{"id":"W4362696919","doi":"10.1016/j.xgen.2023.100294","title":"Genome graphs detect human polymorphisms in active epigenomic state during influenza infection","year":2023,"lang":"en","type":"article","venue":"Cell Genomics","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Alliance de recherche numérique du Canada; Genome Canada; Canada Research Chairs; McGill University","keywords":"Epigenomics; Epigenome; Biology; Genetics; Epigenetics; Genome; Chromatin; Chromatin immunoprecipitation; Expression quantitative trait loci; International HapMap Project; Computational biology; Gene; Human genome; DNA methylation; Gene expression; Single-nucleotide polymorphism; Promoter; Genotype","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001829305,0.0002061289,0.0002410532,0.0005678497,0.0003101859,0.00002136063,0.0001641945,0.0001537031,0.000207336],"category_scores_gemma":[0.00001085057,0.0002127001,0.0001023995,0.0003776588,0.0001184338,0.00007811149,0.000149125,0.0003432917,0.005967741],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004176988,"about_ca_system_score_gemma":0.00008601695,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007577213,"about_ca_topic_score_gemma":0.0005161031,"domain_scores_codex":[0.9984679,0.0001413507,0.0002867461,0.0003737587,0.00003267352,0.0006975861],"domain_scores_gemma":[0.9994919,0.0000512872,0.00008663152,0.0002927801,0.00002454323,0.00005284536],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001547194,0.00007150645,0.01969096,0.00001620244,0.0001015154,0.00005856302,0.001244854,0.0003595397,0.9767729,0.000007885249,0.00001879908,0.001502556],"study_design_scores_gemma":[0.00202595,0.000155984,0.6247093,0.000005720572,0.00001282006,0.00001350975,0.00006944677,0.000001311676,0.3685036,0.0004297719,0.003871819,0.0002007513],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975656,0.0007931773,0.000006138738,0.00001258702,0.000176037,0.0004276902,0.0001172072,0.0001279202,0.0007736121],"genre_scores_gemma":[0.9970099,0.0006351636,0.00001100916,0.0000192698,0.00001719139,0.00007681842,0.0002864547,0.00003746749,0.001906718],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6082693,"threshold_uncertainty_score":0.9948062,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01797987208214317,"score_gpt":0.2580812433282336,"score_spread":0.2401013712460904,"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."}}