{"id":"W4408724690","doi":"10.1101/gr.279240.124","title":"Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA","year":2025,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University and Génome Québec Innovation Centre; McGill Genome Centre; Montreal Heart Institute","funders":"","keywords":"Biology; DNA methylation; Methylation; CpG site; Genetics; Alu element; Quantitative trait locus; Human genome; Genome; Computational biology; DNA; Gene; Gene expression","routes":{"ca_aff":true,"ca_fund":false,"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":[0.00103597,0.0000873301,0.0001266037,0.0001499021,0.000120994,0.00002343155,0.00009794976,0.0001302524,0.00001528171],"category_scores_gemma":[0.0002072223,0.00008587757,0.00004411732,0.0002537841,0.000170896,0.000003484271,0.00009686191,0.000141503,0.00000167139],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002304949,"about_ca_system_score_gemma":0.0000860736,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005023119,"about_ca_topic_score_gemma":0.00003713939,"domain_scores_codex":[0.9988446,0.0002085009,0.0001819742,0.0003054905,0.0002197805,0.0002396998],"domain_scores_gemma":[0.9994224,0.00006612721,0.00004075941,0.0001437065,0.0002706849,0.00005630587],"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":[0.0001064923,0.00003419678,0.0007973242,0.00006624846,0.00005901026,4.840934e-7,0.0001506551,0.000006957493,0.9864929,0.0000979948,0.00001227219,0.01217547],"study_design_scores_gemma":[0.0003566551,0.0004240111,0.006660175,0.000008005893,0.000009298252,5.641098e-7,0.0004328713,0.0001945473,0.989761,0.0005014743,0.001567775,0.00008360586],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9684078,0.01170202,0.01848614,0.00008024543,0.00002689769,0.0002555528,0.00003627413,0.000004059898,0.001001038],"genre_scores_gemma":[0.9973173,0.0007547169,0.0008781261,0.000007700738,0.00003268673,0.00002992672,0.00009997327,0.00001059958,0.0008690038],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02890949,"threshold_uncertainty_score":0.3501986,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04577309514510525,"score_gpt":0.3812855995158716,"score_spread":0.3355125043707664,"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."}}