{"id":"W2121763778","doi":"10.1101/gr.088260.108","title":"Incorporating nucleosomes into thermodynamic models of transcription regulation","year":2009,"lang":"en","type":"article","venue":"Genome Research","topic":"Gene Regulatory Network Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":104,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Azrieli Foundation; Israel Science Foundation","keywords":"Nucleosome; Biology; Promoter; Cooperativity; Transcription (linguistics); Transcription factor; Computational biology; Genetics; Histone; DNA; Cell biology; Gene expression; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007842604,0.0005627751,0.0009089204,0.0006291077,0.0005974723,0.0009989514,0.001431354,0.001131291,0.001813355],"category_scores_gemma":[0.002103497,0.0005172759,0.0008394099,0.0005966244,0.001236819,0.001658852,0.0008437861,0.0007181208,0.0004752793],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001255587,"about_ca_system_score_gemma":0.0008406014,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005037772,"about_ca_topic_score_gemma":0.004284179,"domain_scores_codex":[0.9996904,0.0001369794,0.00001057324,0.00004981027,0.00006236958,0.0000498901],"domain_scores_gemma":[0.9994346,0.0003844884,0.00004600698,0.00004013133,0.00004963003,0.00004503953],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0000155796,0.00002122696,0.0003389268,0.00002439366,0.00001643168,0.00004533629,0.00004109431,0.9041963,0.002125335,0.09097325,0.0001840799,0.002018041],"study_design_scores_gemma":[0.000005436647,0.000006919404,0.00009247682,0.000002720462,0.000003781572,0.000008236146,0.000005184574,0.9615952,0.000141646,0.03773979,0.0003909848,0.00000765262],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1872742,0.002972524,0.7852933,0.001444196,0.0002200643,0.00007007841,0.0003591402,0.0003720724,0.02199438],"genre_scores_gemma":[0.9614086,0.001878436,0.02653672,0.000224442,0.0001206246,0.0002674598,0.0001754981,0.0001935151,0.009194791],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.005037772,"threshold_uncertainty_score":0.01001692,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03219821159713682,"score_gpt":0.3042016877291,"score_spread":0.2720034761319632,"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."}}