{"id":"W4412494107","doi":"10.1126/sciadv.ads9164","title":"A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage","year":2025,"lang":"en","type":"article","venue":"Science Advances","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Japan Society for the Promotion of Science","keywords":"Endogenous retrovirus; Phylogenetic tree; Biology; Genome; Annotation; Long terminal repeat; Phylogenetics; Retrovirus; Lineage (genetic); Genetics; Evolutionary biology; Computational biology; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004774377,0.0003262448,0.0004177656,0.002062919,0.000784195,0.0005417286,0.0002355042,0.0002979652,0.00158988],"category_scores_gemma":[0.0007065097,0.0001543632,0.0004708931,0.001586571,0.000211109,0.0004587633,0.0006170762,0.0006163025,0.0006345076],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002751125,"about_ca_system_score_gemma":0.0002807099,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008155272,"about_ca_topic_score_gemma":0.001974997,"domain_scores_codex":[0.9997312,0.00004484747,0.00002081167,0.0001228677,0.00004378441,0.00003642685],"domain_scores_gemma":[0.9995244,0.0001323753,0.0001129838,0.00006879122,0.00008333221,0.00007829718],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0007325124,0.00007555317,0.1054545,0.0004891685,0.0001778497,0.0004676438,0.001267057,0.001130018,0.7894879,0.001325458,0.0003672582,0.099025],"study_design_scores_gemma":[0.00005561454,0.0006996536,0.7989782,0.0003350319,0.0007657607,0.006865132,0.002221939,0.04250589,0.09229971,0.004417142,0.05075917,0.00009677681],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9724763,0.002108035,0.02103202,0.0000742409,0.00001362099,0.00003743509,0.001605408,0.0002240577,0.002428957],"genre_scores_gemma":[0.9475248,0.00123994,0.04321954,0.0001210208,0.00003080384,0.00005243718,0.006273638,0.0001111559,0.001426582],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002062919,"threshold_uncertainty_score":0.005318701,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01955235416542643,"score_gpt":0.2468794043810867,"score_spread":0.2273270502156603,"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."}}