{"id":"W2509668036","doi":"10.1016/j.cels.2016.07.001","title":"DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo","year":2016,"lang":"en","type":"article","venue":"Cell Systems","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":150,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"National Institute of General Medical Sciences; National Institutes of Health; Norges Forskningsråd; European Molecular Biology Laboratory; Genome Canada","keywords":"Computational biology; DNA; DNA binding site; Transcription factor; Biology; DNA sequencing; Binding site; Base pair; Genetics; Gene; Gene expression; Promoter","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":[0.00007224578,0.000117843,0.0001086666,0.00004634205,0.00004720492,0.00003090454,0.0001038483,0.0001641791,0.00002107496],"category_scores_gemma":[0.000007359951,0.00008965102,0.00006230483,0.00004493622,0.00002067694,0.000004268677,0.00002348711,0.00004565238,0.00002145095],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004356468,"about_ca_system_score_gemma":0.00002702824,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003925799,"about_ca_topic_score_gemma":0.00007734071,"domain_scores_codex":[0.9992624,0.00003148909,0.0001885948,0.0002519753,0.00007114923,0.0001943711],"domain_scores_gemma":[0.9996341,0.000006789749,0.0000682371,0.0002086738,0.00002648021,0.00005568728],"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":[0.00001048801,0.00002368135,0.001495711,0.00004033916,0.00001000882,0.000001021927,0.00007082845,0.0000388353,0.9973447,0.00001321556,0.0006771649,0.0002739507],"study_design_scores_gemma":[0.002015449,0.0003683259,0.007612211,0.000151346,0.00002731387,0.00002457098,0.0003325557,0.003149399,0.9405631,0.00001405403,0.04519508,0.000546529],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961056,0.000475259,0.0009486316,0.00003017005,0.0006882651,0.0002347487,0.0003611201,0.00001491052,0.001141343],"genre_scores_gemma":[0.9943395,0.0001650822,0.00003103988,0.00001122081,0.0002129369,0.00003151155,0.00004934497,0.00002070354,0.005138687],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05678159,"threshold_uncertainty_score":0.3655863,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005555101801612054,"score_gpt":0.192892097060011,"score_spread":0.1873369952583989,"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."}}