{"id":"W4284896311","doi":"10.1186/s13059-022-02713-y","title":"Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding","year":2022,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill Genome Centre","funders":"Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Mitacs; Compute Canada","keywords":"Biology; DNA methylation; CpG site; Methylation; Genetics; Transcription factor; DNA; Pioneer factor; Epigenetics; Epigenetics of physical exercise; DNA binding site; Computational biology; Promoter; Gene; Gene expression; Histone methyltransferase","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":[0.0001691328,0.00009550528,0.0001488652,0.00008620991,0.00004843808,0.000002166502,0.0001738374,0.00008824815,0.00009105894],"category_scores_gemma":[0.00002686399,0.00007544966,0.0001433077,0.0001473487,0.00004791952,0.000001447107,0.00008255088,0.0000835376,4.596452e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009347605,"about_ca_system_score_gemma":0.0000723382,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001167913,"about_ca_topic_score_gemma":0.00002639557,"domain_scores_codex":[0.9992007,0.0001623547,0.0002468824,0.0001827312,0.00006061864,0.0001467157],"domain_scores_gemma":[0.9995619,0.00001238902,0.0001708916,0.0002091761,0.00002790737,0.00001774106],"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":[0.0001132945,0.00006270703,0.008527333,0.00001034132,0.00002981615,1.429859e-7,0.0001672143,0.007349928,0.9833552,0.0001163734,0.000007246599,0.0002604008],"study_design_scores_gemma":[0.001967926,0.004115855,0.2640321,0.00001324733,0.00003569022,0.00001357986,0.000371413,0.003867254,0.7226689,0.0005387881,0.002004485,0.0003706662],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984794,0.0001948755,0.0003394495,0.000054176,0.0001236861,0.0001890831,0.0005337474,0.000002464598,0.00008308158],"genre_scores_gemma":[0.9995723,0.00004162413,0.00009181327,0.0000198462,0.00002805689,0.00001569218,0.0001868061,0.000009882819,0.00003397411],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2606862,"threshold_uncertainty_score":0.3076748,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01925897478410205,"score_gpt":0.2519897421726791,"score_spread":0.232730767388577,"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."}}