{"id":"W2060012727","doi":"10.1371/journal.pone.0009129","title":"High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences","year":2010,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":176,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Canadian Institutes of Health Research; Genome Canada; Ontario Genomics; Ontario Genomics Institute; Canadian Institute for Advanced Research; Howard Hughes Medical Institute","keywords":"Nucleosome; Chromatin; Enhancer; Promoter; Occupancy; Biology; Histone; Linker DNA; Chromatosome; Regulatory sequence; Genetics; Transcription factor; DNA; Computational biology; Gene; Gene expression","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":[0.00007806381,0.0001402407,0.0001549588,0.00002455559,0.0001499615,0.00002335679,0.0002552553,0.0001883825,0.0002798073],"category_scores_gemma":[0.00001790993,0.0001424955,0.00006134381,0.00003752541,0.0001034765,0.000002784163,0.0001588912,0.0001197974,0.00006810236],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001491297,"about_ca_system_score_gemma":0.00003467074,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002483698,"about_ca_topic_score_gemma":0.0001547181,"domain_scores_codex":[0.9991131,0.00001418148,0.0001804745,0.0003159195,0.0001584279,0.0002179014],"domain_scores_gemma":[0.9992177,0.000003969029,0.00009010284,0.0005355161,0.00006442685,0.00008822834],"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":[0.000008752339,0.0001914363,0.007057508,0.00002573533,0.00008755516,0.000001698702,0.00004365827,0.000001141396,0.9914832,0.0005413576,0.0005114031,0.00004658899],"study_design_scores_gemma":[0.0003116982,0.0001348184,0.01079291,0.00001517373,0.00004200883,0.000004275567,0.00001287,0.00007989251,0.986545,0.0009823566,0.000840882,0.0002380956],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982303,0.0000897872,0.000004165803,0.0001615813,0.00008794701,0.000117556,0.00005422765,0.00002126802,0.001233117],"genre_scores_gemma":[0.9927663,0.00005477969,0.003572357,0.0003052087,0.0002876536,0.00001380736,0.0001426531,0.00002796376,0.002829318],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005464091,"threshold_uncertainty_score":0.5810798,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01422035418086564,"score_gpt":0.2137346276742,"score_spread":0.1995142734933343,"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."}}