{"id":"W3108241513","doi":"10.1371/journal.pcbi.1008482","title":"Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages","year":2020,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; National Institutes of Health","keywords":"Prophage; Biology; Lytic cycle; Genetics; Genome; Gene; Transposase; Lysogenic cycle; Computational biology; Transposable element; Bacteriophage; Escherichia coli; Virus","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":[],"consensus_categories":[],"category_scores_codex":[0.00004286374,0.00007619623,0.0000963669,0.000007779717,0.0001532239,0.00001231659,0.0001950101,0.00003678057,0.0004190622],"category_scores_gemma":[0.00005298301,0.00004332111,0.00004956541,0.00009467042,0.0003239359,0.000050564,0.0001032287,0.00008171486,0.0001113577],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002233992,"about_ca_system_score_gemma":0.00001138708,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002058648,"about_ca_topic_score_gemma":0.0001027938,"domain_scores_codex":[0.9993488,0.000110673,0.0001997384,0.000167513,0.00006444841,0.0001088398],"domain_scores_gemma":[0.9995627,0.000187571,0.0001118493,0.00009000223,0.00002106992,0.00002685545],"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":[0.00004141862,0.00008879668,0.03191124,0.0000135474,0.00006617593,0.000006573055,0.001564782,0.005977733,0.9497505,0.0005436743,0.003302774,0.00673276],"study_design_scores_gemma":[0.0002199538,0.0001712906,0.9741765,0.00001145394,0.00003978966,0.00006454697,0.0001201694,0.01397418,0.006063146,0.001413377,0.003621909,0.0001236905],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9918481,0.0001207915,0.002089866,0.005388422,0.0001045756,0.0002038195,0.0000268835,0.00001866796,0.0001988385],"genre_scores_gemma":[0.9977977,0.000006323937,0.0009128376,0.001086663,0.00009856478,0.00001802431,0.00002010558,0.000005454526,0.00005429386],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9436874,"threshold_uncertainty_score":0.4588437,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01603613147626874,"score_gpt":0.2347446801972987,"score_spread":0.21870854872103,"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."}}