{"id":"W4399437507","doi":"10.1038/s41592-024-02298-3","title":"Systematic assessment of long-read RNA-seq methods for transcript identification and quantification","year":2024,"lang":"en","type":"article","venue":"Nature Methods","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":208,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre","funders":"National Institute of Environmental Health Sciences; National Health and Medical Research Council; National Institute of General Medical Sciences; Ministerio de Ciencia e Innovación; Generalitat de Catalunya; Bundesministerium für Bildung und Forschung; Saint Petersburg State University; Ministry of Education, Culture, Sports, Science and Technology; Centres de Recerca de Catalunya; National Human Genome Research Institute; Wellcome Trust; RIKEN; Japan Agency for Medical Research and Development; National Institutes of Health; Pew Charitable Trusts; U.S. Department of Health and Human Services; Ohio State University; Silicon Valley Community Foundation; European Molecular Biology Laboratory; Wellcome; American Concrete Institute Foundation","keywords":"Computational biology; Annotation; Benchmark (surveying); Replicate; Identification (biology); Computer science; Transcriptome; Genome; RNA-Seq; DNA sequencing; Biology; Nanopore sequencing; Reference genome; Bioinformatics; Gene; Genetics; Gene expression","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":[0.002757312,0.0001389484,0.000275527,0.00007224055,0.00005893376,0.00004415907,0.0001265145,0.0002554111,0.000002157457],"category_scores_gemma":[0.0003149797,0.0001158254,0.0001317293,0.0001146411,0.00005401471,0.000001523383,0.00002989855,0.0001222548,2.046113e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000124751,"about_ca_system_score_gemma":0.00004869411,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003386814,"about_ca_topic_score_gemma":0.000003128089,"domain_scores_codex":[0.9986078,0.0004311424,0.0003879495,0.000375128,0.00007510164,0.000122953],"domain_scores_gemma":[0.9991216,0.0002556412,0.0001161237,0.000317041,0.0001557115,0.00003390553],"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":[0.00001021329,0.00001752437,0.00004177738,0.004800205,0.000227875,1.439935e-7,0.0001044794,0.00001077252,0.947479,0.002712832,0.00007187765,0.04452332],"study_design_scores_gemma":[0.0002334616,0.0001613649,0.004494479,0.0005089747,0.0004314706,0.00001260773,0.0001347127,0.005781034,0.9792109,0.002885623,0.005921152,0.0002242534],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.02053732,0.08083611,0.8967777,0.0001985568,0.0008244829,0.0006472846,0.00002881364,0.000006879156,0.0001427981],"genre_scores_gemma":[0.4700979,0.001019331,0.5281841,0.00003422215,0.00008526711,0.0001527829,0.00004532629,0.00002063956,0.0003604706],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.4495606,"threshold_uncertainty_score":0.4723222,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02810561204954477,"score_gpt":0.4453823952405557,"score_spread":0.417276783191011,"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."}}