{"id":"W3092063152","doi":"10.1093/nar/gkaa824","title":"Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis","year":2020,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Institute for Advanced Research","funders":"Weizmann Institute of Science; National Institutes of Health; Human Frontier Science Program; National Institute of Diabetes and Digestive and Kidney Diseases; European Molecular Biology Organization; National Institute of Allergy and Infectious Diseases; Harvard Digestive Diseases Center, Harvard University; Broad Institute; Canadian Institute for Advanced Research; Israel Science Foundation; Israel Cancer Research Fund","keywords":"Biology; Bacteroides fragilis; Phase variation; Genetics; Locus (genetics); Gene; Mutant; Bacteroides thetaiotaomicron; Bacteroidetes; Bacterial genetics; Transcriptome; Bacteroides; Microbiology; Phenotype; Bacteria; Escherichia coli; Gene expression; 16S ribosomal RNA","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":[0.0001051454,0.0001828927,0.0001158415,0.0002768106,0.00009295073,0.0001190984,0.00007975457,0.0001362395,0.0003844568],"category_scores_gemma":[0.0002189442,0.00008895266,0.0001640299,0.0001612057,0.00008531298,0.00005472459,0.0001191542,0.0001469324,0.0001793754],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001234233,"about_ca_system_score_gemma":0.0001357917,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001200423,"about_ca_topic_score_gemma":0.0008447169,"domain_scores_codex":[0.9999205,0.00001384976,0.000005687995,0.00002198637,0.00002172082,0.00001628994],"domain_scores_gemma":[0.9999071,0.00001871898,0.0000373338,0.00001016106,0.00001202867,0.00001464871],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00004314038,0.000005466199,0.001393218,0.00001172043,0.000002230237,0.00002581027,0.0000121297,0.00001875904,0.9976674,0.00001325887,0.000008652301,0.0007981996],"study_design_scores_gemma":[0.00001278842,0.0004451569,0.2060424,0.00001185736,0.0000492468,0.00177647,0.0001538027,0.001469816,0.7876338,0.00008780105,0.002302471,0.00001450074],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968351,0.0003298991,0.002034253,0.0000362947,0.000003786098,0.00001738507,0.0004890662,0.00002842898,0.0002259054],"genre_scores_gemma":[0.9938783,0.000204866,0.004190283,0.0000335205,0.000003962548,0.00001833639,0.001262452,0.00001020298,0.0003980655],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001200423,"threshold_uncertainty_score":0.002386928,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05983530751545092,"score_gpt":0.3372896720900728,"score_spread":0.2774543645746219,"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."}}