{"id":"W2027662098","doi":"10.1016/j.jmb.2004.02.048","title":"Constrained Binding Site Diversity within Families of Transcription Factors Enhances Pattern Discovery Bioinformatics","year":2004,"lang":"en","type":"article","venue":"Journal of Molecular Biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":181,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of British Columbia","funders":"","keywords":"Biology; Computational biology; DNA binding site; Transcription factor; Genetics; Gene; Footprinting; Phylogenetic tree; Binding site; DNA footprinting; Promoter; Bioinformatics; DNA-binding protein; 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":[0.0002064121,0.000147581,0.0002680384,0.0001118158,0.00006635528,0.00001486352,0.0002208662,0.0001666616,0.000002878966],"category_scores_gemma":[0.00004820003,0.0001212152,0.0002140432,0.00006670068,0.0001774993,0.00001394478,0.0001075882,0.0001151304,9.471327e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002600556,"about_ca_system_score_gemma":0.0001035552,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003085776,"about_ca_topic_score_gemma":0.00003423003,"domain_scores_codex":[0.9990742,0.00004636455,0.0004971427,0.0001133149,0.0001089706,0.0001600129],"domain_scores_gemma":[0.99911,0.000009425388,0.0005720386,0.0001386668,0.000114359,0.00005552019],"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":[0.00004042059,0.00004901072,0.007535761,0.00003518743,0.0001362277,0.000006081611,0.0005274971,0.001098404,0.9900713,0.0001114577,0.000003678883,0.0003849666],"study_design_scores_gemma":[0.00118958,0.001086959,0.002123205,0.00005620783,0.00007361218,0.00007123255,0.001095358,0.00007489554,0.9934959,0.0004724274,0.00006603728,0.000194523],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8862366,0.0002289291,0.1130483,0.00004057832,0.0002442923,0.00006139316,0.00009226113,0.000002208531,0.00004541441],"genre_scores_gemma":[0.9962252,0.0003267709,0.003226182,0.00006846263,0.00003551591,3.674392e-7,0.0001014099,0.000009171494,0.000006908704],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1099886,"threshold_uncertainty_score":0.4943011,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00699753906276443,"score_gpt":0.2196670752212404,"score_spread":0.212669536158476,"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."}}