{"id":"W2042392223","doi":"10.1126/science.1162327","title":"Diversity and Complexity in DNA Recognition by Transcription Factors","year":2009,"lang":"en","type":"article","venue":"Science","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1037,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Human Genome Research Institute","keywords":"Genome; Biology; Computational biology; DNA; DNA binding site; Transcription factor; Genetics; DNA sequencing; DNA-binding protein; Transcription (linguistics); Sequence motif; Binding site; Gene; Promoter; Gene expression","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0001090293,0.0000375733,0.00003242631,0.0000199232,0.0002813413,0.00001005335,0.00008345112,0.00002545493,0.000002285094],"category_scores_gemma":[0.00001040598,0.00003714021,0.000009207263,0.00006839873,0.0001347659,0.000005452825,0.00007628983,0.00002306661,4.18091e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000116852,"about_ca_system_score_gemma":0.00001132003,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000232866,"about_ca_topic_score_gemma":0.00005293251,"domain_scores_codex":[0.9996481,0.000006749276,0.00004438172,0.000150266,0.00005814185,0.00009238299],"domain_scores_gemma":[0.9998768,9.312957e-7,0.00001517488,0.0000583313,0.00001599405,0.00003274807],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000004063434,0.00001808909,0.0112798,0.000001189308,3.743935e-7,1.220557e-7,0.0002336375,0.000002274123,0.9866897,0.00001939865,0.00001473686,0.001736654],"study_design_scores_gemma":[0.0002694016,0.000171227,0.8277965,0.00000456409,0.000002439079,0.000002248241,0.0001659227,0.0006772816,0.1672684,0.003325518,0.0001874528,0.0001290352],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9994143,0.00004256077,0.000221854,0.00005942371,0.00003082094,0.00003929083,0.00001213915,0.000002591827,0.0001770049],"genre_scores_gemma":[0.9996442,0.00004455643,0.000184666,0.00008016462,0.000005252764,2.127471e-7,0.00002459308,8.698518e-7,0.00001549745],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8194213,"threshold_uncertainty_score":0.2163878,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03222975422381295,"score_gpt":0.2335535896441704,"score_spread":0.2013238354203575,"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."}}