{"id":"W2572935401","doi":"10.1186/s12864-017-3489-9","title":"Medium throughput bisulfite sequencing for accurate detection of 5-methylcytosine and 5-hydroxymethylcytosine","year":2017,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":37,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University and Génome Québec Innovation Centre; Douglas Mental Health University Institute; McGill University","funders":"Canadian Institutes of Health Research; National Institutes of Health; Fondation Bettencourt Schueller; Fondation pour la Recherche Médicale; National Institute on Drug Abuse; Fondation Fyssen; Canada Research Chairs; Fondation Pierre Deniker pour la Recherche et la Prévention en Santé Mentale; Scottish Rite Charitable Foundation of Canada; American Foundation for Suicide Prevention","keywords":"Bisulfite; Bisulfite sequencing; 5-Methylcytosine; DNA methylation; Biology; Methylated DNA immunoprecipitation; 5-Hydroxymethylcytosine; Computational biology; Epigenetics; DNA; DNA microarray; genomic DNA; DNA nanoball sequencing; DNA sequencing; Sequencing by ligation; Genome; Cytosine; Illumina Methylation Assay; Genetics; Gene; Genomic library; Base sequence; Gene expression","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":[0.0004093941,0.0001471488,0.0001896456,0.00004463297,0.0002511784,0.0000568346,0.0001898741,0.0001662671,0.000001553512],"category_scores_gemma":[0.0003827235,0.0001478134,0.00008099411,0.00002599643,0.0001177441,0.000009711041,0.0001424366,0.00005062021,8.423193e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002410622,"about_ca_system_score_gemma":0.0001057997,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006326044,"about_ca_topic_score_gemma":0.0002964033,"domain_scores_codex":[0.9991138,0.00003167087,0.0002739796,0.0003171651,0.00007622693,0.0001871584],"domain_scores_gemma":[0.9988923,0.00003628803,0.0003442725,0.0005241667,0.0001410253,0.00006193777],"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":[0.00008816268,0.00001033947,0.001496603,0.00005673025,0.00002604819,1.528422e-7,0.00005281961,0.0002494574,0.9935362,0.00002907224,0.000007375558,0.004447029],"study_design_scores_gemma":[0.0007520847,0.0002573676,0.007404774,0.000009879219,0.00003914264,0.000002212501,0.00004338395,0.001536943,0.983945,0.000656754,0.005186216,0.0001662984],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8822505,0.001777362,0.1152143,0.00005397495,0.0002354306,0.0002784994,0.00004064342,0.000006020764,0.0001432633],"genre_scores_gemma":[0.9842228,0.00101608,0.01416382,0.00002315052,0.0003250087,0.00002086903,0.00004910894,0.00003046576,0.0001487071],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1019723,"threshold_uncertainty_score":0.6027656,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03762992640890085,"score_gpt":0.2965026454378771,"score_spread":0.2588727190289763,"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."}}