{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.006434803,0.001277752,0.0008391892,0.003539845,0.0007888764,0.00237076,0.0008498812,0.001063569,0.002028515],"category_scores_gemma":[0.01482985,0.0004635462,0.001132064,0.001916239,0.0006776826,0.001325698,0.001084569,0.00139843,0.001841969],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007590337,"about_ca_system_score_gemma":0.001300502,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007891249,"about_ca_topic_score_gemma":0.001795795,"domain_scores_codex":[0.9963655,0.001052351,0.0004272058,0.001110376,0.0009271682,0.0001173215],"domain_scores_gemma":[0.9898665,0.006047545,0.001467905,0.001080272,0.001274867,0.0002628725],"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":[0.002589944,0.0003562236,0.03216802,0.002828784,0.0008251881,0.001675467,0.001599612,0.01711893,0.5551277,0.007039523,0.01122926,0.3674413],"study_design_scores_gemma":[0.0001534733,0.000615178,0.03970281,0.0005806684,0.0003301684,0.001994557,0.0008865789,0.3659477,0.4955837,0.03699819,0.05685233,0.0003546665],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.06978817,0.001248877,0.8885108,0.0007728607,0.0001921434,0.0003765005,0.01132855,0.02613031,0.001651805],"genre_scores_gemma":[0.1742516,0.0006537312,0.8090998,0.0006828713,0.0001016297,0.0006985363,0.01093001,0.002333278,0.001248561],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.006434803,"threshold_uncertainty_score":0.03403085,"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."}}