{"id":"W4319037052","doi":"10.24072/pci.genomics.100166","title":"A workflow for studying enigmatic non-autonomous transposable elements across bacteria","year":2023,"lang":"en","type":"article","venue":"Peer Community In Genomics","topic":"Infections and bacterial resistance","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"","keywords":"Transposase; Transposable element; Mobile genetic elements; Biology; Genome; Bacterial genome size; Computational biology; Stenotrophomonas maltophilia; Insertion sequence; Workflow; Evolutionary biology; Genetics; Pseudomonas aeruginosa; Computer science; Bacteria; Gene; Database","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0009666217,0.0001359705,0.0001692432,0.00004441211,0.0004065541,0.00007412688,0.0003070058,0.0001063721,0.000008917496],"category_scores_gemma":[0.00007399191,0.0001519192,0.00008033574,0.0001597797,0.00003860507,0.000006115109,0.00014022,0.0001670467,0.00001511839],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006789125,"about_ca_system_score_gemma":0.00006198673,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008631063,"about_ca_topic_score_gemma":0.001785584,"domain_scores_codex":[0.9990395,0.00009801907,0.0002812547,0.0001452386,0.00006549975,0.0003705343],"domain_scores_gemma":[0.9993043,0.00004772795,0.00006338774,0.0004563145,0.00008746271,0.00004080997],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003851563,0.000373503,0.01609472,0.0001971454,0.0001228438,0.000002632006,0.00505577,0.00130365,0.967376,0.0000261037,0.001005532,0.008056924],"study_design_scores_gemma":[0.01237506,0.00196183,0.1710431,0.0002649212,0.0001253495,0.00002077544,0.01194813,0.01010902,0.2618966,0.002246661,0.525615,0.002393611],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9978423,0.00002049622,0.0009287524,0.00009059212,0.0002814227,0.0004208916,0.0001818086,0.0000210461,0.0002126557],"genre_scores_gemma":[0.9955739,0.00007257693,0.002428812,0.00008536697,0.00009808935,0.000153332,0.0007258279,0.00002909,0.0008330414],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7054794,"threshold_uncertainty_score":0.6195086,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03102464476199924,"score_gpt":0.3077212617556718,"score_spread":0.2766966169936726,"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."}}