{"id":"W2254896924","doi":"10.1186/s12864-015-2234-5","title":"Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis","year":2016,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":87,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"Rijksinstituut voor Volksgezondheid en Milieu; Scotland’s Rural College; Queen's University; University of Thessaly; European Commission; Scottish Government; Institut National de la Recherche Agronomique; Rural and Environment Science and Analytical Services Division; Eusko Jaurlaritza; Cork Institute of Technology; AgResearch; Wellcome Trust; Wellcome","keywords":"Biology; Genetics; Genotyping; Phylogenetic tree; Paratuberculosis; Genome; Phylogenetics; Whole genome sequencing; Genetic diversity; Single-nucleotide polymorphism; Typing; Evolutionary biology; Mycobacterium avium subspecies paratuberculosis; Subspecies; Genotype; Mycobacterium; Gene; Population; Zoology","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":[0.0005338992,0.000246652,0.0002633503,0.001342299,0.0003518827,0.0004575457,0.0002473762,0.0004087825,0.0009849492],"category_scores_gemma":[0.001016516,0.0001374186,0.000420951,0.001190883,0.0001931896,0.0002635171,0.0004548812,0.0005191428,0.0002748648],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002297892,"about_ca_system_score_gemma":0.000162758,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000886995,"about_ca_topic_score_gemma":0.001015646,"domain_scores_codex":[0.9997154,0.00005895682,0.00001555083,0.0001136116,0.00003490942,0.00006161405],"domain_scores_gemma":[0.9991571,0.0003688461,0.0002003115,0.00006747647,0.0001032749,0.0001030093],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0008723712,0.0001949987,0.6756214,0.0002866833,0.0004386461,0.0005822992,0.00113222,0.004657321,0.288172,0.000622559,0.0004923166,0.02692709],"study_design_scores_gemma":[0.00001075156,0.0001270659,0.9849449,0.00002216649,0.0001002103,0.0005660878,0.0004140738,0.008244156,0.003678578,0.000349115,0.001532182,0.00001076303],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9974795,0.000202863,0.001194441,0.00004477178,0.000002288853,0.000008373579,0.0007078926,0.00001191024,0.0003480717],"genre_scores_gemma":[0.9951547,0.00008144507,0.001861778,0.00003315257,0.000004596482,0.00001482634,0.002692745,0.00001423417,0.0001424235],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001342299,"threshold_uncertainty_score":0.003294945,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1081281286186307,"score_gpt":0.2936513512844035,"score_spread":0.1855232226657728,"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."}}