{"id":"W4391230939","doi":"10.1099/mgen.0.001186","title":"Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Animal Disease Management and Epidemiology","field":"Agricultural and Biological Sciences","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; University of Saskatchewan","funders":"National Key Research and Development Program of China; Higher Education Discipline Innovation Project; Priority Academic Program Development of Jiangsu Higher Education Institutions","keywords":"African swine fever virus; Biology; Codon usage bias; Clade; Phylogenetic tree; Genome; Adaptation (eye); Gene; Coding region; Genetics; Virus; Host (biology); Host adaptation; Evolutionary biology; Phylogenetics; Virology; Zoology","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":[0.0004925706,0.0001225925,0.0004243305,0.00004713344,0.00008285914,0.0000334017,0.0003154993,0.00005802798,0.0002157188],"category_scores_gemma":[0.00006731599,0.00004726514,0.0002689761,0.0006752625,0.00005016765,0.00005942779,0.0001157352,0.00005949704,0.00001505631],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005441686,"about_ca_system_score_gemma":0.00001007145,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006286178,"about_ca_topic_score_gemma":0.001145236,"domain_scores_codex":[0.998803,0.0001982949,0.0004907748,0.0002319482,0.00009899755,0.0001770178],"domain_scores_gemma":[0.9993551,0.0002304372,0.0002525372,0.00007540215,0.00005171504,0.00003482047],"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":[0.00001701248,0.00002028342,0.001862021,0.0008467962,0.00041031,0.000001504493,0.0004388162,0.0004650936,0.9950506,0.0007232781,0.00004252918,0.0001217473],"study_design_scores_gemma":[0.0001793849,0.0002761593,0.964164,0.00141447,0.004867777,0.00000277343,0.002668203,0.01533724,0.008454059,0.0003687353,0.001620931,0.0006463307],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9977247,0.0007926035,0.0001023658,0.0002479368,0.0001277078,0.0003311556,0.0005238428,0.00001924963,0.0001304274],"genre_scores_gemma":[0.9992139,0.0001709265,0.00002849857,0.0001249863,0.00007665704,0.000005945757,0.00008302448,0.000001563227,0.0002944803],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9865965,"threshold_uncertainty_score":0.236197,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03756748206318438,"score_gpt":0.2345583487589889,"score_spread":0.1969908666958045,"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."}}