy", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "antiviral-state", "label": "Cell-intrinsic antiviral state", "family": "interferon and innate signalling", "aliases": [ "antiviral immunity", "antiviral innate immunity", "antiviral state", "cell-intrinsic immunity", "innate antiviral state", "intrinsic antiviral response" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2015-aguado-microrna-function-is-limited-to-cy", "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "delayed-innate-engagement", "label": "Delayed engagement of host defences", "family": "pandemic pathogenesis", "aliases": [ "delayed innate immune engagement", "delayed innate response", "innate immune response kinetics", "prophylaxis", "prophylaxis versus treatment", "therapeutic time window", "threat-proportional antiviral response" ], "publications": [ "2014-schmid-mitogen-activated-protein-kinase-m", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-oishi-a-diminished-immune-response-under", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "segment-8-splicing", "label": "Segment 8 splicing and the molecular timer", "family": "viral gene expression", "aliases": [ "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": [ "2010-perez-influenza-a-virus-generated-small-", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2013-chua-influenza-a-virus-utilizes-subopti", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "viral-ribonucleoprotein", "label": "Viral ribonucleoprotein complexes", "family": "viral gene expression", "aliases": [ "encapsidated genome", "exportin 1 CRM1-dependent nuclear export", "viral ribonucleoprotein", "viral ribonucleoprotein accessibility", "viral ribonucleoprotein complex", "viral ribonucleoprotein export" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2010-varble-engineered-rna-viral-synthesis-of-", "2013-chua-influenza-a-virus-utilizes-subopti", "2014-shapiro-drosha-as-an-interferon-independen", "2018-aguado-homologous-recombination-is-an-int", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "artificial-microrna", "label": "Artificial microRNAs", "family": "viral engineering and biocontainment", "aliases": [ "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": [ "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-schmid-a-versatile-rna-vector-for-deliver" ] }, { "id": "defective-viral-genomes", "label": "Defective viral genomes", "family": "viral gene expression", "aliases": [ "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": [ "2010-perez-influenza-a-virus-generated-small-", "2012-backes-degradation-of-host-micrornas-by-p", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "extrapulmonary-dissemination", "label": "Extrapulmonary dissemination", "family": "pandemic pathogenesis", "aliases": [ "COVID-19 extrapulmonary involvement", "enteric virus dissemination", "extrapulmonary manifestations", "replication versus inoculum discrimination", "viral RNA dissemination without infectious virus", "viremia", "virus dissemination" ], "publications": [ "2012-pham-replication-in-cells-of-hematopoie", "2020-mccune-rapid-dissemination-and-monopoliza", "2020-yang-a-human-pluripotent-stem-cell-base", "2023-carrau-delayed-engagement-of-host-defense", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "segment-stoichiometry", "label": "Genome segment stoichiometry", "family": "viral gene expression", "aliases": [ "gene expression stoichiometry", "genome segment stoichiometry", "packaging signal duplication", "segment packaging signals", "segment-specific regulation" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2013-chua-influenza-a-virus-utilizes-subopti", "2013-langlois-microrna-based-strategy-to-mitigat", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "host-dependency-factors", "label": "Host dependency factors", "family": "host factors", "aliases": [ "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": [ "2013-varble-an-in-vivo-rnai-screening-approach", "2018-han-genome-wide-crispr-cas9-screen-ide", "2018-m-ller-mirna-mediated-targeting-of-human-", "2021-daniloski-identification-of-required-host-fa", "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "host-pathogen-arms-race", "label": "Host-pathogen arms race", "family": "population genetics and evolution", "aliases": [ "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": [ "2016-tenoever-the-evolution-of-antiviral-defense", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2021-daniloski-the-spike-d614g-mutation-increases", "2021-horiuchi-immune-memory-from-sars-cov-2-infe", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "nucleoprotein", "label": "Influenza nucleoprotein", "family": "viral gene expression", "aliases": [ "influenza nucleoprotein", "nucleoprotein", "nucleoprotein scaffold", "ribonucleoprotein protection of genomes", "viral nucleoprotein" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-perez-influenza-a-virus-generated-small-", "2012-langlois-hematopoietic-specific-targeting-o", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "isre", "label": "Interferon-stimulated