{"id":"W2123128942","doi":"10.1093/bioinformatics/btr184","title":"Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data","year":2011,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":45,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; BC Cancer Agency","funders":"Canadian Institutes of Health Research","keywords":"Genome; Computational biology; LNCaP; Biology; RNA-Seq; Gene; Genetics; Gene expression; Prostate cancer; Cancer; Transcriptome","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":[0.0001284209,0.00009477208,0.0001901435,0.00006352087,0.00002803009,0.000005977187,0.0002133136,0.00006466467,0.000007821685],"category_scores_gemma":[0.00003191283,0.00008443341,0.00003710466,0.0001470124,0.00008694155,0.000003410928,0.0001956575,0.00002844309,4.101237e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004502321,"about_ca_system_score_gemma":0.00001851841,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001189845,"about_ca_topic_score_gemma":0.0000285271,"domain_scores_codex":[0.999384,0.00001524329,0.0003088068,0.000117479,0.0000777521,0.00009675125],"domain_scores_gemma":[0.9992249,0.000006926333,0.0002112507,0.0004443325,0.00008010573,0.00003248972],"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":[0.00003684402,0.00002994443,0.001916567,0.00005361097,0.0006019557,1.162289e-7,0.0003863619,0.00001768118,0.9938856,0.000002851181,0.00009461675,0.002973821],"study_design_scores_gemma":[0.0008136742,0.0004815148,0.02169103,0.00002185042,0.0007539019,0.000001912238,0.0006636972,0.01686217,0.9514531,0.00002808186,0.006901983,0.0003271043],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9883481,0.0004930252,0.009047937,0.000002515282,0.00004220933,0.0001080562,0.001459791,0.000001811815,0.0004965339],"genre_scores_gemma":[0.9955086,0.001326542,0.00247814,0.00002777818,0.000005917913,0.000002754935,0.0006080272,0.000005313569,0.0000369518],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04243255,"threshold_uncertainty_score":0.3443095,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03551003974175679,"score_gpt":0.2413429233919114,"score_spread":0.2058328836501546,"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."}}