{"id":"W4410418781","doi":"10.1101/2025.05.09.653178","title":"Spatial epigenomic niches underlie glioblastoma cell state plasticity","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"Alberta Children's Hospital; University of Calgary","funders":"","keywords":"Epigenomics; Glioblastoma; Biology; Ecological niche; Phenotypic plasticity; Neuroscience; Ecology; Cancer research; DNA methylation; Genetics; Habitat","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000265787,0.0007851768,0.0006267443,0.0002011113,0.0002081042,0.0001833228,0.0008385875,0.0008685864,0.00003045093],"category_scores_gemma":[0.0001087264,0.0008984903,0.0003174501,0.0001986447,0.0001897806,0.000007863242,0.0006871761,0.0007367958,0.00004528232],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001686296,"about_ca_system_score_gemma":0.001233055,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002651071,"about_ca_topic_score_gemma":0.0001285748,"domain_scores_codex":[0.9967402,0.0001588999,0.0006492704,0.001418843,0.0002874622,0.000745284],"domain_scores_gemma":[0.9978557,0.00004521963,0.0003545267,0.001116797,0.000332122,0.0002955905],"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":[0.0002752833,0.0002587073,0.003151943,0.0004581968,0.0002003381,0.00002258068,0.000007800883,0.0008232789,0.9942884,0.00001953604,0.00048551,0.000008428006],"study_design_scores_gemma":[0.0008808782,0.0002487762,0.008444651,0.0001568188,0.0001429227,1.466192e-8,0.000001685373,0.0006161078,0.9796339,0.000003890858,0.008911782,0.0009585929],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9690774,0.001347864,0.02590813,0.00005830075,0.001814511,0.0006227018,0.0009496041,0.0001626811,0.00005879484],"genre_scores_gemma":[0.9960909,0.0006854823,0.001966413,0.0002754975,0.0006730932,0.00008829244,0.000003111918,0.0001265093,0.0000906261],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02701356,"threshold_uncertainty_score":0.9993466,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00969396850329924,"score_gpt":0.2026389596664168,"score_spread":0.1929449911631176,"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."}}