{"id":"W3016851473","doi":"10.1093/bioinformatics/btaa248","title":"Codon optimization: a mathematical programing approach","year":2020,"lang":"en","type":"article","venue":"Bioinformatics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":76,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"","keywords":"Codon usage bias; Heuristics; Computer science; Genetic code; Solver; Mathematical optimization; Computational biology; Mathematics; Biology; Genetics; Amino acid; Programming language; Gene; 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":[0.0001143907,0.0001190087,0.0001212756,0.00001400852,0.00006678555,0.00005234069,0.0001699912,0.0001142895,0.00004377085],"category_scores_gemma":[0.0001167101,0.0001023548,0.00006319818,0.00008507867,0.0000329645,0.000006928649,0.00008265915,0.00004559601,0.0000550983],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003971304,"about_ca_system_score_gemma":0.00002522494,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":1.98744e-7,"about_ca_topic_score_gemma":3.092017e-8,"domain_scores_codex":[0.9993057,0.00001871197,0.0002465547,0.0001191163,0.0001410792,0.000168805],"domain_scores_gemma":[0.9995716,0.000005749515,0.00008150076,0.0001846955,0.00003820213,0.0001182568],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001125741,0.001623982,0.0006245795,0.007725392,0.001164076,0.00002733021,0.01697081,0.09462583,0.3806181,0.04458036,0.03766958,0.4132442],"study_design_scores_gemma":[0.001007479,0.0008169835,0.0000118252,0.00004680915,0.00006083704,0.00006901293,0.001485001,0.8060309,0.1367591,0.0002219205,0.05274379,0.0007462986],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.002997749,0.00008884338,0.979807,0.0002586894,0.00003031486,0.000375838,0.000006747791,0.00004732722,0.01638746],"genre_scores_gemma":[0.1167488,0.00003990032,0.8815429,0.001061976,0.0002235323,0.00005236128,0.0001375695,0.00002568563,0.0001673317],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.7114051,"threshold_uncertainty_score":0.4173908,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02247114369986499,"score_gpt":0.2304318839690389,"score_spread":0.2079607402691739,"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."}}