response element", "family": "interferon and innate signalling", "aliases": [ "interferon regulatory factor binding element", "interferon-stimulated response element", "IRF7 as transactivator of interferon-stimulated response elements" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2014-schmid-mitogen-activated-protein-kinase-m", "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "lineage-tracing", "label": "Lineage tracing of infected cells", "family": "cell identity and development", "aliases": [ "bronchiolar epithelium", "cell survival of lytic infection", "club cells", "lineage tracing of infected cells", "peribronchiolar metaplasia", "tissue repair", "virulence independent of replication" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi", "2017-morales-sars-cov-encoded-small-rnas-contri", "2019-tenoever-synthetic-virology-building-viruse", "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "rna-virus-vectors", "label": "RNA virus vectors", "family": "viral engineering and biocontainment", "aliases": [ "engineered viral vectors", "replication-incompetent vector", "reporter virus design", "RNA virus vectors", "vector cytotoxicity", "vector tropism" ], "publications": [ "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2014-schmid-a-versatile-rna-vector-for-deliver", "2018-m-ller-mirna-mediated-targeting-of-human-", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "small-viral-rna", "label": "Small viral RNA", "family": "viral gene expression", "aliases": [ "mini-viral RNA", "small viral RNA", "svRNA" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2012-langlois-hematopoietic-specific-targeting-o", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2017-morales-sars-cov-encoded-small-rnas-contri", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "microprocessor", "label": "The microprocessor and Drosha-DGCR8 processing", "family": "small RNA biology", "aliases": [ "DGCR8 dependence", "Drosha", "Drosha and DGCR8 processing", "microprocessor", "microprocessor independence", "microRNA biogenesis machinery" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k" ] }, { "id": "fitness-landscape", "label": "Viral fitness landscapes", "family": "population genetics and evolution", "aliases": [ "fitness-based genetic selection", "forward genetic screening", "natural selection as screen readout", "positive selection survival screen", "viral fitness landscape" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "interferon-antagonism", "label": "Viral interferon antagonism", "family": "interferon and innate signalling", "aliases": [ "interferon antagonism", "NS1 antagonist", "NS1 interferon antagonism", "type I interferon antagonism", "viral interferon antagonism" ], "publications": [ "2013-chua-influenza-a-virus-utilizes-subopti", "2015-benitez-in-vivo-rnai-screening-identifies-", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "viral-rna-polymerase", "label": "Viral RNA-dependent RNA polymerase", "family": "viral gene expression", "aliases": [ "encapsidating polymerase", "RNA-dependent RNA polymerase", "steric hindrance of RNA-dependent RNA polymerase", "viral RNA-dependent RNA polymerase" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2016-tenoever-the-evolution-of-antiviral-defense", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "viral-tropism", "label": "Viral tropism and cell-type permissiveness", "family": "host factors", "aliases": [ "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": [ "2012-pham-replication-in-cells-of-hematopoie", "2014-varble-influenza-a-virus-transmission-bot", "2018-m-ller-mirna-mediated-targeting-of-human-", "2020-yang-a-human-pluripotent-stem-cell-base", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "capicua", "label": "Capicua and transcriptional gatekeeping", "family": "interferon and innate signalling", "aliases": [ "ATXN1L", "Capicua", "capicua and ATXN1 corepressor", "CIC binding site motif", "GAF complex", "low-complexity acidic region" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan", "2018-han-genome-wide-crispr-cas9-screen-ide", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "homologous-recombination", "label": "Homologous recombination in RNA viruses", "family": "population genetics and evolution", "aliases": [ "genome polarity", "homologous recombination", "negative-sense RNA virus constraints", "no DNA intermediate", "positive-strand RNA virus specificity", "template switching" ], "publications": [ "2014-schmid-a-versatile-rna-vector-for-deliver", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2018-aguado-homologous-recombination-is-an-int", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "host-directed-antivirals", "label": "Host-directed antiviral strategies", "family": "host factors", "aliases": [ "alectinib repurposing", "antiviral drug target selection", "drug