{"id":"W2029201460","doi":"10.1371/journal.pcbi.1003214","title":"The Next Generation of Transcription Factor Binding Site Prediction","year":2013,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":217,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; National Institutes of Health","keywords":"DNA binding site; ENCODE; Computational biology; Transcription factor; Binding site; Computer science; DNA microarray; DNA; Data mining; Genetics; Biology; 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":[0.00004956753,0.00007406109,0.00006903696,0.00002563134,0.0001130184,0.00002327401,0.00008212796,0.00009055222,0.00002311722],"category_scores_gemma":[0.00002370627,0.00005735976,0.00004573839,0.00003878812,0.00006312988,0.000005458114,0.00002265566,0.00004050522,0.0000247304],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001175542,"about_ca_system_score_gemma":0.00003013283,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008912476,"about_ca_topic_score_gemma":0.000008629366,"domain_scores_codex":[0.9994318,0.00005025386,0.0002055925,0.0001492978,0.00005696953,0.000106054],"domain_scores_gemma":[0.9996281,0.00002588993,0.00009226429,0.00009403311,0.0001353307,0.00002433295],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.000006056305,0.00002326707,0.002227052,0.00000511426,0.00003861027,2.311512e-8,0.00003345871,0.002166117,0.9927469,0.0006167812,0.0002168529,0.001919745],"study_design_scores_gemma":[0.0009542715,0.0008483556,0.04412465,0.00001427788,0.00003680195,0.00001442257,0.00009472168,0.7609854,0.1833596,0.003677124,0.00556156,0.0003288045],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9880442,0.0001976433,0.01107385,0.0001683233,0.0001624795,0.0001713703,0.0000912602,0.000007382806,0.00008349352],"genre_scores_gemma":[0.9959732,0.0001080032,0.001936853,0.00005096347,0.000147719,0.00002517537,0.00169758,0.000007987677,0.00005247898],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8093874,"threshold_uncertainty_score":0.2339063,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03361436893284375,"score_gpt":0.2293162488155568,"score_spread":0.1957018798827131,"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."}}