{"id":"W4409039558","doi":"10.1038/s44321-025-00212-8","title":"Proteomics and personalized PDX models identify treatment for a progressive malignancy within an actionable timeframe","year":2025,"lang":"en","type":"article","venue":"EMBO Molecular Medicine","topic":"Protein Degradation and Inhibitors","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency; McGill University; McGill University Health Centre; University of Ottawa; Canada's Michael Smith Genome Sciences Centre; Jewish General Hospital; Alberta Children's Hospital; University of British Columbia Hospital; Children's Hospital of Eastern Ontario; University of Calgary; BC Children's Hospital; University of British Columbia","funders":"Michael Cuccione Foundation; University of British Columbia; Canada Research Chairs; BC Children's Hospital; Michael Smith Health Research BC; Canadian Institutes of Health Research; Mitacs; Alberta Cancer Foundation; BC Children’s Hospital Foundation; Children's Hospital Foundation","keywords":"Medicine; Proteomics; Precision medicine; Proteogenomics; Malignancy; Oncology; Personalized medicine; Disease; Targeted therapy; Bioinformatics; Proteome; Genomics; Internal medicine; Cancer; Pathology; Genome; Biology; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001683867,0.0001935388,0.0002143786,0.00007918762,0.0001132095,0.00002564052,0.0001006016,0.0001446864,0.00001958914],"category_scores_gemma":[0.0001026942,0.0001567132,0.00006183216,0.00009762686,0.0001498269,0.00001229698,0.00003798488,0.00005603593,9.470095e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003520325,"about_ca_system_score_gemma":0.0001381859,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000297959,"about_ca_topic_score_gemma":0.000005720139,"domain_scores_codex":[0.9989598,0.0000599425,0.0002317327,0.0004270251,0.0001295459,0.0001919241],"domain_scores_gemma":[0.999364,0.000007390445,0.0001032084,0.0002870605,0.0001376241,0.0001006891],"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":[0.0003025733,0.0001197284,0.00004018809,0.00006392834,0.0001588272,0.00000960481,0.0002662759,0.0000676276,0.9889422,0.006629004,0.001136043,0.00226397],"study_design_scores_gemma":[0.004974318,0.001765704,0.0000802031,0.0002074954,0.0001403114,0.00002815983,0.0003320721,0.004093695,0.9690219,0.008459828,0.01062041,0.0002758799],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8417719,0.00772997,0.1428933,0.002796,0.000305859,0.002833978,0.00003092623,0.00004874408,0.001589323],"genre_scores_gemma":[0.9716004,0.0002164803,0.01622948,0.001741382,0.0002801862,0.001244892,0.000663834,0.00004623468,0.007977108],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1298285,"threshold_uncertainty_score":0.6390579,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01861357430794619,"score_gpt":0.3185769974544916,"score_spread":0.2999634231465454,"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."}}