{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001984262,0.00007351295,0.0000914199,0.00009571659,0.0001285174,0.00003527293,0.0001514206,0.000118759,0.00003091947],"category_scores_gemma":[0.0001286345,0.00005846913,0.00004464224,0.0001880735,0.0000923227,0.000004650075,0.0001250361,0.0001200877,0.00001802628],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002238265,"about_ca_system_score_gemma":0.0001089263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009462832,"about_ca_topic_score_gemma":0.0000680997,"domain_scores_codex":[0.9986597,0.0003827291,0.0001949358,0.0002035897,0.0003364359,0.0002225546],"domain_scores_gemma":[0.9990665,0.00003109032,0.00005463324,0.0003405641,0.0004290384,0.00007819066],"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":[0.00003353094,0.00002747595,0.0004725851,0.00001084926,0.00001654381,3.055722e-7,0.0001291048,0.0002617185,0.9977513,0.00009466261,0.0001345323,0.001067381],"study_design_scores_gemma":[0.0003641924,0.0004519954,0.00542394,0.000003773413,0.000008318148,8.219861e-7,0.00006275659,0.000102647,0.9807934,0.001615809,0.01109072,0.00008157818],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942874,0.0008523819,0.001029589,0.00006483798,0.0001305089,0.0002215779,0.00000832866,0.00000467406,0.003400702],"genre_scores_gemma":[0.9985386,0.000248502,0.0001393586,0.000004660676,0.0004319024,0.00001520707,0.0001285149,0.00001486751,0.0004784073],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01695787,"threshold_uncertainty_score":0.2384302,"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."}}