repurposing", "host-directed antiviral strategy", "host-directed antiviral therapy", "kinase inhibitor repurposing" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "imbalanced-host-response", "label": "Imbalanced host response", "family": "pandemic pathogenesis", "aliases": [ "attenuated type I and III interferon signaling", "imbalanced host response" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "mapk-signalling", "label": "MAPK signalling", "family": "interferon and innate signalling", "aliases": [ "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": [ "2014-schmid-mitogen-activated-protein-kinase-m", "2020-bouhaddou-the-global-phosphorylation-landsca", "2022-yaron-host-protein-kinases-required-for-", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "microrna-turnover", "label": "MicroRNA turnover and terminal modification", "family": "small RNA biology", "aliases": [ "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": [ "2012-backes-degradation-of-host-micrornas-by-p", "2014-backes-the-mammalian-response-to-virus-in", "2015-aguado-microrna-function-is-limited-to-cy", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "pattern-recognition-receptors", "label": "Pattern recognition receptors", "family": "interferon and innate signalling", "aliases": [ "pathogen-associated molecular patterns", "pattern recognition receptor", "pattern recognition receptors" ], "publications": [ "2015-benitez-in-vivo-rnai-screening-identifies-", "2016-tenoever-the-evolution-of-antiviral-defense", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "rig-i-like-receptors", "label": "RIG-I-like receptors", "family": "interferon and innate signalling", "aliases": [ "MDA5", "RIG-I", "RIG-I sensing of alphavirus", "RIG-I-like receptor", "RIG-I-like receptors" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o", "2013-varble-an-in-vivo-rnai-screening-approach", "2015-benitez-in-vivo-rnai-screening-identifies-", "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "transcription-to-replication-switch", "label": "Transcription to replication switch", "family": "viral gene expression", "aliases": [ "cRNA intermediate", "cRNA synthesis", "polymerase processivity", "primary transcription", "replicase complex assembly", "transcription to replication switch", "vRNA synthesis" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "isg-repression", "label": "Transcriptional repression of interferon-stimulated genes", "family": "interferon and innate signalling", "aliases": [ "cytokine derepression", "KLF4-mediated repression of antiviral induction", "transcriptional repression", "transcriptional repression of interferon-stimulated genes" ], "publications": [ "2015-aguado-microrna-function-is-limited-to-cy", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-eggenberger-type-i-interferon-response-impairs", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "transmission-bottleneck", "label": "Transmission bottlenecks", "family": "population genetics and evolution", "aliases": [ "barcode control for drift", "founder effects", "founder population", "population bottlenecks", "stochastic transmission", "transmission bottleneck" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach", "2014-varble-influenza-a-virus-transmission-bot", "2019-tenoever-synthetic-virology-building-viruse", "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "type-i-interferon-induction", "label": "Type I interferon induction", "family": "interferon and innate signalling", "aliases": [ "feed forward amplification of innate immunity", "interferon beta enhanceosome", "interferon induction", "type I interferon induction" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2012-langlois-hematopoietic-specific-targeting-o", "2014-schmid-mitogen-activated-protein-kinase-m", "2021-nilsson-payant-reduced-nucleoprotein-availability" ] }, { "id": "viral-population-dynamics", "label": "Viral population dynamics", "family": "population genetics and evolution", "aliases": [ "barcoded library competition assay", "population monopolization", "viral population dynamics", "viral quasispecies", "virus population dynamics", "within-population competition" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot", "2018-aguado-homologous-recombination-is-an-int", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "virtrons", "label": "Virtrons", "family": "small RNA biology", "aliases": [ "viral microRNA synthesis", "virtron", "virtrons", "virus-encoded microRNA" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr" ] }, { "id": "adar1", "label": "ADAR1 and RNA editing", "family": "small RNA biology", "aliases": [ "ADAR1", "ADAR1 deficiency", "ADAR1 p110 and p150 isoforms", "adenosine to inosine RNA editing", "hypermutation" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2023-paget-stress-granules-are-shock-absorber", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "age-and-immunosenescence", "label": "Age and