{"id":"W2134957137","doi":"10.1038/nbt.2798","title":"Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape","year":2014,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":478,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"Institute of Genetics; National Institute of Dental and Craniofacial Research; Common Fund; National Institute of Biomedical Imaging and Bioengineering; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Neurological Disorders and Stroke; Harvard Stem Cell Institute; National Institutes of Health; National Human Genome Research Institute; Massachusetts Institute of Technology","keywords":"Chromatin; Chromatin immunoprecipitation; Transcription factor; Biology; Computational biology; Population; Binding site; Genome; DNase I hypersensitive site; Genetics; Deoxyribonuclease I; Gene; Promoter; Gene expression; Base sequence","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003378348,0.0003074103,0.0002198259,0.0001358717,0.0002038965,0.0005733499,0.0005601886,0.0004305376,0.0007143785],"category_scores_gemma":[0.0007881348,0.0004115773,0.0002811085,0.0001409602,0.0002484595,0.0004357278,0.0002040679,0.0005738906,0.0001680783],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008570114,"about_ca_system_score_gemma":0.0006981416,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002080677,"about_ca_topic_score_gemma":0.004248091,"domain_scores_codex":[0.9999621,0.000005125523,0.000001682797,0.00001089656,0.00001408422,0.000006152821],"domain_scores_gemma":[0.9998348,0.00008278112,0.00002126311,0.00001812254,0.00001701687,0.00002598841],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002955799,0.0001276033,0.0045093,0.0001309472,0.00003732809,0.0001567337,0.0001206708,0.5928338,0.3372246,0.03634601,0.0007097358,0.0275077],"study_design_scores_gemma":[0.0000248287,0.00002310378,0.0002503799,0.000001763903,0.000006561001,0.00001521751,0.00001419201,0.9657997,0.03103737,0.002196018,0.0006224397,0.000008342957],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7482415,0.0003192475,0.2450428,0.000306734,0.00003355251,0.0000682495,0.0001542842,0.0004790602,0.005354475],"genre_scores_gemma":[0.9378693,0.0003020753,0.06002495,0.00002507555,0.000005970297,0.0000476032,0.00007559398,0.00006203857,0.001587376],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002080677,"threshold_uncertainty_score":0.006218076,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.002807850877465943,"score_gpt":0.1942205810885083,"score_spread":0.1914127302110423,"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."}}