{"id":"W4416300386","doi":"10.1101/2025.11.17.687821","title":"Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"interferon and immune responses","field":"Immunology and Microbiology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; University of Toronto","funders":"","keywords":"Effector; Functional genomics; ORFS; Genetic screen; Function (biology); Pathogen; Model organism; Open reading frame","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":[0.0006421584,0.0003606803,0.0005327394,0.000611213,0.0002314784,0.0006604396,0.0002712958,0.0002872698,0.001182539],"category_scores_gemma":[0.000467349,0.0001512697,0.000464663,0.0004584772,0.0002505928,0.0003344195,0.000495107,0.0005818717,0.0005176949],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002921342,"about_ca_system_score_gemma":0.0005660124,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003431466,"about_ca_topic_score_gemma":0.0005397836,"domain_scores_codex":[0.9996927,0.0000513149,0.00002136395,0.0001146067,0.0000794479,0.00004059222],"domain_scores_gemma":[0.9997104,0.0001192271,0.00005337587,0.00005626025,0.00003136238,0.00002931509],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0005902816,0.00005943234,0.01115941,0.000494884,0.00008465871,0.0003161412,0.0001092442,0.001749165,0.9211544,0.001917613,0.001188401,0.06117634],"study_design_scores_gemma":[0.00006244357,0.0004468132,0.05845352,0.0002024986,0.0002676313,0.001843126,0.0002443825,0.01386027,0.8626136,0.006369068,0.05558119,0.00005554799],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9211321,0.006886089,0.05365535,0.0007321774,0.00005718467,0.00008999947,0.01203246,0.001470451,0.003944138],"genre_scores_gemma":[0.8869695,0.002950845,0.09211127,0.0003683759,0.00003490636,0.00006002863,0.01573967,0.0002454594,0.001519962],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001182539,"threshold_uncertainty_score":0.00395596,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0121139576836882,"score_gpt":0.231344980115309,"score_spread":0.2192310224316208,"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."}}