{"id":"W4403971339","doi":"10.1021/acs.jproteome.4c00116","title":"Proteomics Can Rise to the Challenge of Pseudogenes’ Coding Nature","year":2024,"lang":"en","type":"review","venue":"Journal of Proteome Research","topic":"Cell Image Analysis Techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre Hospitalier Universitaire de Sherbrooke; Université de Sherbrooke","funders":"Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; Fonds Québécois de la Recherche sur la Nature et les Technologies; Université de Sherbrooke","keywords":"Pseudogene; Proteomics; Proteogenomics; Computational biology; Coding (social sciences); Biology; Computer science; Genetics; Genomics; Genome; Gene; Sociology","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":["research_integrity"],"consensus_categories":[],"category_scores_codex":[0.005734813,0.0003123261,0.001103824,0.0008019143,0.00009762731,0.000100146,0.001553766,0.0006955878,0.00001915072],"category_scores_gemma":[0.0009849373,0.00017868,0.0009477051,0.0009226371,0.0001456869,0.000004783322,0.0008120754,0.002802033,0.00001530707],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001470157,"about_ca_system_score_gemma":0.001194235,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000151165,"about_ca_topic_score_gemma":0.00002782637,"domain_scores_codex":[0.9964483,0.0007460002,0.0009901699,0.0004132212,0.0009794683,0.000422876],"domain_scores_gemma":[0.9971155,0.00005996839,0.0005671958,0.00089794,0.001184712,0.0001746734],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001995465,0.0003784149,0.000003780786,0.04573581,0.003563134,0.0004668615,0.0003126753,0.000004579289,0.1004287,0.0002058598,0.09947286,0.7492278],"study_design_scores_gemma":[0.00006605806,0.0006447354,2.275705e-7,0.006005969,0.0003948084,0.0001731448,0.00003174995,0.00000250839,0.02325663,0.0001265792,0.9691178,0.0001797869],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0001109213,0.9963539,0.0001926472,0.0009240932,0.00005721875,0.001924897,0.00002446403,0.00000491776,0.000406969],"genre_scores_gemma":[0.0005557539,0.9949034,0.002003987,0.00001436754,0.001169059,0.0002116833,0.00001313982,0.00008089952,0.001047671],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.8696449,"threshold_uncertainty_score":0.9994985,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07986774858860578,"score_gpt":0.4555836910437678,"score_spread":0.375715942455162,"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."}}