{"id":"W4367317956","doi":"10.3389/fbinf.2023.1127661","title":"Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy","year":2023,"lang":"en","type":"article","venue":"Frontiers in Bioinformatics","topic":"Extracellular vesicles in disease","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Stan Cassidy Foundation; Dr. Georges-L.-Dumont University Hospital Centre; Atlantic Cancer Research Institute; Vitalité Health Network; Beatrice Hunter Cancer Research Institute; Université de Moncton","funders":"","keywords":"Computational biology; Annotation; RNA; Biomarker discovery; Computer science; Sequence analysis; Biology; Bioinformatics; Proteomics; Gene; Genetics","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":[0.0005533526,0.0001287898,0.0002247744,0.0004460805,0.00002915229,0.00003821885,0.0004684717,0.0001248179,8.558487e-7],"category_scores_gemma":[0.0006774148,0.0001358556,0.00008645403,0.001173209,0.00008108219,0.00007986413,0.0001958844,0.0000510048,0.000002644043],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004985483,"about_ca_system_score_gemma":0.0001076749,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001787384,"about_ca_topic_score_gemma":0.0000268376,"domain_scores_codex":[0.9987502,0.00002935292,0.0005971462,0.0002453334,0.0001432294,0.0002347019],"domain_scores_gemma":[0.9987783,0.00006373588,0.0002226972,0.0008386846,0.00005310674,0.00004347374],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001949481,0.0004740498,0.2313625,0.002459241,0.002044023,0.00002323523,0.002395001,0.09406878,0.5369441,0.0006375813,0.02584902,0.1017931],"study_design_scores_gemma":[0.0008250193,0.00008478922,0.01290865,0.00004528153,0.0001966117,0.000001278823,0.001756205,0.9578761,0.02477155,0.0003521022,0.0008729549,0.0003094081],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.3769528,0.0002510444,0.6215732,0.00003482442,0.0001134737,0.0003999389,0.0005788514,0.00001167045,0.00008429029],"genre_scores_gemma":[0.8971704,0.0001745616,0.09343863,0.00004523781,0.00002925973,0.00007249657,0.009014023,0.00001685543,0.00003857302],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8638074,"threshold_uncertainty_score":0.5540031,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0274389689924735,"score_gpt":0.2896958859495523,"score_spread":0.2622569169570788,"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."}}