{"id":"W2808484533","doi":"10.1186/s12864-018-4835-2","title":"Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)","year":2018,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Genetic Syndromes and Imprinting","field":"Biochemistry, Genetics and Molecular Biology","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; Simon Fraser University; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Killam Trusts; U.S. Department of Veterans Affairs","keywords":"Epigenomics; Biology; Indel; Allele; Genetics; Computational biology; DNA methylation; Epigenome; Gene; Gene expression; Single-nucleotide polymorphism; Genotype","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":[0.0002456225,0.0001118862,0.0001731458,0.00007267579,0.00006171792,0.00001878923,0.0001119412,0.00008571952,0.000002470212],"category_scores_gemma":[0.00001414383,0.0001109029,0.00004396341,0.00007804521,0.00007599058,0.000001947586,0.00008408998,0.00002140486,9.914415e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001413214,"about_ca_system_score_gemma":0.00005561952,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000267409,"about_ca_topic_score_gemma":0.0003460395,"domain_scores_codex":[0.9992108,0.00002003581,0.0002589838,0.0003290413,0.0000407741,0.0001403311],"domain_scores_gemma":[0.9994838,0.000008693758,0.0001144503,0.0002363304,0.00009555086,0.00006117515],"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":[0.0000443955,0.00002608111,0.002463874,0.00001604092,0.0001344317,3.238118e-8,0.000284053,0.00009771138,0.8275405,0.00002284593,0.00001718787,0.1693528],"study_design_scores_gemma":[0.001095689,0.0002754616,0.0440014,0.000003501956,0.000194919,0.000009719596,0.0007030893,0.02117237,0.7953445,0.00009821053,0.1367367,0.0003644057],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7336602,0.000470509,0.2656442,0.000005048731,0.00001874534,0.0001751531,0.00001394745,0.000003424577,0.000008728289],"genre_scores_gemma":[0.8094134,0.00014469,0.1900492,0.00002006093,0.00007675932,0.00001793614,0.0002395434,0.00001388717,0.00002444402],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1689884,"threshold_uncertainty_score":0.452249,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01811735396814028,"score_gpt":0.2562407394253032,"score_spread":0.2381233854571629,"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."}}