{"id":"W3089926889","doi":"10.1128/mbio.02259-20","title":"Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments","year":2020,"lang":"en","type":"article","venue":"mBio","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":48,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Canadian Institutes of Health Research; National Institutes of Health; National Institute of General Medical Sciences; Government of Canada","keywords":"Escherichia coli; Gene; Computational biology; Context (archaeology); Function (biology); Biology; Carbon source; Genome; Genetics; Biochemistry","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":[0.0000698252,0.0001052442,0.0001215243,0.00001399763,0.000009072251,0.000005372915,0.00008013297,0.00008934637,0.000009237826],"category_scores_gemma":[0.00004012908,0.00009557216,0.00003011338,0.00007176537,0.00002571959,0.000001317072,0.00006070883,0.00009768042,0.000003559815],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002089505,"about_ca_system_score_gemma":0.000007061891,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009249681,"about_ca_topic_score_gemma":0.00006986695,"domain_scores_codex":[0.9993168,0.00003682592,0.0001458909,0.0002998873,0.00005247224,0.0001480861],"domain_scores_gemma":[0.9997594,9.548517e-7,0.00002240156,0.0001654142,0.00000294781,0.00004887291],"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":[0.00003749507,0.00007056697,0.02541736,0.00001172402,0.000005066528,0.000001196242,0.00006142809,0.000107333,0.9738554,0.000002248368,0.00002721248,0.0004029186],"study_design_scores_gemma":[0.0003281365,0.00006202424,0.1930343,0.000003769576,0.000003281253,5.766187e-7,0.00001020172,0.000147954,0.8029959,0.00000521019,0.003297791,0.0001108877],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9990316,0.0002432513,0.00005808489,0.0003302337,0.0001226289,0.0001330205,0.000005661995,0.00000651137,0.00006903269],"genre_scores_gemma":[0.9993525,0.00010969,0.0001103286,0.0001261597,0.0001704638,0.000009675176,0.00003782447,0.000009639421,0.00007373845],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1708596,"threshold_uncertainty_score":0.3897319,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00825327424468841,"score_gpt":0.1947504239394687,"score_spread":0.1864971496947803,"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."}}