{"id":"W2565108179","doi":"10.1139/gen-2016-0129","title":"Analysis of codon usage patterns in <i>Morus notabilis</i> based on genome and transcriptome data","year":2017,"lang":"en","type":"article","venue":"Genome","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":48,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Fundamental Research Funds for the Central Universities; China Postdoctoral Science Foundation; National Natural Science Foundation of China","keywords":"Biology; Codon usage bias; Gene; Housekeeping gene; Genome; Genetics; Synonymous substitution; Stop codon; Transcriptome; Translational efficiency; Computational biology; Gene expression; Messenger RNA; Translation (biology)","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000445596,0.0001411008,0.0002838946,0.0001308047,0.00009761656,0.00005126067,0.0006723351,0.0001125164,0.00007248689],"category_scores_gemma":[0.00005407842,0.0001342755,0.00007811925,0.00007297276,0.0001088964,0.000007409987,0.0001506377,0.00005473588,0.000002358094],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007557189,"about_ca_system_score_gemma":0.00003083341,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002053669,"about_ca_topic_score_gemma":0.0004372843,"domain_scores_codex":[0.9989089,0.00006809247,0.0002200408,0.0004749107,0.000129402,0.0001986239],"domain_scores_gemma":[0.9980564,0.0000156964,0.0001307197,0.001710906,0.0000216897,0.00006465253],"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":[0.00008476125,0.00005619744,0.01350761,0.00002664851,0.0001138916,0.00000601589,0.00005080828,0.000154445,0.9847114,0.000009034092,0.000001152493,0.00127805],"study_design_scores_gemma":[0.001393751,0.0005073562,0.8008108,0.00003114389,0.0004568723,0.000002171876,0.00007930076,0.001262585,0.1845009,0.00003665093,0.01039249,0.0005259423],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955836,0.0003548951,0.002372392,0.0001743879,0.00004466864,0.0001873996,0.000852961,0.000003718826,0.0004259912],"genre_scores_gemma":[0.9987565,0.0001527573,0.0002944994,0.0001952708,0.00004461451,0.00001264081,0.000449015,0.00001572805,0.0000789449],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8002104,"threshold_uncertainty_score":0.5475594,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02757044713263464,"score_gpt":0.2660688212864813,"score_spread":0.2384983741538467,"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."}}