{"id":"W2096878654","doi":"10.1007/s00438-014-0937-y","title":"Limitations of the ‘ambush hypothesis’ at the single-gene scale: what codon biases are to blame?","year":2014,"lang":"en","type":"article","venue":"Molecular Genetics and Genomics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Manitoba","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Codon usage bias; Genetics; Genetic code; Open reading frame; Gene; Frameshift mutation; Synonymous substitution; Stop codon; Computational biology; Genome; Mutation; Peptide sequence","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":[0.000236778,0.0001874028,0.0001677338,0.00002881327,0.0002060971,0.00008217147,0.0003489549,0.0001268593,0.000004753649],"category_scores_gemma":[0.0002530485,0.0001323418,0.0001276306,0.00009795595,0.0001430708,0.000002650842,0.0003424822,0.00004977976,0.000006947997],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001518174,"about_ca_system_score_gemma":0.00003045479,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004970575,"about_ca_topic_score_gemma":0.0001236205,"domain_scores_codex":[0.9988768,0.0001628578,0.0002366916,0.0003376604,0.0001599239,0.0002261208],"domain_scores_gemma":[0.9988309,0.00009002016,0.0001507535,0.0007414884,0.00009358541,0.00009323979],"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":[0.00002535441,0.00002988318,0.0001588382,0.000006614604,0.00003573771,4.355092e-7,0.0000908591,0.001229569,0.9660416,0.00004237804,0.0001453306,0.03219338],"study_design_scores_gemma":[0.0001603294,0.0001903962,0.0022319,0.00002671436,0.00005466468,0.00001172227,0.0001384592,0.00006723007,0.9563348,0.0004672846,0.04013815,0.0001783447],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.989166,0.0045455,0.004171312,0.001349846,0.0001680263,0.0003769413,0.00003238279,0.000004573001,0.0001854256],"genre_scores_gemma":[0.9919422,0.00232276,0.003435136,0.001810028,0.00009195224,0.00003042933,0.00001448806,0.00004233649,0.0003107245],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03999282,"threshold_uncertainty_score":0.539674,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04039430584689236,"score_gpt":0.2120212660049274,"score_spread":0.1716269601580351,"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."}}