immunosenescence", "family": "immunology", "aliases": [ "IL-17 and neutrophil recruitment", "immunosenescence", "immunosuppression", "neutrophil recruitment and transmigration" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r", "2022-oishi-a-diminished-immune-response-under", "2023-carrau-delayed-engagement-of-host-defense" ] }, { "id": "host-range-and-adaptation", "label": "Host range restriction and adaptation", "family": "population genetics and evolution", "aliases": [ "host adaptation", "host range restriction", "host tropism", "pandemic emergence", "PB2 627 polymorphism" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "ikk-related-kinases", "label": "IKK-related kinases", "family": "interferon and innate signalling", "aliases": [ "IKK-related kinases", "IKKepsilon", "IKKε", "TBK1", "virus-activated kinase" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2007-tenoever-multiple-functions-of-the-ikk-rela", "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "interferon-and-cell-identity", "label": "Interferon and cell identity", "family": "cell identity and development", "aliases": [ "cellular reprogramming", "differentiation potential", "germ layer specification", "piRNA pathway", "pluripotency", "pluripotency and RNAi competence" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2016-tenoever-the-evolution-of-antiviral-defense", "2019-eggenberger-type-i-interferon-response-impairs" ] }, { "id": "irf3-activation", "label": "IRF3 activation", "family": "interferon and innate signalling", "aliases": [ "C-terminal phosphorylation", "IRF-3 activation", "IRF3", "sequential multisite phosphorylation" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2010-schmid-transcription-factor-redundancy-en", "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "irf7-activation", "label": "IRF7 activation", "family": "interferon and innate signalling", "aliases": [ "IRF-7 activation", "IRF3 and IRF7 heterodimer", "IRF7" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira", "2010-schmid-transcription-factor-redundancy-en", "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "isgf3", "label": "ISGF3", "family": "interferon and innate signalling", "aliases": [ "ISGF3", "ISGF3 assembly" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela", "2010-schmid-transcription-factor-redundancy-en", "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "live-attenuated-vaccine-design", "label": "Live attenuated vaccine design", "family": "viral engineering and biocontainment", "aliases": [ "live attenuated influenza vaccine", "live attenuated vaccine design", "live-attenuated vaccine design" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2013-tenoever-rna-viruses-and-the-host-microrna-", "2015-benitez-engineered-mammalian-rnai-can-elic" ] }, { "id": "mavs-signalling", "label": "MAVS signalling", "family": "interferon and innate signalling", "aliases": [ "MAVS signaling", "MDA5 and MAVS signaling", "RIG-I and MAVS signalling" ], "publications": [ "2021-nilsson-payant-reduced-nucleoprotein-availability", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "nf-kb-signalling", "label": "NF-kappaB signalling", "family": "interferon and innate signalling", "aliases": [ "NF-kappaB signalling", "NF-kB-driven chemokine response", "NF-κB signalling" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "rnase-iii-nucleases", "label": "RNase III nucleases as antiviral effectors", "family": "small RNA biology", "aliases": [ "interferon-independent antiviral defense", "interferon-independent defense", "microRNA-independent antiviral activity", "RNA stem loop recognition", "RNase III independence", "RNase III nucleases" ], "publications": [ "2014-shapiro-drosha-as-an-interferon-independen", "2017-aguado-rnase-iii-nucleases-from-diverse-k", "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "self-targeting-virus", "label": "Self-targeting viruses", "family": "viral engineering and biocontainment", "aliases": [ "self-targeting virus", "viral self-targeting" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2015-benitez-engineered-mammalian-rnai-can-elic", "2015-benitez-in-vivo-rnai-screening-identifies-" ] }, { "id": "viral-suppressors-of-rna-silencing", "label": "Viral suppressors of RNA silencing", "family": "small RNA biology", "aliases": [ "NS1 and small RNA silencing", "viral suppressor of RNA silencing", "viral suppressors of RNA silencing" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica", "2015-benitez-engineered-mammalian-rnai-can-elic", "2023-uhl-adar1-biology-can-hinder-effective" ] }, { "id": "anosmia", "label": "Anosmia and olfactory disruption", "family": "pandemic pathogenesis", "aliases": [ "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": [ "2022-frere-sars-cov-2-infection-in-hamsters-a", "2022-zazhytska-non-cell-autonomous-disruption-of-" ] }, { "id": "chromatin-accessibility", "label": "Chromatin accessibility", "family": "interferon and innate signalling", "aliases": [ "chromatin accessibility" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2025-manivasagam-transcriptional-repressor-capicua-" ] }, { "id": "mouse-genome-writing", "label": "Mammalian genome writing", "family": "viral engineering and biocontainment", "aliases": [ "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": [ "2009-perez-microrna-mediated-species-specific", "2023-zhang-mouse-genome-rewriting-and-tailori" ] }, { "id": "molecular-biocontainment", "label": "Molecular biocontainment", "family": "viral engineering and biocontainment", "aliases": [ "biocontainment kill switch", "gain-of-function research biosafety", "molecular biocontainment" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat", "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "oas-rnase-l", "label": "OAS and RNase L system", "family": "interferon and innate signalling", "aliases": [ "OAS and RNase L", "OAS and RNase L system" ], "publications": [ "2015-benitez-in-vivo-rnai-screening-identifies-", "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "post-acute-sequelae", "label": "Post-acute sequelae of SARS-CoV-2 infection", "family": "pandemic pathogenesis", "aliases": [ "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": [ "2022-frere-sars-cov-2-infection-in-hamsters-a", "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "prokaryotic-defence", "label": "Prokaryotic and plant defence systems", "family": "small RNA biology", "aliases": [ "antisense RNA defense", "CRISPR-Cas", "kink-turn RNA structure", "L30 protein family", "L7Ae", "prokaryotic Argonaute", "restriction modification systems" ], "publications": [ "2016-tenoever-the-evolution-of-antiviral-defense", "2023-oishi-archaeal-kink-turn-binding-protein" ] }, { "id": "type-iii-interferon", "label": "Type III interferon", "family": "interferon and innate signalling", "aliases": [ "type III interferon", "type III interferon signaling" ], "publications": [ "2010-schmid-transcription-factor-redundancy-en", "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "airway-host-response", "label": "Airway host response", "family": "general virology", "aliases": [ "airway host response" ], "publications": [ "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "allele-a-and-allele-b-ns-segments", "label": "Allele A and allele B NS segments", "family": "viral gene expression", "aliases": [ "allele A and allele B NS segments" ], "publications": [ "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "allosteric-enhancer-rna", "label": "Allosteric enhancer RNA", "family": "interferon and innate signalling", "aliases": [ "allosteric enhancer RNA" ], "publications": [ "2012-perez-a-small-rna-enhancer-of-viral-poly" ] }, { "id": "anp32a", "label": "ANP32A", "family": "host factors", "aliases": [ "ANP32A" ], "publications": [ "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "antagomir-antiviral-strategy", "label": "Antagomir antiviral strategy", "family": "viral engineering and biocontainment", "aliases": [ "antagomir antiviral strategy" ], "publications": [ "2017-morales-sars-cov-encoded-small-rnas-contri" ] }, { "id": "arp2-and-arp3-complex", "label": "ARP2 and ARP3 complex", "family": "host factors", "aliases": [ "ARP2 and ARP3 complex" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "bystander-versus-infected-cell-responses", "label": "Bystander versus infected cell responses", "family": "general virology", "aliases": [ "bystander versus infected cell responses" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don" ] }, { "id": "cell-cycle-arrest", "label": "Cell cycle arrest", "family": "cell identity and development", "aliases": [ "cell cycle arrest" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca" ] }, { "id": "cholesterol-biosynthesis", "label": "Cholesterol biosynthesis", "family": "host factors", "aliases": [ "cholesterol biosynthesis" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "class-3-pi3k", "label": "Class 3 PI3K", "family": "host factors", "aliases": [ "class 3 PI3K" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "cmp-sialic-acid-transport", "label": "CMP-sialic acid transport", "family": "host factors", "aliases": [ "CMP-sialic acid transport" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "coinfection", "label": "Coinfection", "family": "general virology", "aliases": [ "coinfection" ], "publications": [ "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "commander-complex", "label": "Commander complex", "family": "host factors", "aliases": [ "Commander complex" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "criteria-for-demonstrating-antiviral-rnai", "label": "Criteria for demonstrating antiviral RNAi", "family": "small RNA biology", "aliases": [ "criteria for demonstrating antiviral RNAi" ], "publications": [ "2013-cullen-is-rna-interference-a-physiologica" ] }, { "id": "demyelination-signature", "label": "Demyelination signature", "family": "pandemic pathogenesis", "aliases": [ "demyelination signature" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "dorsal-root-ganglia", "label": "Dorsal root ganglia", "family": "general virology", "aliases": [ "dorsal root ganglia" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "endosomal-trafficking", "label": "Endosomal trafficking", "family": "host factors", "aliases": [ "endosomal trafficking" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "enhancer-remodelling", "label": "Enhancer remodelling", "family": "interferon and innate signalling", "aliases": [ "enhancer remodelling" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "filopodial-protrusions", "label": "Filopodial protrusions", "family": "general virology", "aliases": [ "filopodial protrusions" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca" ] }, { "id": "gamma-activated-sequence", "label": "Gamma-activated sequence", "family": "interferon and innate signalling", "aliases": [ "gamma-activated sequence" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "gastrointestinal-barrier", "label": "Gastrointestinal barrier", "family": "general virology", "aliases": [ "gastrointestinal barrier" ], "publications": [ "2020-mccune-rapid-dissemination-and-monopoliza" ] }, { "id": "hemagglutinin-segment-engineering", "label": "Hemagglutinin segment engineering", "family": "viral gene expression", "aliases": [ "hemagglutinin segment engineering" ], "publications": [ "2013-langlois-microrna-based-strategy-to-mitigat" ] }, { "id": "hepatocyte-and-cholangiocyte-infection", "label": "Hepatocyte and cholangiocyte infection", "family": "general virology", "aliases": [ "hepatocyte and cholangiocyte infection" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "host-transcriptome-modulation", "label": "Host transcriptome modulation", "family": "general virology", "aliases": [ "host transcriptome modulation" ], "publications": [ "2014-shapiro-drosha-as-an-interferon-independen" ] }, { "id": "host-transcriptome-remodelling", "label": "Host transcriptome remodelling", "family": "general virology", "aliases": [ "host transcriptome remodelling" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "ie2-autorepression-through-the-cis-repression-sequence", "label": "IE2 autorepression through the cis-repression sequence", "family": "general virology", "aliases": [ "IE2 autorepression through the cis-repression sequence" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "il-6", "label": "IL-6", "family": "general virology", "aliases": [ "IL-6" ], "publications": [ "2020-blanco-melo-imbalanced-host-response-to-sars-c" ] }, { "id": "ilf3", "label": "ILF3", "family": "interferon and innate signalling", "aliases": [ "ILF3" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "immediate-early-gene-circuitry", "label": "Immediate early gene circuitry", "family": "general virology", "aliases": [ "immediate early gene circuitry" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "immune-mediated-apoptosis", "label": "Immune-mediated apoptosis", "family": "pandemic pathogenesis", "aliases": [ "immune-mediated apoptosis" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "in-vivo-rna-interference-screening", "label": "In vivo RNA interference screening", "family": "general virology", "aliases": [ "in vivo RNA interference screening" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach" ] }, { "id": "infected-versus-bystander-cells", "label": "Infected versus bystander cells", "family": "general virology", "aliases": [ "infected versus bystander cells" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "innate-sensing-compartment", "label": "Innate sensing compartment", "family": "interferon and innate signalling", "aliases": [ "innate sensing compartment" ], "publications": [ "2012-langlois-hematopoietic-specific-targeting-o" ] }, { "id": "interferon-response", "label": "Interferon response", "family": "interferon and innate signalling", "aliases": [ "interferon response" ], "publications": [ "2014-backes-the-mammalian-response-to-virus-in" ] }, { "id": "limbal-stem-cell-niche", "label": "Limbal stem cell niche", "family": "cell identity and development", "aliases": [ "limbal stem cell niche" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don" ] }, { "id": "mechanical-hypersensitivity", "label": "Mechanical hypersensitivity", "family": "pandemic pathogenesis", "aliases": [ "mechanical hypersensitivity" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "microglial-and-myeloid-activation", "label": "Microglial and myeloid activation", "family": "general virology", "aliases": [ "microglial and myeloid activation" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a" ] }, { "id": "negative-feedback-by-apoptotic-caspases", "label": "Negative feedback by apoptotic caspases", "family": "general virology", "aliases": [ "negative feedback by apoptotic caspases" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "neuropathic-transcriptome", "label": "Neuropathic