{"id":"W4413376873","doi":"10.1101/2025.08.13.670096","title":"PAM adenine methylation and flanking sequence regulate SaCas9 activity in bacteria","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"Canadian Institutes of Health Research","keywords":"Methylation; Sequence (biology); Genetics; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002024765,0.0004237718,0.0003155792,0.0001487043,0.0001232683,0.0003716924,0.0001825599,0.0003152154,0.0006117981],"category_scores_gemma":[0.0005778491,0.0001550875,0.0002731236,0.0001217109,0.0001947635,0.0001775945,0.0002429302,0.0004765304,0.0003981592],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003917948,"about_ca_system_score_gemma":0.0002617043,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001684911,"about_ca_topic_score_gemma":0.001229897,"domain_scores_codex":[0.999822,0.00002810381,0.0000148143,0.0000547585,0.00005181702,0.0000285393],"domain_scores_gemma":[0.9997683,0.00008579406,0.00005134433,0.00002124117,0.00003359763,0.00003965093],"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":[0.0001570733,0.00005038821,0.004127967,0.00004059148,0.0000160066,0.00002622558,0.00001896246,0.008665513,0.9828675,0.0001308774,0.00006896551,0.003829856],"study_design_scores_gemma":[0.000009102144,0.0002923123,0.01377011,0.000008069807,0.00001367335,0.00009301415,0.00004451111,0.08261333,0.9018286,0.0002484357,0.001057517,0.00002124678],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9926428,0.0003166536,0.005591942,0.00005630784,0.000009857564,0.00001051327,0.0004959502,0.0001775016,0.0006985628],"genre_scores_gemma":[0.9958829,0.0001024345,0.003117932,0.00001340349,0.000001424194,0.000008830148,0.0005385883,0.00001978457,0.0003147286],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001684911,"threshold_uncertainty_score":0.003350198,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01170514641715334,"score_gpt":0.2673943966714492,"score_spread":0.2556892502542958,"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."}}