{"id":"W3185845130","doi":"10.1016/j.molcel.2021.06.009","title":"Transcription-mediated supercoiling regulates genome folding and loop formation","year":2021,"lang":"en","type":"article","venue":"Molecular Cell","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":114,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"European Social Fund; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Division of Civil, Mechanical and Manufacturing Innovation; H2020 Marie Skłodowska-Curie Actions; Guangzhou Regenerative Medicine and Health Guangdong Laboratory; Agencia Estatal de Investigación; Horizon 2020; Faculty of Science and Engineering, University of Manchester; University of California, San Francisco; National Institutes of Health; Research Executive Agency; National Natural Science Foundation of China; University of Oxford; Centres de Recerca de Catalunya; National Institute of General Medical Sciences; European Commission; Ministerio de Ciencia e Innovación; Generalitat de Catalunya; University of Edinburgh; European Regional Development Fund; Broad Institute; European Molecular Biology Laboratory; University of Pennsylvania; University of Michigan; Albert Ellis Institute; Institute of Genetics; Agència de Gestió d'Ajuts Universitaris i de Recerca; National Science Foundation","keywords":"Chromatin; Cohesin; Biology; DNA supercoil; Cell biology; Transcription (linguistics); Biophysics; DNA; Genetics; DNA replication","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":[0.0002977182,0.0003130298,0.0003200428,0.0003129919,0.0004133356,0.001164632,0.0003161504,0.0004217333,0.002208188],"category_scores_gemma":[0.0005265611,0.0002948975,0.0003599008,0.0001768432,0.0005227313,0.0006242679,0.0004855752,0.0008221972,0.0008042706],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008556927,"about_ca_system_score_gemma":0.0002782564,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001007612,"about_ca_topic_score_gemma":0.001308545,"domain_scores_codex":[0.9997098,0.00004422844,0.00001306194,0.00009034698,0.00006331354,0.00007917658],"domain_scores_gemma":[0.9995561,0.0001366108,0.00006592331,0.00005379523,0.00007771331,0.0001098616],"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":[0.0001322511,0.00002130256,0.0006147159,0.00001628103,0.000002646111,0.00002934263,0.00004350972,0.0001993157,0.9964217,0.0006867516,0.0000746419,0.001757569],"study_design_scores_gemma":[0.0000139658,0.00005004753,0.007274332,0.000005115136,0.000003460553,0.0000473396,0.00006291271,0.004116614,0.9869849,0.0004242566,0.001008787,0.000008220837],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9795943,0.001454586,0.01504711,0.0003680059,0.0001030207,0.0000240693,0.0002083456,0.0004998596,0.002700735],"genre_scores_gemma":[0.9965894,0.0001576375,0.001296515,0.00004264239,0.0000154476,0.000008786514,0.0002294096,0.00007280099,0.001587349],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002208188,"threshold_uncertainty_score":0.007387161,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004482778490302261,"score_gpt":0.1823629174231754,"score_spread":0.1778801389328731,"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."}}