{"id":"W2970153829","doi":"10.1093/gbe/evz184","title":"Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes","year":2019,"lang":"en","type":"review","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":81,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Metagenomics; Biology; Horizontal gene transfer; Computational biology; Genome; Gene; Context (archaeology); Contig; Gene duplication; Genetics; Shotgun sequencing","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003220244,0.000358895,0.0008200102,0.0001392435,0.00008871839,0.00001042188,0.0001448495,0.000373753,0.000001670733],"category_scores_gemma":[0.00001486674,0.0003094918,0.0001478849,0.0001024884,0.00007645492,0.00000145329,0.0002244978,0.0001555409,0.000009769988],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004998257,"about_ca_system_score_gemma":0.0000921956,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001491507,"about_ca_topic_score_gemma":0.00003173852,"domain_scores_codex":[0.9983125,0.000168955,0.0003914289,0.0007447875,0.00004437159,0.0003379847],"domain_scores_gemma":[0.9995852,0.00001412087,0.0000715987,0.0002289105,0.00001706744,0.00008309026],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001090335,0.0001522967,0.009306388,0.006347475,0.0009138978,0.000001744678,0.0003413153,0.00001030517,0.04478536,0.0005565161,0.00001377223,0.9374619],"study_design_scores_gemma":[0.000782653,0.0007293817,0.0657023,0.0006968929,0.0007339328,0.0000765918,0.00005834776,0.000003748214,0.0001073108,0.0004763868,0.9295003,0.001132195],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.1744068,0.8240293,0.0003618184,0.00001089862,0.0002667908,0.0008040065,0.0001008907,0.000002331638,0.00001713895],"genre_scores_gemma":[0.120011,0.8791878,0.0001628089,0.00000750432,0.0002135732,0.0001157051,0.0002459319,0.0000249036,0.00003081253],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9363297,"threshold_uncertainty_score":0.9999357,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1047116907146183,"score_gpt":0.3239519014606665,"score_spread":0.2192402107460482,"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."}}