{"id":"W1998847489","doi":"10.1073/pnas.0811669106","title":"Pathogenic adaptation of intracellular bacteria by rewiring a <i>cis</i> -regulatory input function","year":2009,"lang":"en","type":"article","venue":"Proceedings of the National Academy of Sciences","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":63,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada; McMaster University","funders":"Ontario Ministry of Research and Innovation; Canadian Institutes of Health Research; National Institute of General Medical Sciences; Public Health Agency; Public Health Agency of Canada; National Institutes of Health; National Science Foundation","keywords":"Biology; Horizontal gene transfer; Genetics; Gene; Salmonella; Regulator gene; Pathogenicity island; Mutation; Adaptation (eye); Regulatory sequence; Regulation of gene expression; Pathogen; Mutant; Function (biology); Computational biology; Bacteria; Phylogenetics","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002103256,0.0004374828,0.0002418166,0.0002051719,0.000126865,0.0003690581,0.000290519,0.0002633503,0.0009602376],"category_scores_gemma":[0.0003171068,0.0001597548,0.0002691518,0.00009285736,0.0003085919,0.0002338393,0.000357818,0.0005738307,0.0003272347],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003133355,"about_ca_system_score_gemma":0.0001899141,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002981335,"about_ca_topic_score_gemma":0.0005001873,"domain_scores_codex":[0.999832,0.00002213616,0.0000093648,0.00004697115,0.00005371215,0.00003562077],"domain_scores_gemma":[0.9998216,0.00003728798,0.00004548005,0.00004662144,0.00002108353,0.00002789595],"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":[0.00001542806,0.00000827955,0.0003879063,0.000005382875,0.000001884226,0.00002022466,0.000006696791,0.0001341968,0.998325,0.0001069944,0.000004482138,0.0009835013],"study_design_scores_gemma":[0.00000724658,0.0001898791,0.006108777,0.000004906977,0.00001759365,0.0004267862,0.00003575044,0.005316632,0.9869077,0.0002329304,0.0007446682,0.000007054593],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895371,0.0001503057,0.008887324,0.00005201173,0.000008887446,0.00001140273,0.00004412225,0.0001499536,0.001158837],"genre_scores_gemma":[0.9940279,0.00009501391,0.004976098,0.00003854188,0.000003926139,0.00001093132,0.00007381296,0.00003554985,0.0007383708],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009602376,"threshold_uncertainty_score":0.003212273,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01460026739400609,"score_gpt":0.2354800798567121,"score_spread":0.220879812462706,"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."}}