{"id":"W2149582283","doi":"10.1093/sysbio/syt003","title":"Lateral Gene Transfer from the Dead","year":2013,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":135,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Institut National de Physique Nucléaire et de Physique des Particules; Agence Nationale de la Recherche","keywords":"Biology; Phylogenetics; Phylogenetic tree; Lineage (genetic); Horizontal gene transfer; Evolutionary biology; Macroevolution; Genetic algorithm; Molecular phylogenetics; Gene; Genetics","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":[0.0001397517,0.0001395427,0.0002373887,0.000009559015,0.00008195612,0.00002299222,0.0002588,0.000129265,0.00004332565],"category_scores_gemma":[0.00003725511,0.00007878902,0.00009207593,0.00002646994,0.00008888632,3.705704e-7,0.00009939037,0.00005036112,0.00009762994],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004482223,"about_ca_system_score_gemma":0.00001677736,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002697343,"about_ca_topic_score_gemma":0.00005408667,"domain_scores_codex":[0.9990605,0.0001821336,0.0002754384,0.000239032,0.00003834055,0.0002046271],"domain_scores_gemma":[0.9994145,0.00005081011,0.00004004818,0.0004020499,0.00005554192,0.00003703907],"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":[0.000005525806,0.00001346524,0.01930327,0.000210131,0.000233003,3.289669e-7,0.0002310322,0.000006366985,0.9792933,0.0003736465,0.0002532758,0.000076631],"study_design_scores_gemma":[0.003727603,0.001475076,0.4311943,0.0009223433,0.0006267574,0.0001287913,0.001970805,0.0008212213,0.5184484,0.03398626,0.004532355,0.002166027],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9933366,0.003735212,0.001358356,0.0004471749,0.0002616158,0.0006265136,0.00003113936,0.000004393292,0.0001990596],"genre_scores_gemma":[0.9983619,0.00005792099,0.0003517696,0.0006629096,0.0002203461,0.000217832,0.00003676569,0.00001164054,0.00007894052],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4608449,"threshold_uncertainty_score":0.3212923,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01152736331802217,"score_gpt":0.2133231248667484,"score_spread":0.2017957615487262,"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."}}