{"id":"W2603511150","doi":"10.1101/gr.213983.116","title":"Combinatorial DNA methylation codes at repetitive elements","year":2017,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":47,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institut National Du Cancer; Ligue Contre le Cancer; Université de Strasbourg; Alliance Nationale pour les Sciences de la Vie et de la Santé; Agence Nationale de la Recherche; Centre National de la Recherche Scientifique; CNIB; Fondation pour la Recherche Médicale; Institut National de la Santé et de la Recherche Médicale; Ministry of Higher Education and Scientific Research","keywords":"Biology; DNA methylation; Epigenetics; Transposable element; Genetics; Genome; Repeated sequence; DNA; Epigenomics; RNA-Directed DNA Methylation; Retrotransposon; Methylation; Interspersed repeat; 5-Methylcytosine; Human genome; Gene; Gene expression","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":[0.001818167,0.00009934489,0.0001083213,0.00007049991,0.0009467072,0.0001235762,0.0003792734,0.0001442089,0.00009136288],"category_scores_gemma":[0.0006061553,0.0001000298,0.00005645154,0.00004883746,0.0001849524,0.00000601597,0.000570994,0.000130021,0.0000973339],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007134139,"about_ca_system_score_gemma":0.00007907638,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004931523,"about_ca_topic_score_gemma":0.0000659162,"domain_scores_codex":[0.9984024,0.0002177008,0.0001897652,0.0003887126,0.0004333085,0.0003680885],"domain_scores_gemma":[0.9985941,0.00003131098,0.0001089678,0.0007866411,0.0003698576,0.0001091415],"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":[0.00009456101,0.00003711434,0.006475708,0.000008787048,0.00004069962,0.000002892465,0.00004601688,0.00000604896,0.9894474,0.0008386428,0.0001230119,0.002879126],"study_design_scores_gemma":[0.0007247766,0.0003659192,0.06733354,0.000005463182,0.000006826248,6.479382e-7,0.000032344,0.00002319987,0.8041481,0.004154003,0.1230512,0.0001539775],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9735565,0.0009662951,0.0002383631,0.0001920036,0.0002661721,0.0002891337,0.0000315746,0.000006135469,0.02445379],"genre_scores_gemma":[0.995255,0.0008330114,0.0002593969,0.000008477816,0.0005449105,0.00003491037,0.0002276877,0.00002051804,0.00281609],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1852993,"threshold_uncertainty_score":0.7281402,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06940763368328212,"score_gpt":0.400592951207161,"score_spread":0.3311853175238789,"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."}}