{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001399759,0.001135653,0.0009003807,0.0008553406,0.000313039,0.0006953643,0.0005916604,0.0008346571,0.000863751],"category_scores_gemma":[0.002650658,0.0003599442,0.001019549,0.0006742413,0.0002816783,0.0008933426,0.0004973194,0.0007166803,0.0008090691],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004749131,"about_ca_system_score_gemma":0.0004534236,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005699618,"about_ca_topic_score_gemma":0.00781468,"domain_scores_codex":[0.9994841,0.0001625995,0.00002797067,0.0001895055,0.00009794167,0.00003789047],"domain_scores_gemma":[0.9986034,0.0008420811,0.000120242,0.0002048876,0.0001605124,0.0000689189],"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":[0.0007312909,0.0001869116,0.04378073,0.0001465564,0.0003104565,0.000110977,0.00004468261,0.8368855,0.05696125,0.0003664302,0.001376022,0.05909926],"study_design_scores_gemma":[0.00001627372,0.00009286241,0.005619096,0.000005928699,0.00002781118,0.00003652661,0.00001608799,0.9828621,0.01018855,0.0006240686,0.0004959328,0.00001464113],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9395887,0.0008493216,0.05314301,0.0001569485,0.00003595453,0.00002106458,0.003018932,0.002099775,0.001086302],"genre_scores_gemma":[0.9699526,0.0002384048,0.0214446,0.00006984779,0.00001668202,0.00001831578,0.007652446,0.0001323345,0.0004747707],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005699618,"threshold_uncertainty_score":0.01133287,"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."}}