{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008670043,0.00009901742,0.0001453093,0.0001842285,0.0001270964,0.00001856465,0.0002286473,0.0001302058,0.00001911428],"category_scores_gemma":[0.00001793611,0.00009838137,0.0001018846,0.0004014996,0.0001057868,0.000008677581,0.00004531732,0.0001089957,0.000006221477],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004049188,"about_ca_system_score_gemma":0.00008147298,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002407668,"about_ca_topic_score_gemma":0.00002856508,"domain_scores_codex":[0.9986164,0.0002055499,0.0002453626,0.0003035806,0.0003711231,0.0002580058],"domain_scores_gemma":[0.9991554,0.000008014687,0.00007086583,0.0004258043,0.0002723109,0.00006757947],"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":[0.00004664548,0.00003690798,0.0001075031,0.00001564184,0.00003208812,4.785376e-7,0.0001380665,0.01759348,0.9716794,0.00106307,0.00002946604,0.009257277],"study_design_scores_gemma":[0.001571848,0.002080614,0.08071068,0.00008109833,0.00008845727,0.00001521825,0.0007979659,0.2318358,0.4797811,0.2003451,0.001811272,0.0008807919],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.986096,0.001613336,0.01012792,0.0002035704,0.00001454397,0.0001782505,0.000002592579,0.000009548516,0.001754254],"genre_scores_gemma":[0.9975225,0.0001689378,0.001727993,0.00001516812,0.0001335526,0.000007060851,0.0001046709,0.00001570857,0.0003043524],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4918983,"threshold_uncertainty_score":0.4011876,"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."}}