{"id":"W4408129732","doi":"10.1016/j.molp.2025.03.002","title":"SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing","year":2025,"lang":"en","type":"article","venue":"Molecular Plant","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"National Major Science and Technology Projects of China","keywords":"Biology; Genome editing; Computational biology; Genome; Genetics; Mutation; Gene","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":[0.002241578,0.001709304,0.001551752,0.00216001,0.0005620145,0.001505718,0.002542888,0.0009757585,0.008228576],"category_scores_gemma":[0.003461806,0.001478341,0.001544627,0.0007938539,0.0006703253,0.00135797,0.002536526,0.002303243,0.005271365],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007500552,"about_ca_system_score_gemma":0.001730485,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001762533,"about_ca_topic_score_gemma":0.002653398,"domain_scores_codex":[0.9985402,0.0001927622,0.0001807953,0.0004480515,0.0004968613,0.0001414086],"domain_scores_gemma":[0.9981823,0.0008164452,0.0002912686,0.0002693049,0.0002803874,0.0001602829],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004271242,0.0005596406,0.01363177,0.004523284,0.001546425,0.002281265,0.001670596,0.02088543,0.4796839,0.01360719,0.1354688,0.3218705],"study_design_scores_gemma":[0.000550912,0.0007179888,0.01281551,0.0005373178,0.0003917981,0.0023744,0.0002953991,0.193614,0.5234635,0.01303548,0.2513013,0.0009023749],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.01878087,0.0007319367,0.6437271,0.0001831039,0.0001977674,0.0005852392,0.01830403,0.3145047,0.002985283],"genre_scores_gemma":[0.07091855,0.001087147,0.8356386,0.0005863305,0.00005706695,0.003189991,0.03880287,0.04141125,0.008308163],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.008228576,"threshold_uncertainty_score":0.02752733,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006852138082357719,"score_gpt":0.2859818688953309,"score_spread":0.2791297308129732,"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."}}