{"id":"W4412708068","doi":"10.1038/s41587-025-02739-0","title":"Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis","year":2025,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Austrian Science Fund; Keio University; European Commission; HORIZON EUROPE Framework Programme; Rijksuniversiteit Groningen; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; York University","keywords":"RNA; Untranslated region; Computational biology; Biology; Transcriptome; Nucleic acid structure; Messenger RNA; Genetics; Gene; Gene expression","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":[0.0002810701,0.0001507996,0.0002366443,0.0003673739,0.0001993678,0.000319171,0.0002409528,0.0002094231,0.0004042565],"category_scores_gemma":[0.0005109656,0.0001444314,0.0002160312,0.000295895,0.000307957,0.0003929787,0.0002988378,0.0004302459,0.0001029474],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002935897,"about_ca_system_score_gemma":0.0002012022,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006053815,"about_ca_topic_score_gemma":0.001162098,"domain_scores_codex":[0.9998878,0.00001471498,0.00000498689,0.00004887575,0.00003100965,0.00001262506],"domain_scores_gemma":[0.999772,0.00007914874,0.00006598415,0.00003709397,0.00002340804,0.00002233443],"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":[0.00004274886,0.00001743031,0.003792253,0.0000247347,0.0000150737,0.00003373892,0.00004791345,0.003753278,0.9813106,0.001111957,0.00004353235,0.009806817],"study_design_scores_gemma":[0.000008270884,0.0001129447,0.04087359,0.000007796045,0.00002602044,0.0002127735,0.0001021214,0.2415807,0.7109231,0.004730638,0.001382104,0.00003997329],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8091099,0.0002241493,0.188897,0.00006258478,0.000009956904,0.0000217512,0.000264062,0.0005648677,0.0008457036],"genre_scores_gemma":[0.9390576,0.0001522956,0.06014078,0.00003762383,0.000007676766,0.00003105928,0.0002393713,0.00006516097,0.000268452],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0006053815,"threshold_uncertainty_score":0.002130091,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00535572621737268,"score_gpt":0.2286342412362775,"score_spread":0.2232785150189048,"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."}}