{"id":"W1999659528","doi":"10.1371/journal.ppat.1001165","title":"Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite","year":2010,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"Malaria Research and Control","field":"Medicine","cited_by":296,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; National Institute of General Medical Sciences; College of Veterinary Medicine, Cornell University; Arnold and Mabel Beckman Foundation; Office of the Dean for Research, Princeton University; National Institutes of Health; National Science Foundation","keywords":"Biology; Plasmodium falciparum; Gene; Genetics; Transcriptional regulation; DNA; DNA-binding protein; Computational biology; Genome; Sequence motif; Regulatory sequence; Protein family; Regulation of gene expression; DNA sequencing; Transcription factor; Malaria","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005106759,0.00008867047,0.0001931123,0.00005881997,0.0001278804,0.00002399558,0.0001277366,0.00007560536,0.00004969907],"category_scores_gemma":[0.0005049692,0.00005204747,0.00008257233,0.0001037672,0.0001774024,0.00005099022,0.00002932726,0.0001619816,0.000003042515],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001148956,"about_ca_system_score_gemma":0.00005088899,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000381659,"about_ca_topic_score_gemma":0.00002532265,"domain_scores_codex":[0.9990181,0.00004776281,0.0003013045,0.0001741422,0.0002990109,0.0001596641],"domain_scores_gemma":[0.9985332,0.0006416754,0.0001558515,0.0004294272,0.0001823051,0.00005751345],"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":[0.000210389,0.00004569335,0.05694312,0.00004652574,0.0001565393,7.779719e-7,0.0004788676,9.443343e-7,0.9397551,0.001661227,0.0000940082,0.0006068043],"study_design_scores_gemma":[0.0007286847,0.00009922247,0.9354469,0.00003388547,0.0002743368,0.000001922943,0.0009855386,0.00166238,0.0597988,0.0004634669,0.0004621251,0.00004279162],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9947691,0.0003069892,0.00119423,0.001648046,0.0001368419,0.001031657,0.0007912882,0.00001574405,0.0001061169],"genre_scores_gemma":[0.9989082,0.0001271332,0.0002179269,0.00004109564,0.0002674168,0.00008728153,0.00008017912,0.00001516286,0.0002556586],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8799563,"threshold_uncertainty_score":0.2122434,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02569137894692053,"score_gpt":0.2456402880767693,"score_spread":0.2199489091298488,"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."}}