{"id":"W4386637239","doi":"10.1038/s41467-023-41265-y","title":"Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries","year":2023,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":50,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"National Institute of General Medical Sciences; Agence Nationale de la Recherche; Fondation Bettencourt Schueller; Oxford Nanopore Technologies; Centre National de la Recherche Scientifique; Laboratoire d’excellence Physique Atomes Lumière Matière; Fondation pour la Recherche Médicale; Fondation de Coopération Scientifique Campus Paris-Saclay; Eunice Kennedy Shriver National Institute of Child Health and Human Development; European Commission; National Institute on Drug Abuse; National Science Foundation","keywords":"Robustness (evolution); Extrusion; Loop (graph theory); Blocking (statistics); Cluster analysis; Domain (mathematical analysis); Computer science; CTCF; Feature (linguistics); Topology (electrical circuits); Biological system; Algorithm; Computational biology; Statistical physics; Physics; Mathematics; Materials science; Biology; Artificial intelligence; Genetics; Combinatorics; Mathematical analysis; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001078399,0.0001277271,0.0002807204,0.0002831543,0.0003099233,0.0005425856,0.0004271246,0.0004407548,0.001198169],"category_scores_gemma":[0.0005313038,0.0002713594,0.000207684,0.0001768945,0.0004136504,0.0003547106,0.0004762343,0.0004382465,0.0002881946],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004587946,"about_ca_system_score_gemma":0.0001943024,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008943084,"about_ca_topic_score_gemma":0.001265441,"domain_scores_codex":[0.9997934,0.00001186855,0.000008117348,0.0000583064,0.00006673085,0.00006169176],"domain_scores_gemma":[0.9995066,0.00008424107,0.0001059819,0.0001310949,0.00005459248,0.0001175167],"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":[0.0000657098,0.0000159983,0.001500955,0.00001479962,0.000008210971,0.00007344753,0.00002257069,0.001682862,0.994224,0.000355206,0.00006119046,0.001975096],"study_design_scores_gemma":[0.00003284378,0.000149479,0.05731945,0.000008818901,0.00002753454,0.0005888953,0.0001369115,0.0567229,0.8817763,0.0009655078,0.002240437,0.00003095098],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9913413,0.00006018398,0.00767127,0.00002138571,0.000003836335,0.000005266713,0.00003732115,0.0001373606,0.0007222171],"genre_scores_gemma":[0.9981272,0.00001063394,0.001515975,0.00001288196,0.000001098809,0.000005143131,0.00005263533,0.00001837955,0.0002561798],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001198169,"threshold_uncertainty_score":0.004008293,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0196476771006077,"score_gpt":0.2978010228625673,"score_spread":0.2781533457619596,"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."}}