{"id":"W2159380553","doi":"10.1093/genetics/165.2.695","title":"Likelihood Models of Somatic Mutation and Codon Substitution in Cancer Genes","year":2003,"lang":"en","type":"article","venue":"Genetics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":46,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"National Human Genome Research Institute","keywords":"Biology; Genetics; Missense mutation; Mutation rate; Nonsense mutation; Mutation; Germline mutation; Silent mutation; Gene; Transversion; Synonymous substitution; Codon usage bias; Genome","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":[0.00662277,0.001345042,0.002680754,0.002785761,0.0007890791,0.002757087,0.00424141,0.003286613,0.005810862],"category_scores_gemma":[0.02739789,0.000988378,0.002287404,0.002682283,0.002869012,0.002929637,0.001504494,0.002738981,0.001957573],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002861269,"about_ca_system_score_gemma":0.001105941,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007186344,"about_ca_topic_score_gemma":0.00405264,"domain_scores_codex":[0.9975225,0.00150524,0.00008640315,0.0003182512,0.0003419344,0.0002256175],"domain_scores_gemma":[0.977295,0.0199047,0.001150591,0.0004805216,0.0006781384,0.0004909793],"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":[0.0001649671,0.00003893046,0.002742651,0.00008789177,0.00007471538,0.0003503612,0.0001584901,0.8898739,0.0003966373,0.09768012,0.001469787,0.00696157],"study_design_scores_gemma":[0.0000306478,0.00001881552,0.0002857593,0.00001022568,0.00001326276,0.00008067631,0.0000131537,0.9373946,0.00007175965,0.06141712,0.0006427097,0.00002124448],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1187243,0.002840079,0.8597999,0.003587619,0.0001937263,0.0002224721,0.001317036,0.001089817,0.01222496],"genre_scores_gemma":[0.8674349,0.002703245,0.0876633,0.0007371241,0.0003904769,0.00101238,0.002090326,0.0004608763,0.03750728],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.007186344,"threshold_uncertainty_score":0.035025,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01373980624748314,"score_gpt":0.2507101516144761,"score_spread":0.236970345366993,"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."}}