{"id":"W2758677856","doi":"10.1093/gbe/evx207","title":"Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species","year":2017,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":49,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Plastid; Genome; Genetics; Intergenic region; Transcription (linguistics); Organelle; Gene; RNA; Nuclear gene; Non-coding RNA; Computational biology; Mitochondrial DNA; Chloroplast","routes":{"ca_aff":true,"ca_fund":true,"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":[0.00009060858,0.0001445796,0.0001945797,0.00002224905,0.0005755479,0.00002590126,0.0001295485,0.0001711565,0.000006461957],"category_scores_gemma":[0.00004822641,0.0001361392,0.00005129104,0.00001453034,0.0006193974,0.000003790364,0.0002134501,0.00005641882,0.000002181684],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001141189,"about_ca_system_score_gemma":0.00001975437,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007902523,"about_ca_topic_score_gemma":0.000114201,"domain_scores_codex":[0.9992216,0.00002967513,0.0001630315,0.0003245054,0.00003658274,0.0002246675],"domain_scores_gemma":[0.9994743,0.00001198253,0.0001752147,0.0002224501,0.00006262911,0.000053436],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001371994,0.00001409029,0.1317152,0.00002051675,0.00007982894,5.368109e-7,0.0003109975,0.00001296295,0.867026,0.0002163407,0.00004396121,0.0004223607],"study_design_scores_gemma":[0.0007888825,0.0003920298,0.9784442,0.000008138075,0.00003688295,0.0000138643,0.0006325508,0.0000158503,0.01265515,0.0002808475,0.00655403,0.000177577],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9930948,0.005508083,0.0004232484,0.00006620593,0.0003479392,0.0001347471,0.0002085951,0.000002883799,0.0002134896],"genre_scores_gemma":[0.9956712,0.003378976,0.0004240089,0.00001460658,0.0002826838,0.000008241468,0.00004194237,0.000008668198,0.0001696327],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8543709,"threshold_uncertainty_score":0.5551596,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01902389678654699,"score_gpt":0.2491061630626162,"score_spread":0.2300822662760692,"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."}}