{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007996892,0.0001231074,0.0001022086,0.00002779612,0.00007375364,0.00004931706,0.00007246493,0.0001163782,0.00001606572],"category_scores_gemma":[0.00001781439,0.0001399539,0.00006674392,0.00006962594,0.0000253561,0.000005642323,0.00005655841,0.00005810525,0.000006458643],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001303273,"about_ca_system_score_gemma":0.00003549088,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003555405,"about_ca_topic_score_gemma":0.00001078775,"domain_scores_codex":[0.9992752,0.00003522442,0.0001702801,0.0002552597,0.00007931628,0.0001847382],"domain_scores_gemma":[0.9996046,0.000004604497,0.00003678426,0.0002172078,0.00006931899,0.00006744906],"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":[0.000005315035,0.00002204956,0.00007228701,0.00004629297,0.00001565192,0.00001911369,0.00008540478,0.000407711,0.9989403,0.00004883706,0.00001711344,0.0003199199],"study_design_scores_gemma":[0.000465576,0.00005072598,0.0003042427,0.000008946575,0.00002509906,0.00003811305,0.0002173309,0.004143811,0.9903677,0.0001329819,0.004043082,0.0002023704],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.985775,0.003494305,0.009560768,0.00009295817,0.00005356558,0.00008174746,0.00001578741,0.00001188338,0.0009139806],"genre_scores_gemma":[0.9956595,0.0005993273,0.002487784,0.000221317,0.00003191957,0.000005897833,0.0006825983,0.00002524291,0.0002863775],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.009884531,"threshold_uncertainty_score":0.5707154,"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."}}