{"id":"W4410694920","doi":"10.1093/ismeco/ycaf087","title":"Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals","year":2025,"lang":"en","type":"article","venue":"ISME Communications","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Université du Québec à Montréal","funders":"Université de Montréal; Vetenskapsrådet","keywords":"Archaea; Phylogenetic tree; Oxidizing agent; Gene; Ammonia; Biology; Evolutionary biology; Genetics; Computational biology; Chemistry; Biochemistry; Organic chemistry","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":[0.0006797564,0.0004594408,0.0003565263,0.001475663,0.0002799482,0.000611431,0.0002393973,0.0003613221,0.0006838171],"category_scores_gemma":[0.001935642,0.00019368,0.0005360664,0.0009754433,0.000227598,0.0004340306,0.0004454644,0.0003345493,0.0002898053],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002527669,"about_ca_system_score_gemma":0.0002878302,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002102124,"about_ca_topic_score_gemma":0.002005534,"domain_scores_codex":[0.9997556,0.00006944705,0.00001128859,0.0001044719,0.0000329176,0.00002629097],"domain_scores_gemma":[0.9994488,0.0002954383,0.00007902972,0.00003110727,0.00009457447,0.0000510084],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001091413,0.0001885281,0.5002424,0.0003935667,0.0002790014,0.0004422939,0.000361888,0.1669377,0.2323627,0.002253294,0.001118705,0.0943284],"study_design_scores_gemma":[0.00002685324,0.000161937,0.1117812,0.00003589983,0.00007144111,0.0002708984,0.0002509394,0.8672948,0.01448548,0.004064624,0.001525784,0.00003012673],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9660826,0.0002699701,0.03134874,0.00006537738,0.000008526667,0.00001132274,0.001401826,0.000259647,0.0005519629],"genre_scores_gemma":[0.98523,0.00009040244,0.0126757,0.0000160046,0.000007053408,0.000009371082,0.00179626,0.00002656679,0.0001485556],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002102124,"threshold_uncertainty_score":0.004179776,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03463248501067207,"score_gpt":0.3016043232704398,"score_spread":0.2669718382597677,"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."}}