{"id":"W4307379589","doi":"10.1186/s12915-022-01433-w","title":"The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB","year":2022,"lang":"en","type":"article","venue":"BMC Biology","topic":"Wheat and Barley Genetics and Pathology","field":"Agricultural and Biological Sciences","cited_by":67,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; University of Alberta; Agriculture and Agri-Food Canada","funders":"Saskatchewan Wheat Development Commission; Alberta Wheat Commission; Agriculture and Agri-Food Canada; University of Carthage","keywords":"Biology; Effector; Genome; Genetics; Transposable element; Gene; Horizontal gene transfer; Comparative genomics; Genome evolution; Pyrenophora; Genomics; Cell 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":[],"consensus_categories":[],"category_scores_codex":[0.0004252639,0.0001275441,0.0002257561,0.000008510645,0.0006707011,0.0000157428,0.000315971,0.0000899566,0.00008202858],"category_scores_gemma":[0.00003770589,0.00003638588,0.00009207589,0.0002649757,0.000267189,0.000009918716,0.0001213061,0.0001460493,7.309176e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000013436,"about_ca_system_score_gemma":0.00001535931,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001342769,"about_ca_topic_score_gemma":0.001140061,"domain_scores_codex":[0.9987294,0.000432839,0.0001992545,0.0002492346,0.0000979446,0.0002913153],"domain_scores_gemma":[0.9992249,0.0004948259,0.0001017874,0.0000952475,0.00003809196,0.00004512298],"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":[0.00007063067,0.00006529958,0.0537416,0.000004572193,0.00002243719,0.000001117511,0.00007493171,0.000006050022,0.942523,0.0003972493,0.00005539661,0.003037711],"study_design_scores_gemma":[0.0006523923,0.002539515,0.9779931,0.00001694651,0.00007567449,0.0000472474,0.0002927344,0.00002418633,0.004447924,0.001161396,0.01251864,0.0002302273],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955739,0.001573041,0.000004946374,0.00167734,0.000181327,0.0003723614,0.0005264915,0.00001373775,0.00007689027],"genre_scores_gemma":[0.9992515,0.0001305315,0.00002667456,0.0001714065,0.00006104482,0.00006767293,0.00006927104,0.000001683604,0.0002201959],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9380751,"threshold_uncertainty_score":0.5158558,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0182810822913678,"score_gpt":0.1995397272330815,"score_spread":0.1812586449417137,"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."}}