{"id":"W2159324718","doi":"10.1038/nbt.2486","title":"Evaluation of methods for modeling transcription factor sequence specificity","year":2013,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":411,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto","funders":"National Cancer Institute; National Human Genome Research Institute; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory; Tel Aviv University; Canadian Institute for Advanced Research; Israel Science Foundation; Academy of Finland; National Institutes of Health; Ontario Genomics; March of Dimes Foundation; Genome Canada; National Institute on Minority Health and Health Disparities; Ontario Genomics Institute; John Simon Guggenheim Memorial Foundation; Canadian Institutes of Health Research; National Science Foundation","keywords":"Computational biology; Transcription factor; Biology; Sequence motif; DNA binding site; Degeneracy (biology); DNA; Binding site; Genetics; DNA sequencing; Sequence (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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00420694,0.001343122,0.001000246,0.0009466638,0.0008264175,0.0009321079,0.002334694,0.001619791,0.00271912],"category_scores_gemma":[0.01197358,0.0005949858,0.0008947333,0.0007734453,0.0005041228,0.001365575,0.0007738427,0.00139164,0.000394393],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001953228,"about_ca_system_score_gemma":0.001563113,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01317678,"about_ca_topic_score_gemma":0.00742008,"domain_scores_codex":[0.9991401,0.0004251398,0.00003613851,0.0001138534,0.0002249214,0.00005985731],"domain_scores_gemma":[0.9921887,0.006393542,0.0002237604,0.0004370774,0.0006204452,0.0001364315],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001744927,0.0001442134,0.001253401,0.0001198843,0.00005260465,0.00004839397,0.00007711829,0.9550725,0.004299123,0.01077191,0.0004176176,0.02756868],"study_design_scores_gemma":[0.00001488288,0.00001734744,0.0000592884,0.000004287185,0.00000636886,0.000006774561,0.000008290825,0.9966794,0.001465089,0.001585961,0.0001476429,0.000004784552],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1754907,0.0005114362,0.8157209,0.000384372,0.00007280614,0.0002134525,0.0003719858,0.001861417,0.005373066],"genre_scores_gemma":[0.6442063,0.0004416286,0.3517249,0.0001230252,0.00003914768,0.0004197044,0.0004414993,0.0007985231,0.001805306],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01317678,"threshold_uncertainty_score":0.02620018,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04364750028958875,"score_gpt":0.3522073939154018,"score_spread":0.308559893625813,"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."}}