{"id":"W2619023647","doi":"10.1089/aid.2017.0061","title":"HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences","year":2017,"lang":"en","type":"article","venue":"AIDS Research and Human Retroviruses","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"National Institute of Allergy and Infectious Diseases; Medical Research Council; Klaus Tschira Stiftung; Engineering and Physical Sciences Research Council; NHLBI Division of Intramural Research; Ministry of Business, Innovation and Employment; Fogarty International Center; Department for International Development; Imperial College London; Bill and Melinda Gates Foundation; Austrian Science Fund; National Institutes of Health; University of Auckland; Division of Intramural Research, National Institute of Allergy and Infectious Diseases","keywords":"Phylogenetics; Genome; Human immunodeficiency virus (HIV); Virology; Biology; Genetics; Evolutionary biology; Computational biology; Gene","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":[0.008243217,0.0004985245,0.0008132898,0.000480208,0.0009230065,0.0009704216,0.0009409725,0.001115205,0.001159911],"category_scores_gemma":[0.03054174,0.0005612048,0.0008674283,0.0005645536,0.0009484058,0.001686559,0.0009822302,0.00152288,0.0001356604],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001050354,"about_ca_system_score_gemma":0.0009442007,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01149131,"about_ca_topic_score_gemma":0.01503865,"domain_scores_codex":[0.997583,0.001712764,0.00008705704,0.0003059023,0.0001435585,0.0001676469],"domain_scores_gemma":[0.9856166,0.01156992,0.0008812934,0.000916523,0.0005204446,0.000495226],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"observational","study_design_scores_codex":[0.0003255818,0.00005048895,0.06199852,0.00009660586,0.0002018511,0.0001846329,0.0002484336,0.9275818,0.001280053,0.001797538,0.0003350585,0.005899533],"study_design_scores_gemma":[0.00006599385,0.0001605828,0.01540355,0.00005552642,0.00005561387,0.0001102011,0.0001534239,0.9796199,0.0007514831,0.003192273,0.000403226,0.00002809035],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9842704,0.0003431148,0.01394471,0.0003674592,0.00002110804,0.00004593913,0.0003340263,0.0001030552,0.0005700843],"genre_scores_gemma":[0.9931026,0.00009304791,0.006073264,0.00008343004,0.000007498342,0.00004050497,0.0004521836,0.00002748336,0.0001200522],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01149131,"threshold_uncertainty_score":0.04359484,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1778245725768024,"score_gpt":0.3869087264383318,"score_spread":0.2090841538615294,"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."}}