{"id":"W19422881","doi":"10.1101/gr.192005.115","title":"Bacterial infection remodels the DNA methylation landscape of human dendritic cells","year":2015,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":240,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University and Génome Québec Innovation Centre; University of British Columbia; Child and Family Research Institute; Université de Montréal; Centre Hospitalier Universitaire Sainte-Justine","funders":"National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; Canadian Institutes of Health Research; National Institutes of Health; Compute Canada; Canada Research Chairs; Canadian Institute for Advanced Research","keywords":"Biology; DNA demethylation; DNA methylation; Epigenetics; Chromatin; Histone; Epigenomics; Epigenetics of physical exercise; Enhancer; DNA; Cell biology; Methylation; Regulation of gene expression; Genetics; Demethylation; Transcription (linguistics); Gene; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001101614,0.00009263607,0.0001289086,0.0001926172,0.0001248207,0.0002221989,0.00007847208,0.0001306356,0.0006559927],"category_scores_gemma":[0.0001894627,0.00010717,0.0001095761,0.0001394884,0.0001108509,0.00007952719,0.0001634886,0.0002105429,0.0002383653],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001505596,"about_ca_system_score_gemma":0.0001624285,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001218461,"about_ca_topic_score_gemma":0.001539538,"domain_scores_codex":[0.9999229,0.0000112789,0.000004540429,0.00002385368,0.00001826877,0.0000192786],"domain_scores_gemma":[0.9999434,0.00001244829,0.00001178971,0.000009380647,0.00001200768,0.00001095739],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001194406,0.000007960006,0.004551814,0.00001400194,0.000007732848,0.00002728098,0.00003604883,0.00006930235,0.9925289,0.00003523714,0.00003196403,0.002570411],"study_design_scores_gemma":[0.00002939678,0.0002563564,0.1852804,0.00001006463,0.0000339209,0.0005845235,0.0002113379,0.001903841,0.8072848,0.000340971,0.004050562,0.00001386694],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9971297,0.0008637395,0.001181311,0.00005044525,0.00000554588,0.000007474122,0.0003026155,0.00001749455,0.0004416016],"genre_scores_gemma":[0.9978448,0.0004585159,0.0006806757,0.00004084872,0.000004261688,0.000007970946,0.000418684,0.000007231451,0.0005369835],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001218461,"threshold_uncertainty_score":0.00242269,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08844769575239227,"score_gpt":0.3669222423589964,"score_spread":0.2784745466066041,"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."}}