{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006492986,0.0001785373,0.0002616474,0.0006453453,0.0004227647,0.001093058,0.0003514811,0.0004513698,0.0007583209],"category_scores_gemma":[0.00260197,0.0002032781,0.0004225651,0.0004694886,0.0005748903,0.0006767097,0.000573009,0.0004802418,0.00009122785],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004239682,"about_ca_system_score_gemma":0.0004296346,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001442918,"about_ca_topic_score_gemma":0.001533394,"domain_scores_codex":[0.9998179,0.00004989222,0.000009048874,0.00006358422,0.00003302707,0.00002656947],"domain_scores_gemma":[0.9993609,0.0004045697,0.0001015077,0.0000483783,0.00002640678,0.00005830375],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0005348481,0.0002087101,0.3278023,0.0001794737,0.0002624714,0.0006238488,0.0005767071,0.5478392,0.07407119,0.01997194,0.0003281045,0.02760123],"study_design_scores_gemma":[0.00002491789,0.00006838179,0.06794665,0.000009525498,0.00003448731,0.0002486529,0.0002217899,0.9183244,0.003308189,0.009389395,0.0003999616,0.00002371472],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9940222,0.0000350208,0.005428952,0.00005471328,0.000001201081,0.00000344929,0.00004104386,0.00003258065,0.0003808911],"genre_scores_gemma":[0.9956007,0.00005110622,0.004087096,0.00001699203,0.000002075172,0.00001171483,0.0001013787,0.0000121371,0.0001168425],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001442918,"threshold_uncertainty_score":0.003433883,"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."}}