{"id":"W4388341825","doi":"10.1038/s41467-023-42916-w","title":"Mutational spectra are associated with bacterial niche","year":2023,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Fondation Botnar; Cystic Fibrosis Trust; Wellcome Trust; Wellcome","keywords":"Biology; Clade; Niche; Ecological niche; Context (archaeology); Genetics; Evolutionary biology; Phylogenetics; Computational biology; Gene; Ecology","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004530248,0.0003192705,0.0003009502,0.00190973,0.0002801258,0.0006178419,0.0002335263,0.0004097721,0.001109255],"category_scores_gemma":[0.001765588,0.00023677,0.0003533476,0.0009869293,0.0003831975,0.0004513997,0.0005849411,0.0004028111,0.0003832852],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000181679,"about_ca_system_score_gemma":0.0001267683,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006479263,"about_ca_topic_score_gemma":0.0008899956,"domain_scores_codex":[0.9997185,0.00005586378,0.00001765724,0.0001085532,0.00005519926,0.0000442525],"domain_scores_gemma":[0.9989836,0.0002716368,0.0003548819,0.0001627398,0.0001419406,0.00008519793],"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":[0.0005500751,0.00005706878,0.3144904,0.0001591555,0.0001199516,0.000299227,0.0006148924,0.01016768,0.6468006,0.00121212,0.0002484709,0.0252804],"study_design_scores_gemma":[0.00001603944,0.0001842058,0.8408451,0.00005195173,0.0001314811,0.001681898,0.0009379163,0.07185953,0.07677483,0.004256151,0.003183071,0.00007777115],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.99188,0.0001665607,0.006907846,0.00002124062,0.000002508237,0.000005580423,0.0002938207,0.00009626363,0.0006260464],"genre_scores_gemma":[0.9941583,0.00008551359,0.005091123,0.00001370059,0.000002364942,0.000006180858,0.0004551407,0.00005305514,0.0001346157],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00190973,"threshold_uncertainty_score":0.003710806,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01779359154961452,"score_gpt":0.2726861846739955,"score_spread":0.254892593124381,"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."}}