{"id":"W4396241746","doi":"10.1038/s41592-024-02256-z","title":"Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput","year":2024,"lang":"en","type":"article","venue":"Nature Methods","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of British Columbia","funders":"National Institute of Allergy and Infectious Diseases; Howard Hughes Medical Institute; National Cancer Institute; National Science Foundation; National Institutes of Health; National Human Genome Research Institute; University of California, San Diego; Michael Smith Health Research BC; National Center for Research Resources; National Institute of General Medical Sciences; Stem Cell Network","keywords":"Phosphoproteomics; Phosphorylation; NFAT; Biology; Computational biology; Function (biology); Phenotype; Regulation of gene expression; Signal transduction; Cell biology; Protein phosphorylation; Gene; Transcription factor; Genetics; Protein kinase A","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":[0.0006911089,0.0001396229,0.0001137364,0.0001165566,0.00004013312,0.00004018213,0.00009540305,0.0003322269,0.00005843078],"category_scores_gemma":[0.0002476507,0.0001381226,0.00007500565,0.0003746547,0.00001400345,0.00000826582,0.00003287825,0.0003113608,0.00001549873],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003125707,"about_ca_system_score_gemma":0.00008465901,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003327226,"about_ca_topic_score_gemma":0.00003553999,"domain_scores_codex":[0.9988936,0.0001190975,0.0002021468,0.0004219224,0.0001908951,0.0001722928],"domain_scores_gemma":[0.9994316,0.0001033107,0.00001975672,0.000235483,0.0001381152,0.00007175266],"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":[0.0001062977,0.00006647356,0.002760744,0.00007951396,0.00005891653,0.000003886325,0.0001112148,0.01884373,0.9407597,0.001784826,0.00739601,0.02802868],"study_design_scores_gemma":[0.000617815,0.0001420396,0.2203028,0.0000601412,0.0000628988,0.00001314431,0.00004659055,0.01631907,0.3948648,0.0007445946,0.3662353,0.0005907906],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.106667,0.005260771,0.8824121,0.001301488,0.003691376,0.0002439437,0.0001717379,0.00003900324,0.000212639],"genre_scores_gemma":[0.7824149,0.00004784372,0.2131208,0.0003565416,0.002861164,0.00003341795,0.0008531748,0.00002434112,0.0002878542],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.6757479,"threshold_uncertainty_score":0.5632477,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01906636675796761,"score_gpt":0.3943247207630588,"score_spread":0.3752583540050912,"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."}}