{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003249828,0.0002041128,0.0001978019,0.0002701435,0.0005685235,0.0001549054,0.0001607182,0.0002987411,0.0001172193],"category_scores_gemma":[0.0007760964,0.0002100613,0.00006342331,0.0003779677,0.0001093432,0.00003590996,0.0003899221,0.0002617149,0.00004893615],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004363165,"about_ca_system_score_gemma":0.00009702263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009963985,"about_ca_topic_score_gemma":0.00005995532,"domain_scores_codex":[0.996637,0.001094444,0.0004665815,0.0007073482,0.0005170926,0.0005775023],"domain_scores_gemma":[0.9984064,0.0002860947,0.0001773452,0.0004676274,0.0004791107,0.0001834163],"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":[0.00002418805,0.00001974396,0.000348573,0.00001634545,0.00003637933,6.553091e-7,0.0002222837,0.003116361,0.9697821,0.00004337792,0.00005449912,0.02633551],"study_design_scores_gemma":[0.0005288133,0.000450701,0.05195538,0.00002454996,0.00003157379,0.000002726624,0.0002002547,0.0419586,0.8903058,0.01003326,0.004136927,0.000371473],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7137936,0.005209669,0.279275,0.0001768712,0.0001496015,0.0005243676,0.00001841249,0.00002331579,0.0008291425],"genre_scores_gemma":[0.8454117,0.0003766148,0.1526898,0.00001921957,0.0004909125,0.0001433354,0.0003610403,0.00003812924,0.0004692592],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1316181,"threshold_uncertainty_score":0.8566049,"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."}}