{"id":"W2916101679","doi":"10.1038/s41598-019-39369-x","title":"An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria","year":2019,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":55,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","keywords":"Transfer RNA; Codon usage bias; Biology; Genetics; Gene; RNA; Computational biology; Genome","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":[0.0006494939,0.00008390599,0.0001181936,0.00004027754,0.00007835064,0.00004834257,0.00008982297,0.00005141697,0.000005280647],"category_scores_gemma":[0.00003076785,0.00006283337,0.00002430921,0.00008580718,0.00008125645,0.000003863721,0.00008885009,0.00003334464,0.000001419331],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007846592,"about_ca_system_score_gemma":0.00002697846,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003383898,"about_ca_topic_score_gemma":0.000031991,"domain_scores_codex":[0.999051,0.00004192774,0.0002680748,0.0004040748,0.00009863988,0.0001362969],"domain_scores_gemma":[0.9992455,0.000007549508,0.0001594936,0.0004963497,0.00005014881,0.00004092735],"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":[0.00001301775,0.00001156589,0.05048776,0.000009982372,0.000004731331,5.979839e-7,0.0001781207,0.0001866521,0.9459637,8.097284e-7,0.0001338272,0.003009215],"study_design_scores_gemma":[0.0001289289,0.0001115734,0.3453936,0.00002076538,0.000006367517,0.000005025772,0.00003810812,0.0003662032,0.6508943,0.0002627141,0.002681578,0.00009080863],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9983572,0.0001346125,0.000456049,0.00006964526,0.0006014184,0.0003190271,0.000008382836,0.000001652926,0.00005203113],"genre_scores_gemma":[0.9984293,0.000007734741,0.001262401,0.00002461076,0.0000395682,0.00001155425,0.00005635767,0.000006995831,0.0001614582],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2950694,"threshold_uncertainty_score":0.256227,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007081083127976392,"score_gpt":0.2416125915468011,"score_spread":0.2345315084188248,"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."}}