{"id":"W2019581511","doi":"10.1101/gr.150482.112","title":"DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types","year":2013,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Human Genome Research Institute; Natural Sciences and Engineering Research Council of Canada; National Institutes of Health; University of Chicago","keywords":"Nucleosome; Biology; Histone; Chromatin; SWI/SNF; Hypersensitive site; Deoxyribonuclease I; DNase I hypersensitive site; DNA; Genetics; Micrococcal nuclease; Biophysics; Cell biology; Base sequence","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004925648,0.00009902377,0.0001190238,0.0000457345,0.000239685,0.00003921746,0.0003531561,0.0001215095,0.0003120255],"category_scores_gemma":[0.0000594624,0.00009752803,0.00007230005,0.0001304505,0.0003005113,0.00000579541,0.0004061741,0.0001552466,0.00009927089],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003806964,"about_ca_system_score_gemma":0.0001180093,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001801413,"about_ca_topic_score_gemma":0.00007791741,"domain_scores_codex":[0.998659,0.0001053498,0.0002176162,0.0003103058,0.0003051894,0.000402535],"domain_scores_gemma":[0.9988488,0.00002627821,0.00006078089,0.0004858802,0.0004507541,0.0001274967],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00001423666,0.0001415764,0.004422914,0.00006562605,0.00002621451,0.00000109992,0.0003367133,0.00009434469,0.9938223,0.0002438723,0.0006563623,0.0001747711],"study_design_scores_gemma":[0.003243848,0.002328478,0.5340841,0.00004366902,0.00003192015,0.00001518238,0.007293948,0.001563371,0.4185664,0.01137743,0.02042847,0.00102319],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9963502,0.0002217766,0.00006423652,0.0001045989,0.00003019662,0.0003621829,0.0001832318,0.000006640489,0.002676881],"genre_scores_gemma":[0.9976593,0.00009379421,0.0005320697,0.00001544042,0.0001030254,0.00004316051,0.0002781492,0.00001926136,0.00125583],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5752558,"threshold_uncertainty_score":0.3977078,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04844681308948119,"score_gpt":0.327362137324569,"score_spread":0.2789153242350878,"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."}}