{"id":"W2989638633","doi":"10.1186/s13059-019-1853-6","title":"EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation","year":2019,"lang":"en","type":"article","venue":"Genome biology","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":44,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of General Medical Sciences; National Institutes of Health; School of Medicine, New York University; York University","keywords":"DNA methylation; CTCF; Biology; Chromatin; Computational biology; DNA; Transcription factor; ChIP-sequencing; Bisulfite sequencing; Methylation; Genetics; Epigenetics; Gene; Enhancer; Gene expression; Chromatin remodeling","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001067715,0.0009160898,0.0007439507,0.0008544738,0.000384622,0.0007125342,0.0009877251,0.0008319701,0.003992532],"category_scores_gemma":[0.001050513,0.0006933117,0.0004346224,0.0005642105,0.0005243671,0.0007331693,0.001058801,0.001660578,0.001671093],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003207673,"about_ca_system_score_gemma":0.0004006426,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004636925,"about_ca_topic_score_gemma":0.001978666,"domain_scores_codex":[0.9991392,0.0001243334,0.00005976422,0.000335154,0.000256945,0.00008460721],"domain_scores_gemma":[0.9991984,0.0003065707,0.000132709,0.0001269407,0.0001304435,0.0001050151],"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":[0.00008604422,0.00001423153,0.0003833343,0.0000825789,0.00001732723,0.00001721822,0.00002016926,0.00006665787,0.9947884,0.0001839465,0.0002044824,0.004135595],"study_design_scores_gemma":[0.000020261,0.0001181201,0.004933739,0.000009797525,0.00002350053,0.0001685905,0.00001740178,0.003697831,0.985212,0.0002724372,0.005499379,0.00002698129],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2820395,0.002343419,0.6954423,0.0003807535,0.0002598991,0.0005159046,0.008433859,0.004881218,0.005703275],"genre_scores_gemma":[0.3438368,0.002531594,0.6223354,0.0008927567,0.0001333116,0.002075216,0.0118005,0.001168658,0.01522573],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003992532,"threshold_uncertainty_score":0.01335633,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01028221844830421,"score_gpt":0.2517364274065773,"score_spread":0.2414542089582731,"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."}}