{"id":"W2109203567","doi":"10.1186/s12859-015-0805-8","title":"Revisiting operons: an analysis of the landscape of transcriptional units in E. coli","year":2015,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":48,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Andlinger Center for Energy and the Environment, Princeton University; U.S. Department of Energy; Canadian Association for the Study of the Liver; National Science Foundation","keywords":"Operon; Computational biology; DNA microarray; Biology; Genetics; Escherichia coli; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004495615,0.00006585087,0.0001571781,0.00007910754,0.00001683978,0.000006750407,0.0001961574,0.0000774872,0.00001106399],"category_scores_gemma":[0.0001440558,0.00004712184,0.00006989622,0.0004032267,0.00003426388,0.000008048381,0.00003471639,0.00003072558,7.008739e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005099154,"about_ca_system_score_gemma":0.0001265952,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001730786,"about_ca_topic_score_gemma":0.00007384804,"domain_scores_codex":[0.9993055,0.00006683208,0.0003342546,0.0000599315,0.0001457291,0.00008769424],"domain_scores_gemma":[0.9994235,0.00001162814,0.0001485033,0.0002584849,0.0001201719,0.00003771232],"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":[0.0006209496,0.0003353651,0.2727769,0.0008728532,0.0009875729,8.356926e-7,0.007914798,0.07152759,0.6171441,0.01043767,0.000404644,0.01697676],"study_design_scores_gemma":[0.002650215,0.0008133422,0.1073262,0.0003047129,0.0008691284,0.00000968413,0.0156375,0.3582092,0.5091246,0.0003332315,0.004067015,0.0006552009],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9861371,0.0002287566,0.01219537,0.00002063399,0.00003995295,0.0001388533,0.00005836436,0.000002469586,0.001178533],"genre_scores_gemma":[0.9871497,0.00002556256,0.01262376,0.00004987574,0.00002211476,0.00000522293,0.00007269,0.00000449247,0.00004660925],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2866816,"threshold_uncertainty_score":0.1921573,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04254395801968929,"score_gpt":0.2615126920627316,"score_spread":0.2189687340430423,"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."}}