{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003664118,0.0001315463,0.0003096556,0.0001041647,0.00007498674,0.00001071283,0.0001832636,0.0001184023,0.000108437],"category_scores_gemma":[0.00047998,0.00007860309,0.0001864163,0.0001958108,0.0001869191,0.0001555489,0.00008701072,0.0001284897,0.00004140318],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001319603,"about_ca_system_score_gemma":0.0003021309,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002862179,"about_ca_topic_score_gemma":0.00009204787,"domain_scores_codex":[0.9987013,0.000159735,0.0004602438,0.0001965883,0.0002465306,0.0002355623],"domain_scores_gemma":[0.998558,0.0003539785,0.0002246366,0.0005543541,0.0001837112,0.0001252471],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00007124719,0.00005135172,0.6283342,0.00009164281,0.00004777976,3.206115e-7,0.0004178828,0.000003994474,0.3696757,0.0004933989,0.0003389343,0.0004734808],"study_design_scores_gemma":[0.0006392772,0.0001187203,0.8303887,0.00007322925,0.00009771898,0.000001999889,0.0002623103,0.00000391326,0.166852,0.0005044071,0.0009782037,0.00007955403],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.996538,0.0001072591,0.0007098931,0.001082861,0.0001096631,0.0004592916,0.0002976944,0.0000145285,0.0006807827],"genre_scores_gemma":[0.9981804,0.000307787,0.0008597212,0.00001723324,0.0002423746,0.00002605169,0.00003317001,0.0000219014,0.0003113246],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2028238,"threshold_uncertainty_score":0.3205341,"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."}}