{"id":"W4385836593","doi":"10.1186/s13059-023-03029-1","title":"BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens","year":2023,"lang":"en","type":"article","venue":"Genome biology","topic":"Immunotherapy and Immune Responses","field":"Immunology and Microbiology","cited_by":23,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Institute for Research in Immunology and Cancer","funders":"Common Fund; National Institute of Neurological Disorders and Stroke; National Cancer Institute; NIH Office of the Director; National Institute on Drug Abuse; Fonds De La Recherche Scientifique - FNRS; Fonds de Recherche du Québec - Santé; Canadian Institutes of Health Research; National Institutes of Health; National Heart, Lung, and Blood Institute; National Institute of Mental Health; Fonds Léon Fredericq; Koning Boudewijnstichting; National Human Genome Research Institute; Canadian Cancer Society","keywords":"Biology; Computational biology; Immunogenicity; Antigen; RNA; Major histocompatibility complex; RNA-Seq; Genetics; Gene; Transcriptome; Gene expression","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001529461,0.002338463,0.001255675,0.001683346,0.000733409,0.001803324,0.001201096,0.001120315,0.01097001],"category_scores_gemma":[0.001728304,0.001021076,0.0007843812,0.00109244,0.0004806716,0.001626238,0.001061217,0.002233191,0.006541465],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004528029,"about_ca_system_score_gemma":0.0006735281,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006584536,"about_ca_topic_score_gemma":0.0008966992,"domain_scores_codex":[0.9995891,0.00006941829,0.00003693386,0.0001126527,0.0001390757,0.00005277696],"domain_scores_gemma":[0.9992126,0.000459605,0.0001177085,0.00006762841,0.00006169834,0.0000806972],"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":[0.002211422,0.000291801,0.002940496,0.001932938,0.0002725366,0.001224499,0.000659581,0.002174934,0.810069,0.005068387,0.05191954,0.1212349],"study_design_scores_gemma":[0.0004732904,0.0004065488,0.006588258,0.0002286732,0.0001441374,0.002234987,0.00020956,0.04951341,0.7527825,0.008122648,0.1790104,0.0002856361],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.05096534,0.00287172,0.6996135,0.0008824745,0.0002940729,0.0005621195,0.04517588,0.1938076,0.005827349],"genre_scores_gemma":[0.1246832,0.002792728,0.750577,0.0009016789,0.0001336936,0.001925184,0.06628577,0.04222609,0.01047455],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01097001,"threshold_uncertainty_score":0.0366984,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02682303842877963,"score_gpt":0.2636125920558422,"score_spread":0.2367895536270626,"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."}}