[ { "id": "innate-immune-signaling", "name": "Innate Immune Signaling and the Interferon Response", "short": "How the interferon response is wired, tuned and held in check", "question": "What determines which genes the interferon system turns on, how strongly, and for how long?", "themes": [ "ikk-kinases-and-irf-activation", "transcription-factor-selectivity", "homeostatic-repression-of-isgs", "interferon-and-cell-identity", "sensing-aberrant-rna", "calibration-of-interferon-in-vivo" ], "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", "2012-langlois-hematopoietic-specific-targeting-o", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-mitogen-activated-protein-kinase-m", "2015-benitez-in-vivo-rnai-screening-identifies-", "2016-tenoever-the-evolution-of-antiviral-defense", "2018-han-genome-wide-crispr-cas9-screen-ide", "2019-eggenberger-type-i-interferon-response-impairs", "2020-blanco-melo-imbalanced-host-response-to-sars-c", "2021-hoagland-leveraging-the-antiviral-type-i-in", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2021-nilsson-payant-the-nf-b-transcriptional-footprint", "2023-carrau-delayed-engagement-of-host-defense", "2023-paget-stress-granules-are-shock-absorber", "2025-manivasagam-transcriptional-repressor-capicua-" ], "url": "https://tenoeverlab.us/research/innate-immune-signaling/", "discoveries": [ "claim-03", "claim-04", "claim-05", "claim-06", "claim-10", "claim-12", "claim-13", "claim-14" ] }, { "id": "small-rna-antiviral-defense", "name": "Small RNA Biology and the Limits of Antiviral Silencing", "short": "Why vertebrates abandoned RNA silencing as an antiviral system, and what that costs them", "question": "Do mammals use small RNAs against viruses, and if not, why not?", "themes": [ "noncanonical-microrna-biogenesis", "does-mammalian-antiviral-rnai-exist", "reconstructing-antiviral-rnai", "rnase-iii-antiviral-effectors", "limits-of-microrna-function", "evolution-of-antiviral-defense" ], "publications": [ "2010-shapiro-noncanonical-cytoplasmic-processin", "2010-varble-engineered-rna-viral-synthesis-of-", "2012-backes-degradation-of-host-micrornas-by-p", "2012-langlois-in-vivo-delivery-of-cytoplasmic-rn", "2012-shapiro-evidence-for-a-cytoplasmic-micropr", "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-aguado-microrna-function-is-limited-to-cy", "2015-benitez-engineered-mammalian-rnai-can-elic", "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", "2023-oishi-archaeal-kink-turn-binding-protein", "2023-uhl-adar1-biology-can-hinder-effective" ], "url": "https://tenoeverlab.us/research/small-rna-antiviral-defense/", "discoveries": [ "claim-06", "claim-07", "claim-08", "claim-09" ] }, { "id": "programmable-virology", "name": "Programmable Virology", "short": "Treating a virus as a genetic circuit that can be rewritten to answer a question", "question": "If a virus can be redesigned, what can be learned that cannot be learned any other way?", "themes": [ "microrna-mediated-viral-attenuation", "cell-type-restriction-as-a-tool", "molecular-biocontainment", "rna-vectors-for-delivery", "in-vivo-screening-through-fitness", "lineage-tracing-of-infection", "synthetic-virology-as-method" ], "publications": [ "2009-perez-microrna-mediated-species-specific", "2010-varble-engineered-rna-viral-synthesis-of-", "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", "2013-varble-an-in-vivo-rnai-screening-approach", "2014-heaton-long-term-survival-of-influenza-vi", "2014-schmid-a-versatile-rna-vector-for-deliver", "2015-benitez-in-vivo-rnai-screening-identifies-", "2018-han-genome-wide-crispr-cas9-screen-ide", "2018-m-ller-mirna-mediated-targeting-of-human-", "2019-tenoever-synthetic-virology-building-viruse", "2021-daniloski-identification-of-required-host-fa", "2023-zhang-mouse-genome-rewriting-and-tailori" ], "url": "https://tenoeverlab.us/research/programmable-virology/", "discoveries": [ "claim-10", "claim-14" ] }, { "id": "influenza-genome-regulation", "name": "Influenza Genome Regulation and Replication", "short": "The timing and stoichiometry that govern an eight-segment genome", "question": "How does influenza A virus control the order and amount of its own gene expression?", "themes": [ "small-viral-rnas", "splicing-and-temporal-control", "polymerase-nucleoprotein-host-factors", "ns1-and-interferon-antagonism" ], "publications": [ "2010-perez-influenza-a-virus-generated-small-", "2012-perez-a-small-rna-enhancer-of-viral-poly", "2013-chua-influenza-a-virus-utilizes-subopti", "2017-morales-sars-cov-encoded-small-rnas-contri", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2021-nilsson-payant-reduced-nucleoprotein-availability", "2022-nilsson-payant-the-host-factor-anp32a-is-required", "2023-oishi-archaeal-kink-turn-binding-protein" ], "url": "https://tenoeverlab.us/research/influenza-genome-regulation/", "discoveries": [ "claim-01", "claim-02", "claim-03", "claim-11" ] }, { "id": "pandemic-host-response", "name": "Pandemic Host Response and Disease", "short": "What SARS-CoV-2 does to the host, acutely and long after clearance", "question": "Why does SARS-CoV-2 produce the pattern of disease it does, and what part of that is the host's own response?", "themes": [ "imbalanced-host-response", "interferon-as-intervention", "host-factors-and-druggable-signaling", "tropism-and-permissive-tissues", "post-acute-sequelae", "immunity-age-and-reinfection", "models-for-pandemic-virology" ], "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-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" ], "url": "https://tenoeverlab.us/research/pandemic-host-response/", "discoveries": [ "claim-12", "claim-13", "claim-14" ] }, { "id": "viral-populations-evolution", "name": "Viral Populations, Evolution and Transmission", "short": "Viruses as populations passing through bottlenecks and selective landscapes", "question": "What survives when a viral population moves between hosts, tissues or species?", "themes": [ "transmission-bottlenecks", "fitness-landscapes", "recombination-and-escape", "historical-virus-movement" ], "publications": [ "2014-varble-influenza-a-virus-transmission-bot", "2015-benitez-engineered-mammalian-rnai-can-elic", "2018-aguado-homologous-recombination-is-an-int", "2019-munoz-moreno-viral-fitness-landscapes-in-divers", "2020-mccune-rapid-dissemination-and-monopoliza", "2021-guzman-solis-ancient-viral-genomes-reveal-intro", "2023-uhl-adar1-biology-can-hinder-effective" ], "url": "https://tenoeverlab.us/research/viral-populations-evolution/", "discoveries": [ "claim-09", "claim-11" ] } ]