transcriptome", "family": "pandemic pathogenesis", "aliases": [ "neuropathic transcriptome" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "neuroplasticity", "label": "Neuroplasticity", "family": "pandemic pathogenesis", "aliases": [ "neuroplasticity" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "ns1-protein", "label": "NS1 protein", "family": "viral gene expression", "aliases": [ "NS1 protein" ], "publications": [ "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "nucleocapsid-sr-rich-domain", "label": "Nucleocapsid SR-rich domain", "family": "viral gene expression", "aliases": [ "nucleocapsid SR-rich domain" ], "publications": [ "2022-yaron-host-protein-kinases-required-for-" ] }, { "id": "ocular-route-of-sars-cov-2-entry", "label": "Ocular route of SARS-CoV-2 entry", "family": "pandemic pathogenesis", "aliases": [ "ocular route of SARS-CoV-2 entry" ], "publications": [ "2021-eriksen-sars-cov-2-infects-human-adult-don" ] }, { "id": "pa-rna-binding-cleft", "label": "PA RNA binding cleft", "family": "general virology", "aliases": [ "PA RNA binding cleft" ], "publications": [ "2012-perez-a-small-rna-enhancer-of-viral-poly" ] }, { "id": "paleovirology", "label": "Paleovirology and historical virus movement", "family": "population genetics and evolution", "aliases": [ "ancient DNA authentication", "Cocoliztli", "Colonial epidemics", "cross-population transmission", "host genetic ancestry", "molecular tip calibration", "paleovirology", "transatlantic slave trade", "viral genotype geography" ], "publications": [ "2021-guzman-solis-ancient-viral-genomes-reveal-intro" ] }, { "id": "pancreatic-beta-cell-infection", "label": "Pancreatic beta cell infection", "family": "general virology", "aliases": [ "pancreatic beta cell infection" ], "publications": [ "2020-yang-a-human-pluripotent-stem-cell-base" ] }, { "id": "pkr", "label": "PKR", "family": "interferon and innate signalling", "aliases": [ "PKR" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "promoter-motif-specificity", "label": "Promoter motif specificity", "family": "interferon and innate signalling", "aliases": [ "promoter motif specificity" ], "publications": [ "2010-schmid-transcription-factor-redundancy-en" ] }, { "id": "promoter-panhandle", "label": "Promoter panhandle", "family": "interferon and innate signalling", "aliases": [ "promoter panhandle" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-" ] }, { "id": "promoter-selectivity", "label": "Promoter selectivity", "family": "interferon and innate signalling", "aliases": [ "promoter selectivity" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela" ] }, { "id": "promyelocytic-leukemia-nuclear-bodies", "label": "Promyelocytic leukemia nuclear bodies", "family": "general virology", "aliases": [ "promyelocytic leukemia nuclear bodies" ], "publications": [ "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "renal-tubular-atrophy", "label": "Renal tubular atrophy", "family": "pandemic pathogenesis", "aliases": [ "renal tubular atrophy" ], "publications": [ "2022-frere-sars-cov-2-infection-in-hamsters-a" ] }, { "id": "replication-kinetics", "label": "Replication kinetics", "family": "viral gene expression", "aliases": [ "replication kinetics" ], "publications": [ "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "retromer-complex", "label": "Retromer complex", "family": "host factors", "aliases": [ "Retromer complex" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "sequential-infection", "label": "Sequential infection", "family": "general virology", "aliases": [ "sequential infection" ], "publications": [ "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "sialic-acid-biosynthesis", "label": "Sialic acid biosynthesis", "family": "host factors", "aliases": [ "sialic acid biosynthesis" ], "publications": [ "2018-han-genome-wide-crispr-cas9-screen-ide" ] }, { "id": "sp100-family", "label": "SP100 family", "family": "general virology", "aliases": [ "SP100 family" ], "publications": [ "2014-schmid-mitogen-activated-protein-kinase-m" ] }, { "id": "stat1-dependent-selection", "label": "STAT1 dependent selection", "family": "interferon and innate signalling", "aliases": [ "STAT1 dependent selection" ], "publications": [ "2019-munoz-moreno-viral-fitness-landscapes-in-divers" ] }, { "id": "stat1-homodimer-interface", "label": "STAT1 homodimer interface", "family": "interferon and innate signalling", "aliases": [ "STAT1 homodimer interface" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "stat1-serine-708-phosphorylation", "label": "STAT1 serine 708 phosphorylation", "family": "interferon and innate signalling", "aliases": [ "STAT1 serine 708 phosphorylation" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "stat1-serine-phosphorylation", "label": "STAT1 serine phosphorylation", "family": "interferon and innate signalling", "aliases": [ "STAT1 serine phosphorylation" ], "publications": [ "2007-tenoever-multiple-functions-of-the-ikk-rela" ] }, { "id": "strain-dependent-virulence", "label": "Strain-dependent