{"id":"W2655883216","doi":"10.1016/j.meegid.2017.06.024","title":"Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family","year":2017,"lang":"en","type":"article","venue":"Infection Genetics and Evolution","topic":"Enterobacteriaceae and Cronobacter Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":117,"is_retracted":false,"has_abstract":false,"ca_institutions":"McMaster University","funders":"","keywords":"Biology; Clade; Polyphyly; Phylogenetic tree; Enterobacteriaceae; Phylogenomics; Evolutionary biology; Genetics; Bacterial taxonomy; Phylogenetics; Gene; Escherichia coli; 16S ribosomal RNA","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":[0.0003297555,0.0001313904,0.0001540653,0.00002433134,0.0004384614,0.00006955777,0.0001726991,0.0000799116,7.874729e-7],"category_scores_gemma":[0.00003880063,0.00007801945,0.00004674076,0.0000308673,0.0007368579,0.00001097424,0.0003450981,0.00009339698,3.107475e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002371517,"about_ca_system_score_gemma":0.0000475468,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001796115,"about_ca_topic_score_gemma":0.0004813393,"domain_scores_codex":[0.9991441,0.0001571074,0.0002642342,0.0002156584,0.00008993727,0.0001289728],"domain_scores_gemma":[0.9990905,0.00001966246,0.0003084627,0.0004269525,0.0001236226,0.00003080157],"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":[0.0001021643,0.00002121626,0.1873575,0.00003550117,0.0001270501,6.677909e-8,0.000472744,0.0001183333,0.8110929,0.0001009225,0.0001007757,0.0004708833],"study_design_scores_gemma":[0.0003981411,0.0002450319,0.9723258,0.00002170593,0.00005973163,0.00001577239,0.0007292664,0.0006929663,0.02452292,0.0001232215,0.0007764146,0.00008901842],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9973576,0.001582073,0.0002349704,0.0002249009,0.0002042106,0.0003007427,0.00003523145,0.000002226182,0.00005804497],"genre_scores_gemma":[0.9953613,0.004329498,0.00007701845,0.00005072243,0.00007472414,0.00001666417,0.00001194109,0.000008086119,0.00007009564],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.78657,"threshold_uncertainty_score":0.3372335,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05666681702130533,"score_gpt":0.3109937017088635,"score_spread":0.2543268846875582,"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."}}