{"id":"W2138300343","doi":"10.1186/1471-2148-9-196","title":"Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis","year":2009,"lang":"en","type":"article","venue":"BMC Evolutionary Biology","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":113,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"McGill University Health Centre; McGill University","keywords":"Biology; Horizontal gene transfer; Genetics; Phylogenetics; Phylogenetic tree; Genome; Gene; Mycobacterium tuberculosis; Comparative genomics; Whole genome sequencing; Genomics; Evolutionary biology; Tuberculosis","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004058375,0.0002164619,0.0002054774,0.0007998907,0.000464017,0.0004671405,0.0001999454,0.0003826813,0.0007090343],"category_scores_gemma":[0.0008636016,0.0001351574,0.00029296,0.0008955785,0.0001997928,0.000239002,0.0003698298,0.0004257334,0.0002556552],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002315557,"about_ca_system_score_gemma":0.0002125188,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000589308,"about_ca_topic_score_gemma":0.0007022614,"domain_scores_codex":[0.9997774,0.00004537511,0.00002033915,0.00006191014,0.00005020971,0.00004481329],"domain_scores_gemma":[0.9993979,0.0002344864,0.0001490567,0.00004831961,0.00009883461,0.0000713502],"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":[0.0009700083,0.0001976087,0.2660054,0.0003801383,0.0001192105,0.0007063269,0.001007889,0.00109606,0.7021928,0.0008001172,0.0001449916,0.0263794],"study_design_scores_gemma":[0.00004967305,0.0008405888,0.8671377,0.0001192581,0.0002764143,0.003261479,0.001019165,0.009410621,0.1130228,0.0008942272,0.003937383,0.00003064672],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972913,0.0002782345,0.00168934,0.00002499563,0.000003136157,0.0000193314,0.0001455328,0.00001629516,0.0005319362],"genre_scores_gemma":[0.995398,0.0001766566,0.003717519,0.00003075504,0.000003323439,0.00001212708,0.0005461927,0.000006746561,0.0001086941],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007998907,"threshold_uncertainty_score":0.002371907,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01701595533410389,"score_gpt":0.273280250490639,"score_spread":0.2562642951565351,"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."}}