{"id":"W4412818268","doi":"10.21769/bioprotoc.5422","title":"Assembly and Mutagenesis of Human Coronavirus OC43 Genomes in Yeast via Transformation-Associated Recombination","year":2025,"lang":"en","type":"article","venue":"BIO-PROTOCOL","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"","keywords":"Coronavirus; Recombination; Mutagenesis; Transformation (genetics); Genetics; Biology; Genome; Yeast; Virology; Mutation; Gene; Computational biology; Coronavirus disease 2019 (COVID-19)","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":[0.0001397809,0.00009315174,0.0001128791,0.00008230437,0.00003518819,0.00001018558,0.0000732631,0.0001108565,0.00001080571],"category_scores_gemma":[0.00001401893,0.00009774061,0.00003494824,0.0001173754,0.00002319873,0.00000385208,0.00002632403,0.00003595532,7.751813e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001888025,"about_ca_system_score_gemma":0.00002612633,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005265794,"about_ca_topic_score_gemma":0.0001507465,"domain_scores_codex":[0.999417,0.00002796469,0.0002366269,0.0001476646,0.0000592705,0.000111438],"domain_scores_gemma":[0.9997638,0.000004794389,0.00005117837,0.0001156091,0.00004244309,0.00002221654],"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":[0.00004231367,0.00007367241,0.009186116,0.0001447252,0.00002581133,4.553912e-7,0.00007725568,0.00005342892,0.964143,0.00009550628,0.00005172573,0.026106],"study_design_scores_gemma":[0.002196141,0.0002248282,0.1439936,0.00005025976,0.00001072509,9.719846e-7,0.00005663304,0.0003595929,0.8436324,0.0001149023,0.009206787,0.0001531486],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8395976,0.0000536341,0.003507558,0.00006591168,0.00005279628,0.1545191,0.00002036073,0.00002065179,0.002162413],"genre_scores_gemma":[0.877555,0.000003579756,0.00009264437,0.00001823892,0.00001222447,0.1221306,0.00003398255,0.000007820466,0.0001459177],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1348075,"threshold_uncertainty_score":0.3985746,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01263673247965873,"score_gpt":0.3519078569624783,"score_spread":0.3392711244828195,"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."}}