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Cancer Res."},{"key":"10.1016\/j.ajhg.2026.03.012_bib73","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/1471-2105-12-77","article-title":"pROC: an open-source package for R and S+ to analyze and compare ROC curves","volume":"12","author":"Robin","year":"2011","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ajhg.2026.03.012_bib74","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1182\/bloodadvances.2021006941","article-title":"The immune microenvironment shapes transcriptional and genetic heterogeneity in chronic lymphocytic leukemia","volume":"7","author":"Sun","year":"2023","journal-title":"Blood Adv."},{"key":"10.1016\/j.ajhg.2026.03.012_bib75","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1038\/s43587-023-00424-y","article-title":"Human microglia show unique transcriptional changes in Alzheimer\u2019s disease","volume":"3","author":"Prater","year":"2023","journal-title":"Nat. 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Genet."},{"key":"10.1016\/j.ajhg.2026.03.012_bib88","doi-asserted-by":"crossref","first-page":"2522","DOI":"10.1167\/iovs.04-0072","article-title":"Kruppel-like factor 15, a zinc-finger transcriptional regulator, represses the rhodopsin and interphotoreceptor retinoid-binding protein promoters","volume":"45","author":"Otteson","year":"2004","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"10.1016\/j.ajhg.2026.03.012_bib89","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbc.2022.101926","article-title":"Transcription factors KLF15 and PPAR\u03b4 cooperatively orchestrate genome-wide regulation of lipid metabolism in skeletal muscle","volume":"298","author":"Fan","year":"2022","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.ajhg.2026.03.012_bib90","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1126\/science.aba5906","article-title":"Human fetal microglia acquire homeostatic immune-sensing properties early in development","volume":"369","author":"Kracht","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.ajhg.2026.03.012_bib91","doi-asserted-by":"crossref","first-page":"7816","DOI":"10.1038\/s41598-023-34787-4","article-title":"Transcriptomic and glycomic analyses highlight pathway-specific glycosylation alterations unique to Alzheimer\u2019s disease","volume":"13","author":"Tang","year":"2023","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ajhg.2026.03.012_bib92","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1189\/jlb.4A0214-087R","article-title":"Elk-3 is a KLF4-regulated gene that modulates the phagocytosis of bacteria by macrophages","volume":"97","author":"Tsoyi","year":"2015","journal-title":"J. Leukoc. Biol."},{"key":"10.1016\/j.ajhg.2026.03.012_bib93","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1038\/s43018-022-00475-x","article-title":"A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets","volume":"3","author":"Wang","year":"2022","journal-title":"Nat. Cancer"},{"key":"10.1016\/j.ajhg.2026.03.012_bib94","doi-asserted-by":"crossref","first-page":"2236","DOI":"10.1038\/s41467-022-29912-2","article-title":"Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival","volume":"13","author":"Lu","year":"2022","journal-title":"Nat. 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Neurol."},{"key":"10.1016\/j.ajhg.2026.03.012_bib98","first-page":"1613","article-title":"A thirteen-gene set efficiently predicts the prognosis of glioblastoma","volume":"19","author":"Yang","year":"2019","journal-title":"Mol. Med. Rep."},{"key":"10.1016\/j.ajhg.2026.03.012_bib99","first-page":"1017","article-title":"The mechanism of BUD13 m6A methylation mediated MBNL1-phosphorylation by CDK12 regulating the vasculogenic mimicry in glioblastoma cells. Cell Death","volume":"13","author":"Liu","year":"2022","journal-title":"Dis"},{"key":"10.1016\/j.ajhg.2026.03.012_bib100","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/glia.20197","article-title":"Neuregulin-1 enhances survival of human astrocytic glioma cells","volume":"51","author":"Ritch","year":"2005","journal-title":"Glia"},{"key":"10.1016\/j.ajhg.2026.03.012_bib101","article-title":"Integrative analysis of neuregulin family members-related tumor microenvironment for predicting the prognosis in gliomas","volume":"12","author":"Zhao","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ajhg.2026.03.012_bib102","article-title":"MiR-218-5p targets LHFPL3 to regulate proliferation, migration, and epithelial\u2013mesenchymal transitions of human glioma cells","volume":"39","author":"Li","year":"2019","journal-title":"Biosci. Rep."},{"key":"10.1016\/j.ajhg.2026.03.012_bib103","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gpb.2020.10.005","article-title":"Chinese Glioma Genome Atlas (CGGA): a comprehensive resource with functional genomic data from Chinese glioma patients","volume":"19","author":"Zhao","year":"2021","journal-title":"Genomics Proteomics Bioinf"},{"key":"10.1016\/j.ajhg.2026.03.012_bib104","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1038\/onc.2012.137","article-title":"Suppression of proinvasive RGS4 by mTOR inhibition optimizes glioma treatment","volume":"32","author":"Weiler","year":"2013","journal-title":"Oncogene"},{"key":"10.1016\/j.ajhg.2026.03.012_bib105","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0082108","article-title":"Identification of novel genetic alterations in samples of malignant glioma patients","volume":"8","author":"Milinkovic","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.ajhg.2026.03.012_bib106","doi-asserted-by":"crossref","first-page":"3909","DOI":"10.3934\/mbe.2020217","article-title":"Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma","volume":"17","author":"Wei","year":"2020","journal-title":"Math. Biosci. Eng."},{"key":"10.1016\/j.ajhg.2026.03.012_bib107","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1158\/2159-8290.CD-19-0329","article-title":"The Phenotypes of Proliferating Glioblastoma Cells Reside on a Single Axis of Variation","volume":"9","author":"Wang","year":"2019","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ajhg.2026.03.012_bib108","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/nrc1209","article-title":"AP-1: a double-edged sword in tumorigenesis","volume":"3","author":"Eferl","year":"2003","journal-title":"Nat. Rev. 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Transl. Med."},{"key":"10.1016\/j.ajhg.2026.03.012_bib119","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/nature22079","article-title":"T-cell invigoration to tumour burden ratio associated with anti-PD-1 response","volume":"545","author":"Huang","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.ajhg.2026.03.012_bib120","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.137263","article-title":"CCL5 mediates CD40-driven CD4+ T cell tumor infiltration and immunity","volume":"5","author":"Huffman","year":"2020","journal-title":"JCI Insight"},{"key":"10.1016\/j.ajhg.2026.03.012_bib121","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1016\/j.ccell.2019.05.004","article-title":"Cooperation between constitutive and inducible chemokines enables T cell engraftment and immune attack in solid tumors","volume":"35","author":"Dangaj","year":"2019","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ajhg.2026.03.012_bib122","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/s41591-019-0734-6","article-title":"Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma","volume":"26","author":"Fairfax","year":"2020","journal-title":"Nat. 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