{"id":"W1965744864","doi":"10.1186/1471-2105-12-s9-s14","title":"Origin and evolution of gene families in Bacteria and Archaea","year":2011,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genome Rearrangement Algorithms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Laurentian University; McMaster University","funders":"","keywords":"Genome; Biology; Gene; Horizontal gene transfer; Archaea; Gene duplication; Genetics; Gene family; Genome evolution; Bacterial genome size; Gene cluster; Genome size; Evolutionary biology; Computational biology","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000114784,0.00007269144,0.00008898182,0.00006557837,0.00001289804,0.000004715629,0.00005187429,0.0000627261,0.000004202952],"category_scores_gemma":[0.00001708719,0.00006695974,0.00001388503,0.00004782817,0.00008206682,0.000006624122,0.00006529702,0.00002553896,0.000001811676],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007289651,"about_ca_system_score_gemma":0.00002729999,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004264062,"about_ca_topic_score_gemma":0.00006543619,"domain_scores_codex":[0.9995766,0.0000112516,0.0001873689,0.00007030011,0.00004859344,0.0001059067],"domain_scores_gemma":[0.9997584,0.000003472749,0.00006095411,0.000123204,0.00002270121,0.00003122376],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001738847,0.000122601,0.6385551,0.0009434836,0.00007461275,0.000001334295,0.008109519,0.00001723035,0.3360189,0.0009498163,0.0001045933,0.01492888],"study_design_scores_gemma":[0.001875632,0.0005742076,0.876319,0.00004987634,0.00003095105,0.00003632328,0.003326879,0.01220415,0.102767,0.0005328611,0.00187954,0.0004036602],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9872864,0.0004029133,0.01139058,0.000002513604,0.00003225085,0.0001212032,0.00001324801,0.000003472933,0.0007473445],"genre_scores_gemma":[0.7891523,0.0004510565,0.2102798,0.00001044247,0.00001886986,0.000006015786,0.00002807431,0.000006535643,0.00004691429],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2377639,"threshold_uncertainty_score":0.2730539,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02074680044134661,"score_gpt":0.2202355862224828,"score_spread":0.1994887857811362,"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."}}