{"id":"W2128595429","doi":"10.1101/gr.188680.114","title":"Determinants of nucleosome positioning and their influence on plant gene expression","year":2015,"lang":"en","type":"article","venue":"Genome Research","topic":"Plant Molecular Biology Research","field":"Agricultural and Biological Sciences","cited_by":70,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Natural Sciences and Engineering Research Council of Canada; Michigan Department of Agriculture and Rural Development; College of Engineering, Michigan State University; Michigan State University; Central Taiwan University of Science and Technology; National Science Foundation","keywords":"Nucleosome; Biology; Chromatin; Genetics; SWI/SNF; Gene; Gene expression; Histone; Arabidopsis; Transcription factor; Regulation of gene expression; Cell biology; Computational biology; Mutant","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":[0.001171384,0.0000830327,0.0001411966,0.00004860857,0.0001773362,0.0000347727,0.0003064152,0.00009493232,0.00002156373],"category_scores_gemma":[0.0001874803,0.00002986347,0.00002262378,0.0002505099,0.0001991799,0.00005499117,0.0002987962,0.0002213962,0.00004006865],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002455,"about_ca_system_score_gemma":0.00002399927,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001084979,"about_ca_topic_score_gemma":0.00003646394,"domain_scores_codex":[0.9985081,0.0003330301,0.0001356603,0.0002677268,0.0003636934,0.0003917892],"domain_scores_gemma":[0.9992135,0.0003041163,0.00003309263,0.00008084276,0.0001725476,0.0001959382],"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":[0.0001063566,0.00003302557,0.01986968,0.000005249548,0.000002823519,0.0000235523,0.000124177,0.00000411956,0.976133,0.00001506356,0.00002752802,0.003655431],"study_design_scores_gemma":[0.0002149862,0.001404859,0.366275,0.0000771346,9.988536e-7,0.00008405612,0.000379112,0.00008572313,0.6292735,0.0006893515,0.001371194,0.0001440438],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9987851,0.0003629956,6.283738e-7,0.000152715,0.00001094567,0.0001767806,0.0001363458,0.00001212718,0.000362312],"genre_scores_gemma":[0.9996266,0.0001006818,0.00006239252,0.0000266625,0.00004734501,0.00001305942,0.00004713834,9.645967e-7,0.00007510804],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3468595,"threshold_uncertainty_score":0.1363945,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09027955236265407,"score_gpt":0.3195722940208101,"score_spread":0.2292927416581561,"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."}}