{"id":"W2963998247","doi":"10.1371/journal.pgen.1008227","title":"Quantifying immune-based counterselection of somatic mutations","year":2019,"lang":"en","type":"article","venue":"PLoS Genetics","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"Lunenfeld-Tanenbaum Research Institute; Institute of Cancer Research; Ontario Institute for Cancer Research; University of Toronto","funders":"National Human Genome Research Institute; Canadian Institutes of Health Research; National Institutes of Health; National Research Foundation of Korea; Canada Excellence Research Chairs, Government of Canada; National Research Foundation; Broad Institute; Japan Agency for Medical Research and Development; Foundation for the National Institutes of Health","keywords":"Biology; Somatic cell; Major histocompatibility complex; Genetics; Allele; Gene; Immune system; MHC class I","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":[],"consensus_categories":[],"category_scores_codex":[0.0000519714,0.0000908072,0.000117214,0.00004248099,0.00003105377,0.0000138144,0.0001039511,0.00007316196,0.00004109406],"category_scores_gemma":[0.00003852063,0.0001002691,0.00006742507,0.0000660274,0.00003231097,0.000001207392,0.00003152563,0.0000403807,0.00002982947],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001531329,"about_ca_system_score_gemma":0.0001196069,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006850567,"about_ca_topic_score_gemma":0.00002809157,"domain_scores_codex":[0.9993708,0.00001758022,0.0002120964,0.0001634473,0.0001048737,0.0001311839],"domain_scores_gemma":[0.9994441,0.00002729885,0.0001068335,0.0002908392,0.0000993824,0.00003149427],"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":[0.00002255726,0.00008248058,0.01827673,0.0000732966,0.00004069398,2.435934e-7,0.00003594032,0.005946829,0.9752163,0.00004396088,0.00006336579,0.0001976566],"study_design_scores_gemma":[0.0004927426,0.000293924,0.002235713,0.00002591597,0.000042215,0.000001594827,0.00006585915,0.01600786,0.9793299,0.00003950766,0.001333939,0.0001307538],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9969455,0.0009116763,0.001191248,0.0000312643,0.0001908633,0.000203699,0.00002884004,0.000007051719,0.0004898657],"genre_scores_gemma":[0.9982958,0.0001121711,0.001239476,0.00008694885,0.0000604957,0.00001130699,0.0001184758,0.00002158494,0.00005370794],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01604102,"threshold_uncertainty_score":0.4088855,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0181347876038995,"score_gpt":0.2517553244034139,"score_spread":0.2336205367995144,"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."}}