{"id":"W2146837785","doi":"10.1534/genetics.114.172106","title":"A Major Controversy in Codon-Anticodon Adaptation Resolved by a New Codon Usage Index","year":2014,"lang":"en","type":"article","venue":"Genetics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":71,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"","keywords":"Codon usage bias; Transfer RNA; Biology; Translation (biology); Protein biosynthesis; Genetics; Translational efficiency; Adaptation (eye); Gene; Eukaryotic translation; Elongation factor; Messenger RNA; Computational biology; Ribosome; RNA; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003138109,0.0001907941,0.0002033528,0.00005247733,0.00005114691,0.00003989449,0.0002227457,0.0002553843,0.00003966567],"category_scores_gemma":[0.0001670396,0.0001988219,0.00006883319,0.00009220847,0.00003770686,0.000003474501,0.00006979522,0.00008557927,0.00002612261],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001698626,"about_ca_system_score_gemma":0.00007450795,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001434493,"about_ca_topic_score_gemma":0.0004337809,"domain_scores_codex":[0.9986724,0.0001598513,0.0002793557,0.0003796123,0.0001886148,0.0003201221],"domain_scores_gemma":[0.999288,0.00003633432,0.0001129087,0.0003922509,0.00004282816,0.0001276426],"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":[0.0001609431,0.00004049143,0.001751616,0.00001118694,0.00002253908,0.000001522783,0.00007495943,0.0001895883,0.9686297,0.000109805,0.005290641,0.02371706],"study_design_scores_gemma":[0.002217141,0.0005199384,0.001433214,0.00002948313,0.00002761075,0.000005404186,0.00008129751,0.002916259,0.7934848,0.0007289224,0.1981924,0.0003635524],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7056981,0.001790482,0.2898957,0.000478741,0.0002359043,0.0005257784,0.00002843622,0.0000237039,0.001323046],"genre_scores_gemma":[0.9920298,0.00027569,0.005312871,0.00059616,0.0002244125,0.00002154276,0.00009128051,0.0000379548,0.001410297],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2863316,"threshold_uncertainty_score":0.8107722,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01083337905534572,"score_gpt":0.22757918685352,"score_spread":0.2167458077981743,"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."}}