virulence", "family": "general virology", "aliases": [ "strain-dependent virulence" ], "publications": [ "2021-si-a-human-airway-on-a-chip-for-the-r" ] }, { "id": "stress-granules", "label": "Stress granules and biomolecular condensates", "family": "interferon and innate signalling", "aliases": [ "biomolecular condensates", "stress granules" ], "publications": [ "2023-paget-stress-granules-are-shock-absorber" ] }, { "id": "subgenomic-rna", "label": "Subgenomic RNA", "family": "viral gene expression", "aliases": [ "subgenomic RNA" ], "publications": [ "2021-hoagland-leveraging-the-antiviral-type-i-in" ] }, { "id": "synthetic-virology", "label": "Synthetic virology", "family": "viral engineering and biocontainment", "aliases": [ "learning by building", "synthetic virology", "viral genetic circuitry" ], "publications": [ "2019-tenoever-synthetic-virology-building-viruse" ] }, { "id": "tgf-beta-signalling", "label": "TGF-beta signalling", "family": "general virology", "aliases": [ "TGF-beta signalling" ], "publications": [ "2022-oishi-a-diminished-immune-response-under" ] }, { "id": "transcription-factor-complex-competition", "label": "Transcription factor complex competition", "family": "interferon and innate signalling", "aliases": [ "transcription factor complex competition" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "transcription-factor-motif-enrichment", "label": "Transcription factor motif enrichment", "family": "interferon and innate signalling", "aliases": [ "transcription factor motif enrichment" ], "publications": [ "2021-nilsson-payant-the-nf-b-transcriptional-footprint" ] }, { "id": "transcription-factor-nuclear-translocation", "label": "Transcription factor nuclear translocation", "family": "interferon and innate signalling", "aliases": [ "transcription factor nuclear translocation" ], "publications": [ "2003-sharma-triggering-the-interferon-antivira" ] }, { "id": "transcription-factor-redundancy", "label": "Transcription factor redundancy", "family": "interferon and innate signalling", "aliases": [ "transcription factor redundancy" ], "publications": [ "2010-schmid-transcription-factor-redundancy-en" ] }, { "id": "transcriptional-maintenance-of-antiviral-capacity", "label": "Transcriptional maintenance of antiviral capacity", "family": "general virology", "aliases": [ "transcriptional maintenance of antiviral capacity" ], "publications": [ "2013-varble-an-in-vivo-rnai-screening-approach" ] }, { "id": "type-i-interferon-signalling-in-sensory-tissue", "label": "Type I interferon signalling in sensory tissue", "family": "interferon and innate signalling", "aliases": [ "type I interferon signalling in sensory tissue" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "type-i-versus-type-ii-interferon-balance", "label": "Type I versus type II interferon balance", "family": "interferon and innate signalling", "aliases": [ "type I versus type II interferon balance" ], "publications": [ "2011-ng-i-b-kinase-ikk-regulates-the-balan" ] }, { "id": "upstream-regulator-prediction", "label": "Upstream regulator prediction", "family": "general virology", "aliases": [ "upstream regulator prediction" ], "publications": [ "2023-serafini-sars-cov-2-airway-infection-result" ] }, { "id": "vaccine-yield-in-ovo", "label": "Vaccine yield in ovo", "family": "viral engineering and biocontainment", "aliases": [ "vaccine yield in ovo" ], "publications": [ "2009-perez-microrna-mediated-species-specific" ] }, { "id": "vacuolar-atpase", "label": "Vacuolar ATPase", "family": "host factors", "aliases": [ "vacuolar ATPase" ], "publications": [ "2021-daniloski-identification-of-required-host-fa" ] }, { "id": "viral-egress", "label": "Viral egress", "family": "viral gene expression", "aliases": [ "viral egress" ], "publications": [ "2020-bouhaddou-the-global-phosphorylation-landsca" ] }, { "id": "viral-genomic-rna-cleavage", "label": "Viral genomic RNA cleavage", "family": "general virology", "aliases": [ "viral genomic RNA cleavage" ], "publications": [ "2014-shapiro-drosha-as-an-interferon-independen" ] }, { "id": "viral-interference", "label": "Viral interference", "family": "general virology", "aliases": [ "viral interference" ], "publications": [ "2022-oishi-the-host-response-to-influenza-a-v" ] }, { "id": "viral-promoter-mutation", "label": "Viral promoter mutation", "family": "interferon and innate signalling", "aliases": [ "viral promoter mutation" ], "publications": [ "2022-nilsson-payant-the-host-factor-anp32a-is-required" ] }, { "id": "viral-transcriptional-cascade", "label": "Viral transcriptional cascade", "family": "general virology", "aliases": [ "viral transcriptional cascade" ], "publications": [ "2018-m-ller-mirna-mediated-targeting-of-human-" ] }, { "id": "virus-clearance", "label": "Virus clearance", "family": "general virology", "aliases": [ "virus clearance" ], "publications": [ "2014-heaton-long-term-survival-of-influenza-vi" ] } ] }