{"id":"W4405995673","doi":"10.1038/s41564-024-01881-w","title":"Profiling lateral gene transfer events in the human microbiome using WAAFLE","year":2025,"lang":"en","type":"article","venue":"Nature Microbiology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":false,"ca_institutions":"Dalhousie University","funders":"National Institute of Dental and Craniofacial Research; National Institute of Diabetes and Digestive and Kidney Diseases; U.S. Department of Health and Human Services; National Cancer Institute; Crohn's and Colitis Foundation; American Gastroenterological Association","keywords":"Horizontal gene transfer; Biology; Microbiome; Metagenomics; Phylogenetic tree; Genome; Computational biology; Mobile genetic elements; Human microbiome; Gene; Genetics; Evolutionary biology; Fusobacterium nucleatum; Human Microbiome Project; Phylogenetics; Bacteria","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":[0.0002762582,0.0001690815,0.0002142039,0.0006721636,0.0004715001,0.0006557338,0.0001918479,0.0005386319,0.002688981],"category_scores_gemma":[0.0005013209,0.0001584489,0.0003243032,0.0005777442,0.0003261748,0.0004376289,0.0004640601,0.0005815454,0.0008169195],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001515911,"about_ca_system_score_gemma":0.0001769691,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008232206,"about_ca_topic_score_gemma":0.001969184,"domain_scores_codex":[0.9997959,0.00003019371,0.000005184732,0.00005817347,0.00005109101,0.00005942288],"domain_scores_gemma":[0.999788,0.00008506804,0.00004191092,0.0000263801,0.00003157887,0.00002702164],"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":[0.0003330592,0.00003843784,0.009983833,0.00007165057,0.00003175536,0.00007897951,0.0001919179,0.0003665533,0.971728,0.0004925455,0.0002751267,0.01640814],"study_design_scores_gemma":[0.00002768705,0.0005509976,0.1342473,0.00004336826,0.00006564218,0.0007834093,0.00081257,0.01033179,0.8412411,0.001051398,0.01077771,0.0000670305],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9667973,0.001113803,0.02574787,0.0001863717,0.00003893597,0.00005228327,0.003202435,0.0002864867,0.002574479],"genre_scores_gemma":[0.957109,0.0008755457,0.03413588,0.000238137,0.00003348604,0.0001464021,0.002415828,0.0000987471,0.004946972],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002688981,"threshold_uncertainty_score":0.008995533,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00811550989729893,"score_gpt":0.2671464994948146,"score_spread":0.2590309895975157,"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."}}