{"id":"W2780622732","doi":"10.1093/bioinformatics/btx839","title":"ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data","year":2017,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre","funders":"National Human Genome Research Institute; National Institutes of Health","keywords":"Annotation; splice; Sequence assembly; Exon; Computational biology; Genome; Transcriptome; Computer science; Whole genome sequencing; Genome project; Graph; RNA splicing; Genetics; Exon skipping; Gene Annotation; Biology; Alternative splicing; Gene; Theoretical computer science; RNA; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002848815,0.002061295,0.001180176,0.00267412,0.001339379,0.002195249,0.003104749,0.001488314,0.02004436],"category_scores_gemma":[0.008393278,0.001824265,0.001991981,0.002344799,0.001095887,0.0018486,0.003087259,0.002839998,0.01424407],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008010215,"about_ca_system_score_gemma":0.002115256,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003028437,"about_ca_topic_score_gemma":0.005753535,"domain_scores_codex":[0.9984816,0.000207068,0.0001107297,0.0006052184,0.0004473923,0.0001480184],"domain_scores_gemma":[0.9971571,0.001261498,0.0003126732,0.0006915195,0.0003577337,0.0002195241],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001561,0.0002477872,0.009650181,0.004061407,0.0009303084,0.001537126,0.00111613,0.0210465,0.07376696,0.007301114,0.5066823,0.3720993],"study_design_scores_gemma":[0.0009439246,0.0005720584,0.02109412,0.0007886203,0.0004247602,0.002846957,0.0004400713,0.3865239,0.2061403,0.04315842,0.33642,0.0006469381],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01567089,0.00048395,0.4796267,0.0004457476,0.0004237616,0.0006641024,0.05175209,0.4462771,0.004655522],"genre_scores_gemma":[0.04494203,0.0004143003,0.7575334,0.0006462089,0.0001381765,0.001214371,0.13687,0.05313554,0.005105882],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02004436,"threshold_uncertainty_score":0.06705505,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05435405250254151,"score_gpt":0.2784282938971421,"score_spread":0.2240742413946006,"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."}}