{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008773156,0.0008710875,0.0007624276,0.0005082003,0.0003347803,0.001074849,0.0004592779,0.000443225,0.002779061],"category_scores_gemma":[0.0009038635,0.0003356564,0.0004930235,0.000336318,0.0003467109,0.00105917,0.0006500785,0.001100477,0.001021254],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003187009,"about_ca_system_score_gemma":0.0002784448,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002631585,"about_ca_topic_score_gemma":0.0003569875,"domain_scores_codex":[0.9996835,0.00004354101,0.00002555931,0.0001060523,0.0001035787,0.00003792109],"domain_scores_gemma":[0.9994128,0.000280466,0.00007982805,0.00007481629,0.00007299638,0.00007915737],"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":[0.0008615156,0.00006168399,0.001879866,0.0002141315,0.00005011823,0.0001681328,0.00008537593,0.001007527,0.982511,0.0003638908,0.0006063722,0.01219037],"study_design_scores_gemma":[0.00003455042,0.00009682357,0.003850004,0.000008561996,0.00001474999,0.0003419206,0.000026861,0.01467559,0.9769351,0.0002641737,0.003723094,0.00002845438],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7380561,0.001537103,0.2416576,0.0003385159,0.0001480345,0.0001665724,0.005102944,0.01051317,0.002479918],"genre_scores_gemma":[0.6931238,0.001119102,0.2884599,0.0002599728,0.00005008005,0.0003520651,0.007800606,0.003294453,0.005539947],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002779061,"threshold_uncertainty_score":0.009296894,"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."}}