{"id":"W2211682249","doi":"10.1186/s13059-015-0856-1","title":"Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation","year":2015,"lang":"en","type":"article","venue":"Genome biology","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":107,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill Genome Centre; McGill University and Génome Québec Innovation Centre; McGill University","funders":"Division of Mathematical Sciences; Seventh Framework Programme; Fonds de Recherche du Québec - Santé; NIHR Biomedical Research Centre, Royal Marsden NHS Foundation Trust/Institute of Cancer Research; National Institutes of Health; King's College London; Université de Genève; University of Oxford; National Institute for Health and Care Research; McGill University; Génome Québec; Canadian Institutes of Health Research; Wellcome; Queen Mary University of London; Wellcome Trust","keywords":"Biology; DNA methylation; Genetics; CpG site; Epigenetics; Bisulfite sequencing; Methylation; Genetic variation; Population; Enhancer; 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":[0.001092943,0.0001796086,0.0001983194,0.00003650028,0.0002435722,0.00002543131,0.000328864,0.0001826864,0.00001614904],"category_scores_gemma":[0.00006820424,0.0001149099,0.00007951891,0.00008810145,0.0001657302,0.000005528635,0.0002328207,0.00009782048,0.00003073143],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007227579,"about_ca_system_score_gemma":0.00004331185,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006385222,"about_ca_topic_score_gemma":0.00009257926,"domain_scores_codex":[0.9984359,0.0003471352,0.0004034688,0.000364401,0.0001526833,0.0002963979],"domain_scores_gemma":[0.9989591,0.00003205781,0.0003038299,0.0005522313,0.00007970238,0.00007307269],"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":[0.00002077061,0.00001812366,0.002032906,0.000004263988,0.00005314048,3.467446e-7,0.001570996,0.003242638,0.9914714,0.0008182109,0.00000140387,0.0007657859],"study_design_scores_gemma":[0.001735997,0.001941832,0.1599248,0.000008925805,0.0001248082,0.00001284621,0.0009120498,0.0002248899,0.4588152,0.01210441,0.363493,0.0007012596],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9916493,0.002922107,0.004289406,0.0003752927,0.0001465847,0.0003273434,0.00003904149,0.00001090933,0.0002400612],"genre_scores_gemma":[0.9976721,0.0001056879,0.0003341271,0.00008967795,0.0003970745,0.00003070159,0.000766334,0.00002245927,0.0005818126],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5326563,"threshold_uncertainty_score":0.4685891,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03126932285189862,"score_gpt":0.3071811783947347,"score_spread":0.2759118555428361,"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."}}