{"id":"W4414494490","doi":"10.1371/journal.pone.0332950","title":"Framework for analyzing MAE-derived immunopeptidomes from cell lines with shared HLA haplotypes","year":2025,"lang":"en","type":"article","venue":"PLoS ONE","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia; Canada's Michael Smith Genome Sciences Centre","funders":"","keywords":"Human leukocyte antigen; Haplotype; Immune system; Cell culture; Antigen; T cell","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":[0.00006272917,0.0001763682,0.000251132,0.00004790123,0.0001130773,0.0000800974,0.000241325,0.0001524216,0.00002310172],"category_scores_gemma":[0.00008948117,0.0001459906,0.00007817117,0.0001079749,0.00002768136,0.000008808355,0.0001143291,0.00009715262,0.000007495717],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008621346,"about_ca_system_score_gemma":0.00005420011,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002081505,"about_ca_topic_score_gemma":0.00001027081,"domain_scores_codex":[0.9992151,0.00001343213,0.0002353152,0.0002371496,0.00008464031,0.0002143741],"domain_scores_gemma":[0.9992842,0.00004422459,0.0001027801,0.0004103226,0.0001255323,0.00003292392],"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":[0.0004351637,0.0004669891,0.004814886,0.0002326355,0.001002749,3.476448e-7,0.0001557693,0.0000294525,0.9915853,0.000179736,0.0004687604,0.000628281],"study_design_scores_gemma":[0.001069624,0.0003015855,0.003186854,0.0003321643,0.0002778879,2.359714e-7,0.0002895266,0.0007966329,0.991511,0.0007622202,0.001190894,0.0002813125],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9782699,0.003410006,0.01691664,0.0003064511,0.0000370643,0.0003872648,0.00007918843,0.00002884974,0.0005646384],"genre_scores_gemma":[0.8655327,0.0004885712,0.1315921,0.0002682862,0.0001585772,0.0001159509,0.0005982692,0.00003273302,0.001212814],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1146755,"threshold_uncertainty_score":0.5953323,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02343327360236637,"score_gpt":0.2314529046674776,"score_spread":0.2080196310651113,"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."}}