{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003435845,0.0002102946,0.0002973153,0.000108498,0.00005442255,0.000009855818,0.0001767377,0.0003274435,0.0001179089],"category_scores_gemma":[0.0001393673,0.0001607512,0.00008081037,0.0001873955,0.00009320457,0.00000490813,0.00007556282,0.00009565744,0.00004142164],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000216477,"about_ca_system_score_gemma":0.00008115161,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003029961,"about_ca_topic_score_gemma":0.00007069445,"domain_scores_codex":[0.9985899,0.000177602,0.0003558451,0.0004822572,0.0001041988,0.0002902496],"domain_scores_gemma":[0.9989334,0.0001077284,0.0002681629,0.0004375979,0.0001809127,0.00007218063],"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":[0.0004553306,0.00003808908,0.003574485,0.00002649418,0.00008698976,0.000001364464,0.00004409584,0.001836958,0.9834704,0.00003399614,8.198197e-7,0.01043096],"study_design_scores_gemma":[0.0006766705,0.002649889,0.004907553,0.00000625036,0.00003382817,0.000005628398,0.0000382646,0.0002380028,0.9783691,0.0003757873,0.01244165,0.0002573883],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9788054,0.001844671,0.01817312,0.00003945317,0.0001866066,0.0004135918,0.00004630147,0.00001698015,0.0004739162],"genre_scores_gemma":[0.9969886,0.0003413337,0.001354316,0.00005374611,0.0001846506,0.00001750925,0.0003149723,0.00003222514,0.0007126667],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01818322,"threshold_uncertainty_score":0.6555244,"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."}}