{"id":"W2399841009","doi":"10.1186/s12864-016-2690-6","title":"Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements","year":2016,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Fungal and yeast genetics research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":227,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Ministry of Education, Culture, Sports, Science and Technology; Japan Society for the Promotion of Science; Biotechnology and Biological Sciences Research Council; Directorate for Biological Sciences; Gatsby Charitable Foundation","keywords":"Biology; Setaria; Eleusine; Magnaporthe; Oryza sativa; Pyricularia; Nonsynonymous substitution; Genetics; Genome; Monophyly; Oryza; Gene; Magnaporthe grisea; Phylogenetic tree; Botany; Finger millet; Clade","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001397862,0.0000985653,0.00012108,0.00002894011,0.00004012796,0.000006928227,0.0001735011,0.00008011295,0.0000258969],"category_scores_gemma":[0.00003647204,0.00006000255,0.00004216541,0.0001018015,0.0001025895,0.000001814294,0.00008081374,0.00002629773,0.000001986632],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002000742,"about_ca_system_score_gemma":0.0001252848,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000923847,"about_ca_topic_score_gemma":0.0008789163,"domain_scores_codex":[0.9992404,0.00004641701,0.0002008952,0.0001983966,0.0001445094,0.0001693915],"domain_scores_gemma":[0.9994452,0.00001182355,0.0001022979,0.0002418993,0.0001462476,0.00005253389],"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":[0.0001511943,0.00003813557,0.1639653,0.00002331926,0.00004166347,2.85998e-7,0.00008671433,0.00009654229,0.8349963,0.000007990789,0.000046714,0.0005458603],"study_design_scores_gemma":[0.00110216,0.0004578819,0.07300728,0.0000573606,0.00003284094,0.000002626128,0.0000667734,0.0002959051,0.9228258,0.00003443579,0.001959231,0.0001577132],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9976456,0.0002205492,0.001384072,0.00008866514,0.00003540779,0.0002709926,0.0002459821,0.000001931045,0.0001067794],"genre_scores_gemma":[0.9978356,0.0003036066,0.0004103077,0.00003962386,0.00003568659,0.000006565188,0.00002800164,0.00001871632,0.001321861],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.090958,"threshold_uncertainty_score":0.2446833,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01105179087911627,"score_gpt":0.23689570927624,"score_spread":0.2258439183971237,"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."}}