{"id":"W2157251845","doi":"10.1101/gr.099796.109","title":"Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis","year":2009,"lang":"en","type":"article","venue":"Genome Research","topic":"Pluripotent Stem Cells Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":320,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children","funders":"Eunice Kennedy Shriver National Institute of Child Health and Human Development; Canadian Institutes of Health Research; National Institute of Child Health and Human Development; National Institute of General Medical Sciences; National Institutes of Health; International Rett Syndrome Foundation","keywords":"Biology; Replication timing; Epiblast; SOX2; Homeobox protein NANOG; Genetics; Embryonic stem cell; Induced pluripotent stem cell; Cell biology; Chromatin; Gene; Gastrulation","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":[0.002125763,0.0001362405,0.0002754943,0.0003653958,0.00006201547,0.00001380258,0.0006371654,0.0001946921,0.00001260597],"category_scores_gemma":[0.0002490649,0.0001463756,0.00008927649,0.0005677639,0.000142822,0.00000919985,0.0002477697,0.0002276113,0.000007770237],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001487967,"about_ca_system_score_gemma":0.0001844324,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001009549,"about_ca_topic_score_gemma":0.00001863052,"domain_scores_codex":[0.9973693,0.0003166666,0.0004859979,0.0005975561,0.0006446167,0.0005858384],"domain_scores_gemma":[0.9981154,0.00005873687,0.0001104332,0.001140521,0.0004485644,0.000126393],"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":[0.0003270094,0.0001776703,0.0005455055,0.00009025886,0.0000227411,0.000002660616,0.00003860656,0.00111205,0.9957098,0.00002109138,0.0001042885,0.001848307],"study_design_scores_gemma":[0.0005337188,0.0003376411,0.004382006,0.0000140713,0.000004343453,0.000003074939,0.00009759251,0.00443935,0.9893667,0.0002342935,0.0004236853,0.0001634981],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9931148,0.002066265,0.00215078,0.0003729934,0.000007272494,0.0005592959,0.0001070704,0.000005807476,0.001615702],"genre_scores_gemma":[0.9898612,0.00171476,0.0009521297,0.00002027979,0.00002313859,0.000035044,0.000645011,0.00002753694,0.006720911],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006343085,"threshold_uncertainty_score":0.5969024,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03992302647324868,"score_gpt":0.3241959757296273,"score_spread":0.2842729492563786,"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."}}