{"id":"W2156064797","doi":"10.1128/mbio.00579-12","title":"EvolutionaryGenomics of Salmonellaenterica Subspecies","year":2013,"lang":"en","type":"article","venue":"mBio","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":137,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health; United States - Israel Binational Agricultural Research and Development Fund; U.S. Department of Agriculture","keywords":"Subspecies; Salmonella enterica; Biology; Phylogenetics; Nonsynonymous substitution; Evolutionary biology; Gene; Genome; Genetics; Phylogenetic tree; Zoology; Escherichia coli","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":[0.00002743087,0.00007001113,0.00008350654,0.00001517979,0.00003264449,0.000005548234,0.0001014527,0.00004107264,0.00005398288],"category_scores_gemma":[0.00001007598,0.00006499362,0.00005351127,0.00002974562,0.00007486765,2.891676e-7,0.00009375306,0.00001800131,0.00003411707],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005169442,"about_ca_system_score_gemma":0.00001506566,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005095729,"about_ca_topic_score_gemma":0.000004740672,"domain_scores_codex":[0.99959,0.00001007717,0.0001200676,0.0001304408,0.00003557197,0.0001137739],"domain_scores_gemma":[0.9996798,0.00000383915,0.00004358241,0.0001793136,0.00006528138,0.00002820062],"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":[0.000007146969,0.00002669603,0.0176456,0.000004887593,0.00003561684,1.334224e-7,0.00003465506,0.00001790945,0.9750647,0.0001240022,0.006304936,0.0007337265],"study_design_scores_gemma":[0.0004161271,0.0003532816,0.5405571,0.000005380879,0.00001611662,0.00001412573,0.0002485682,0.0000534704,0.3292844,0.0009871194,0.1277933,0.00027094],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9936594,0.001760234,0.0001185757,0.0001121614,0.00009791013,0.00009375092,0.00001392193,0.000001603596,0.004142382],"genre_scores_gemma":[0.9975013,0.0003877551,0.001073678,0.00007437726,0.00009125579,0.00001191992,0.00001319589,0.000008380194,0.0008381517],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6457803,"threshold_uncertainty_score":0.2650363,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006799698446020169,"score_gpt":0.1910100463293617,"score_spread":0.1842103478833416,"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."}}