{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003978557,0.0005039268,0.001423833,0.00184675,0.001004259,0.001351253,0.001558684,0.001145888,0.002668808],"category_scores_gemma":[0.01515222,0.0007551573,0.00100879,0.002543784,0.0008957096,0.002081315,0.002307608,0.001831357,0.001000112],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000492447,"about_ca_system_score_gemma":0.001314636,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009927565,"about_ca_topic_score_gemma":0.003037044,"domain_scores_codex":[0.9967167,0.001479445,0.0002028574,0.0008013116,0.0006192753,0.0001803795],"domain_scores_gemma":[0.9853057,0.009870413,0.0005442311,0.003099061,0.0007356844,0.0004450318],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004144811,0.001179946,0.06135516,0.0006933459,0.0008007059,0.0007539007,0.0006412396,0.2076396,0.243566,0.03141247,0.005723466,0.4420892],"study_design_scores_gemma":[0.0002117859,0.0003650382,0.006644826,0.00003674449,0.0001873321,0.0005509319,0.0001471688,0.8882459,0.03665104,0.06205019,0.00485575,0.00005328994],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.3478683,0.0005749551,0.6424776,0.0005915916,0.00004330391,0.0001739579,0.0009618958,0.003826683,0.003481805],"genre_scores_gemma":[0.7192866,0.0002982266,0.2756397,0.0003507216,0.0000705163,0.00028728,0.002526737,0.000540353,0.0009999411],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.003978557,"threshold_uncertainty_score":0.02104086,"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."}}