{"id":"W4404587478","doi":"10.1016/j.immuni.2024.10.015","title":"Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms","year":2024,"lang":"en","type":"article","venue":"Immunity","topic":"Cytomegalovirus and herpesvirus research","field":"Medicine","cited_by":26,"is_retracted":false,"has_abstract":false,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network; Université de Montréal","funders":"National Institute of General Medical Sciences; National Institute on Aging; Canadian Institutes of Health Research; Dystonia Medical Research Foundation Canada; V Foundation for Cancer Research; Stanford Genome Technology Center; Mark Foundation For Cancer Research; Memorial Sloan-Kettering Cancer Center; Fondation pour la Recherche Médicale; National Institutes of Health; Consejo Nacional de Ciencia y Tecnología; Pershing Square Sohn Cancer Research Alliance; National Cancer Institute; Jane Coffin Childs Memorial Fund for Medical Research; National Institute of Allergy and Infectious Diseases; Howard Hughes Medical Institute","keywords":"Biology; Retrotransposon; Immunogenicity; Cancer; Computational biology; Cancer research; Genetics; Virology; Gene; Immune system; Transposable element; Genome","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0004561586,0.0001659813,0.0003422743,0.0001760611,0.0001300219,0.0000293777,0.0002107734,0.0001495642,0.001578267],"category_scores_gemma":[0.00003982678,0.000130746,0.0002067016,0.0005015432,0.0001042269,0.00009947093,0.0001009669,0.0007112163,0.00007734859],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001647937,"about_ca_system_score_gemma":0.0002064736,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007154577,"about_ca_topic_score_gemma":0.0001408447,"domain_scores_codex":[0.9985207,0.0001255771,0.0003378713,0.0002389468,0.000466727,0.0003102166],"domain_scores_gemma":[0.999006,0.0001324599,0.00004875822,0.0005603367,0.0001260591,0.0001263277],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0005861252,0.0001562691,0.0004425231,0.0004416941,0.00008754029,0.00005381896,0.0003118591,0.000002637907,0.9785256,0.0001250547,0.0004719875,0.01879494],"study_design_scores_gemma":[0.0005715779,0.0002818996,0.01696214,0.000659315,0.00008682402,0.00001194072,0.00004517581,0.0004720104,0.9748175,0.0005203774,0.005434633,0.0001366325],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9888245,0.005224942,0.002678992,0.0001947697,0.0003384559,0.0004087237,0.000136386,0.0001160986,0.002077123],"genre_scores_gemma":[0.9976516,0.0008074851,0.0004270634,0.00002948244,0.00008236283,0.00003341295,0.00003002302,0.00003551715,0.0009030153],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01865831,"threshold_uncertainty_score":0.9994569,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03023688800305665,"score_gpt":0.3313843503377144,"score_spread":0.3011474623346577,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}