{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004948535,0.0001049187,0.0001296791,0.00006329158,0.00003507804,0.000007319718,0.0001929884,0.001074454,0.00001961485],"category_scores_gemma":[0.0002361643,0.00009946884,0.00007917648,0.00007203856,0.00005396002,0.000003386652,0.00003198614,0.0001874727,0.000001388623],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003599986,"about_ca_system_score_gemma":0.00006568825,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001522068,"about_ca_topic_score_gemma":0.00001324906,"domain_scores_codex":[0.9992307,0.00006400375,0.0001924852,0.0002701852,0.0000932086,0.0001493816],"domain_scores_gemma":[0.9991428,0.000008878625,0.00008579861,0.0002991799,0.000442601,0.00002077092],"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":[0.000007381317,0.00001779847,0.00000748502,0.00001209508,0.00002638307,1.083443e-8,0.000009414833,0.0006744125,0.9220806,0.0009596131,0.00003610514,0.07616871],"study_design_scores_gemma":[0.0002932061,0.0001183664,0.00007374363,0.00000416246,0.00003216894,0.000003188793,0.00004084223,0.3249274,0.6671411,0.005995951,0.001270576,0.00009925482],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.731859,0.001286995,0.2658657,0.0002965695,0.0001653795,0.0004254943,0.00002871694,0.00001464117,0.00005742363],"genre_scores_gemma":[0.9009631,0.0001306307,0.09866577,0.00004030178,0.00004733763,0.00005339762,0.00007371469,0.00001279372,0.00001295744],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.324253,"threshold_uncertainty_score":0.8287171,"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."}}