{"id":"W4390011662","doi":"10.21769/bioprotoc.4904","title":"Identifying Antigenic Switching by Clonal Cell Barcoding and Nanopore Sequencing in &lt;em&gt;Trypanosoma brucei&lt;/em&gt;","year":2023,"lang":"en","type":"article","venue":"BIO-PROTOCOL","topic":"Trypanosoma species research and implications","field":"Medicine","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Alliance de recherche numérique du Canada; Islamic Development Bank","keywords":"Biology; Genetics; Gene; Trypanosoma brucei; Population; DNA sequencer; DNA sequencing; Computational biology","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000192608,0.0003983514,0.0005133743,0.0006838372,0.000498138,0.0002955102,0.0003744295,0.0002582054,0.0003482843],"category_scores_gemma":[0.0003214735,0.0003756416,0.0001657178,0.001500704,0.0001194784,0.0004072028,0.000400833,0.0006326983,0.0003044411],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004918657,"about_ca_system_score_gemma":0.000554679,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001041541,"about_ca_topic_score_gemma":0.0001873862,"domain_scores_codex":[0.9961134,0.0001283817,0.00080159,0.0008691834,0.0009385715,0.001148853],"domain_scores_gemma":[0.9982848,0.0001703232,0.0002055983,0.0006724425,0.0001559635,0.0005108365],"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":[0.0001372247,0.00008694247,0.007742587,0.0006954586,0.00003051719,0.0001595155,0.0006260471,0.000002471787,0.9749067,0.0002066698,0.009492178,0.005913647],"study_design_scores_gemma":[0.01130767,0.0007201174,0.5221375,0.001486048,0.00005522146,0.0003230251,0.002718254,0.00272898,0.3174716,0.0009470911,0.1388853,0.00121922],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7379615,0.00007741643,0.0002303396,0.0006719197,0.00009333326,0.2579045,0.00006970911,0.0003773434,0.002613995],"genre_scores_gemma":[0.5889136,0.00003488397,0.001252347,0.0002309281,0.0003377054,0.4068357,0.00009929661,0.0001072645,0.002188282],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6574352,"threshold_uncertainty_score":0.9998695,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04577567489807454,"score_gpt":0.3415799068955034,"score_spread":0.2958042319974288,"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."}}