{"id":"W2124748744","doi":"10.1101/gr.152231.112","title":"Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods","year":2013,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":161,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; University of British Columbia; BC Cancer Agency","funders":"National Institute of Environmental Health Sciences; National Human Genome Research Institute; National Institute on Drug Abuse; Sontag Foundation; National Cancer Institute; March of Dimes Foundation; National Institutes of Health; Edward Mallinckrodt, Jr. Foundation; Dermatology Foundation","keywords":"Methylated DNA immunoprecipitation; Bisulfite sequencing; Illumina Methylation Assay; DNA methylation; Biology; Differentially methylated regions; Computational biology; CpG site; Bisulfite; DNA sequencing; Genetics; Deep sequencing; Genome; Human genome; DNA; Gene; 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":[0.002272205,0.0009226464,0.0006989497,0.001441678,0.0003022715,0.0007219958,0.001030826,0.0008767236,0.001318838],"category_scores_gemma":[0.004529792,0.0006766043,0.00101842,0.0009130738,0.0004219313,0.0008740887,0.0005990666,0.001042141,0.0009158564],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006690874,"about_ca_system_score_gemma":0.000808292,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003787641,"about_ca_topic_score_gemma":0.00528763,"domain_scores_codex":[0.9989837,0.000159335,0.00005492609,0.0003667244,0.0003886241,0.00004672604],"domain_scores_gemma":[0.9987154,0.0007010708,0.0001936235,0.0001537887,0.0002006387,0.00003552003],"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":[0.0005172478,0.0001334484,0.03124419,0.0006554845,0.000392254,0.000111326,0.0001536647,0.2202992,0.48287,0.005385725,0.001367174,0.2568704],"study_design_scores_gemma":[0.00002544676,0.0001910862,0.01447909,0.0000447401,0.00008995269,0.0001652213,0.00003163569,0.764761,0.2088961,0.00716678,0.004068667,0.00008022471],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.06498721,0.0005238803,0.9305967,0.00007777501,0.00001965287,0.00006762535,0.0008911964,0.001847929,0.0009880128],"genre_scores_gemma":[0.2762522,0.0007228167,0.7182902,0.0001052461,0.00002116124,0.0001878623,0.002639505,0.0003500431,0.001430945],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003787641,"threshold_uncertainty_score":0.01201671,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1273657141965672,"score_gpt":0.38973497850028,"score_spread":0.2623692643037129,"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."}}