{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002708419,0.002216096,0.001077674,0.002309494,0.0007649667,0.001850549,0.002040536,0.0009591528,0.009353505],"category_scores_gemma":[0.005112514,0.001106482,0.001811731,0.001212022,0.0004879769,0.001507652,0.002756058,0.002271504,0.00537078],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006776213,"about_ca_system_score_gemma":0.001968067,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002156558,"about_ca_topic_score_gemma":0.00328502,"domain_scores_codex":[0.9989449,0.0001232998,0.0001001721,0.0004254294,0.0003116656,0.0000945882],"domain_scores_gemma":[0.998245,0.0005853527,0.0001866333,0.0003986458,0.0003990367,0.000185396],"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":[0.001920903,0.0002846674,0.01942518,0.002029426,0.001589459,0.00106128,0.001062041,0.01659546,0.4550307,0.00816956,0.08271281,0.4101186],"study_design_scores_gemma":[0.0003230574,0.0004061526,0.032257,0.0001903992,0.00042958,0.001241876,0.0002335175,0.3027535,0.4940225,0.02148373,0.1461733,0.0004854008],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01242399,0.000250703,0.8040555,0.0002505242,0.0001059464,0.0003957556,0.01493172,0.1660622,0.001523731],"genre_scores_gemma":[0.05701795,0.0002795405,0.8918735,0.0003604725,0.00006080505,0.001644884,0.03238479,0.01397147,0.002406621],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.009353505,"threshold_uncertainty_score":0.03129065,"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."}}