{"id":"W4408108012","doi":"10.1016/j.mcpro.2025.100937","title":"PEPSeek-Mediated Identification of Novel Epitopes From Viral and Bacterial Pathogens and the Impact on Host Cell Immunopeptidomes","year":2025,"lang":"en","type":"article","venue":"Molecular & Cellular Proteomics","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"H2020 Marie Skłodowska-Curie Actions; Blood Cancer UK; International Max Planck Research School for Advanced Methods in Process and Systems Engineering; Innovative Medicines Initiative; Universiteit Utrecht; European Commission; Department of Health and Social Care; Georg-August-Universität Göttingen; National Institute for Health and Care Research; NIHR BioResource; Horizon 2020 Framework Programme; Cancer Research UK; International Max Planck Research School for Environmental, Cellular and Molecular Microbiology; Francis Crick Institute; HORIZON EUROPE Framework Programme; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Wellcome Trust; European Research Council; Center for Ocean Leadership; European Federation of Pharmaceutical Industries and Associations; NHS Blood and Transplant","keywords":"Epitope; Identification (biology); Host (biology); Virology; Computational biology; Biology; Microbiology; Antigen; Immunology; Genetics","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":[0.000199358,0.000165791,0.0001992397,0.00003767338,0.0001218538,0.0001017422,0.0001644818,0.00008397236,0.000113991],"category_scores_gemma":[0.00004306645,0.0001197133,0.00009208672,0.000102785,0.0002900937,0.00009838791,0.0001990526,0.0001432616,0.00001968994],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005328536,"about_ca_system_score_gemma":0.00001441417,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001318412,"about_ca_topic_score_gemma":0.00001302142,"domain_scores_codex":[0.9990897,0.00009071054,0.0002964148,0.0002821866,0.00008796577,0.0001529984],"domain_scores_gemma":[0.9994168,0.00006477013,0.0001658368,0.0003009702,0.00001310419,0.00003855102],"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":[0.0001949519,0.000101494,0.0001332466,0.000007003953,0.00003390843,0.000002047208,0.0002510363,0.00005990086,0.9988272,0.0000395084,0.00002485301,0.0003248804],"study_design_scores_gemma":[0.001315114,0.0000498212,0.02728061,0.00001983729,0.00004790382,0.00000182307,0.00005568433,0.001005779,0.969844,0.00007827539,0.0001873329,0.0001138182],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9946728,0.0001644222,0.003809141,0.0001720057,0.0001384548,0.0006253371,0.0001902077,0.00001132545,0.0002162602],"genre_scores_gemma":[0.9985977,0.00008963116,0.0009061545,0.00007107842,0.00001749879,0.00002892348,0.00008214609,0.00001447694,0.0001923197],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02898317,"threshold_uncertainty_score":0.4881766,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003008112812014577,"score_gpt":0.2052054920752156,"score_spread":0.202197379263201,"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."}}