{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002156248,0.0001761436,0.0001852966,0.00008273979,0.0001330214,0.000007782226,0.0003291976,0.0004502113,0.000003810796],"category_scores_gemma":[0.00001004853,0.0001312127,0.00009434347,0.0001445639,0.00008190764,5.565988e-7,0.0001021096,0.0002849538,0.000001820021],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002019221,"about_ca_system_score_gemma":0.00004660168,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001901909,"about_ca_topic_score_gemma":0.00008648165,"domain_scores_codex":[0.9989755,0.000124444,0.0002159003,0.0003586511,0.00002106458,0.0003044076],"domain_scores_gemma":[0.9996422,0.00001196719,0.00002496484,0.0002633367,0.00004407146,0.00001344458],"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":[0.00002550933,0.0000435737,0.01468041,0.00001282441,0.00006661121,0.000002002104,0.00006240053,0.00002358398,0.984618,0.0002200083,0.0001976499,0.00004741853],"study_design_scores_gemma":[0.0008897348,0.00008251506,0.01203932,0.00001628765,0.00003194674,0.00006008425,0.00005457564,0.000004053119,0.9647641,0.0002563361,0.02158883,0.0002121701],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9945639,0.004174064,0.00009062885,0.0002452389,0.0003473258,0.0002960062,0.00005794044,0.000002736116,0.0002221117],"genre_scores_gemma":[0.9973712,0.00005665153,0.0005374356,0.001515274,0.0001142506,0.00001414692,0.0001902183,0.00001163259,0.0001892184],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02139118,"threshold_uncertainty_score":0.5350697,"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."}}