{"id":"W2053812068","doi":"10.1093/nar/gkl365","title":"Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria","year":2006,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Legume Nitrogen Fixing Symbiosis","field":"Agricultural and Biological Sciences","cited_by":120,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Natural Sciences and Engineering Research Council of Canada; Ontario Genomics; Ontario Genomics Institute; Genome Canada","keywords":"Biology; Sinorhizobium meliloti; Genome; Promoter; Genetics; Proteobacteria; Microbiology; Computational biology; Gene; Symbiosis; Bacteria; Gene expression","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":[0.0009090109,0.0001179515,0.0001859578,0.00007314242,0.0001301024,0.00006116183,0.0002473894,0.0001587733,0.0002383096],"category_scores_gemma":[0.00007006041,0.00005397982,0.00004215384,0.0008288283,0.0002219558,0.000166525,0.0001493488,0.0002579301,0.00002301237],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009167893,"about_ca_system_score_gemma":0.00001756603,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001648429,"about_ca_topic_score_gemma":0.000257477,"domain_scores_codex":[0.9981467,0.0002602052,0.0003018178,0.0003681922,0.0004778818,0.0004452499],"domain_scores_gemma":[0.9995076,0.00008582271,0.00006169281,0.00009646935,0.0001738309,0.00007455996],"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":[0.0000634275,0.0001111666,0.04994703,0.00001861055,0.000007181222,0.000004179865,0.00009310492,1.083547e-7,0.9479299,0.0000458399,0.00008604445,0.001693429],"study_design_scores_gemma":[0.0002315444,0.0003601467,0.8393503,0.00003264827,0.000003445484,0.000004942436,0.00009300866,0.00001799561,0.1587718,0.0005838808,0.0004681964,0.00008211932],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.997321,0.00009103538,7.483015e-8,0.0007153527,0.00002986145,0.000678378,0.00006042933,0.00004864011,0.001055305],"genre_scores_gemma":[0.9993905,0.000008172375,0.000122021,0.000007675477,0.0001202567,0.00003719288,0.00006635003,0.000002593727,0.0002451727],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7894033,"threshold_uncertainty_score":0.2609323,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02824391321404294,"score_gpt":0.251606104438919,"score_spread":0.2233621912248761,"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."}}