{"id":"W3008598131","doi":"10.1038/s41467-020-14337-6","title":"RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions","year":2020,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":166,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Occupational Cancer Research Centre; McGill University Health Centre","funders":"RIKEN; Medical Research Council; Ministry of Education, Culture, Sports, Science and Technology; Russian Science Foundation; Ministero dell’Istruzione, dell’Università e della Ricerca; Karolinska Institutet; European Commission; King Abdullah University of Science and Technology; Wellcome Trust; Francis Crick Institute; Vetenskapsrådet; Cancer Research UK","keywords":"Chromatin; ChIA-PET; Genome; Biology; RNA; ENCODE; Computational biology; Genetics; Transcription (linguistics); Gene; Chromosome conformation capture; Long non-coding RNA; Chromatin remodeling; Gene expression; Enhancer","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007031469,0.0001068019,0.0001232916,0.00003136483,0.0001332639,0.00003066921,0.0005371555,0.000139172,0.0000223544],"category_scores_gemma":[0.00007815117,0.0001109486,0.00005566601,0.0001131339,0.0001254919,0.000005626805,0.0004748304,0.0002786635,0.000006477325],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001160718,"about_ca_system_score_gemma":0.0000434217,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005087605,"about_ca_topic_score_gemma":0.00006597545,"domain_scores_codex":[0.9993542,0.00005798836,0.0002394949,0.0001802619,0.00006635147,0.0001017138],"domain_scores_gemma":[0.9988412,0.00003938859,0.0001400991,0.0007896126,0.0001213604,0.00006833096],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00001267913,0.0000587884,0.001893864,0.00002577738,0.00004265475,3.198961e-7,0.0003009474,0.0001770106,0.9934135,0.001421792,0.002520565,0.0001320712],"study_design_scores_gemma":[0.0009976689,0.0002756993,0.07005522,0.0000343141,0.00009832852,0.00002189829,0.001244184,0.0088562,0.2225186,0.0002918534,0.6949685,0.0006375478],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9808999,0.01204951,0.0003481151,0.001791295,0.0000977367,0.0001524336,0.00006383639,0.00001462293,0.004582511],"genre_scores_gemma":[0.9826718,0.00441723,0.01176478,0.000318653,0.00007139266,0.000008775214,0.0004197058,0.00001847358,0.000309215],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7708949,"threshold_uncertainty_score":0.4524351,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01797216490246847,"score_gpt":0.2590328680174855,"score_spread":0.241060703115017,"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."}}