{"id":"W4407107571","doi":"10.1038/s41588-024-02069-y","title":"A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity","year":2025,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Wheat and Barley Genetics and Pathology","field":"Agricultural and Biological Sciences","cited_by":41,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"Carlsbergfondet; Grains Research and Development Corporation; Biotechnology and Biological Sciences Research Council; Rural and Environment Science and Analytical Services Division; Genome Canada","keywords":"Biology; Transcriptome; RNA-Seq; Genome; Genetics; Computational biology; Gene; Gene expression profiling; Reference genome; Gene expression","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":[0.0001988673,0.0001550398,0.0002442988,0.00002701072,0.0001135983,0.00002029958,0.0003232406,0.0003959704,0.0002520471],"category_scores_gemma":[0.00001369502,0.0000705042,0.0001433931,0.0002920634,0.0001217372,0.00001719111,0.00003663811,0.0003146009,0.000007808999],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001403993,"about_ca_system_score_gemma":0.00002226924,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003091112,"about_ca_topic_score_gemma":0.0003435072,"domain_scores_codex":[0.9988604,0.00007507898,0.0002877211,0.0002866507,0.0002308175,0.0002593733],"domain_scores_gemma":[0.9995852,0.00005542446,0.00005579219,0.00009201824,0.0001494013,0.00006218116],"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":[0.00005231984,0.00009259232,0.01051635,0.0000242912,0.00003064589,0.000002831974,0.00005484652,0.000009538204,0.9688439,0.00362913,0.001042783,0.01570079],"study_design_scores_gemma":[0.0004613444,0.0003431573,0.8693693,0.00003929316,0.0000800827,0.000009684428,0.0001128481,0.00004385494,0.05541211,0.01954177,0.05429098,0.0002955365],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9864254,0.007852616,0.00006037327,0.001290785,0.0006016311,0.0002003435,0.0002580856,0.00002813755,0.003282616],"genre_scores_gemma":[0.9969021,0.0004784908,0.0007785098,0.0008804807,0.0001718737,0.000006476278,0.00008734421,0.000001220655,0.0006934662],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9134318,"threshold_uncertainty_score":0.3054086,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02193695844020681,"score_gpt":0.2573770969075235,"score_spread":0.2354401384673167,"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."}}