2020
Glycolytic expression in lower-grade glioma reveals an epigenetic association between IDH mutation status and PDL1/2 expression
Givechian K, Garner C, Benz S, Rabizadeh S, Soon-Shiong P. Glycolytic expression in lower-grade glioma reveals an epigenetic association between IDH mutation status and PDL1/2 expression. Neuro-Oncology Advances 2020, 3: vdaa162. PMID: 33532725, PMCID: PMC7837356, DOI: 10.1093/noajnl/vdaa162.Peer-Reviewed Original ResearchChIP-seq dataEpigenetic linkR132H/Promoter methylationPromoter methylation patternsPromoter H3K4me3Cancer Genome AtlasGenomic analysisDNA methylationRNA-seqImmortalized human astrocytesMethylation patternsMethylation dataEpigenetic associationsCheckpoint genesCell line dataMethylation levelsMethylationWild-type IDHHuman low-grade gliomasGenome AtlasExpression levelsExpression ratioGlycolysisGenes
2019
Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity
Wnuk K, Sudol J, Givechian K, Soon-Shiong P, Rabizadeh S, Szeto C, Vaske C. Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity. IScience 2019, 20: 119-136. PMID: 31563852, PMCID: PMC6823659, DOI: 10.1016/j.isci.2019.09.018.Peer-Reviewed Original ResearchDNA accessibilityChromatin stateOpen chromatin stateChromatin regulationSpecific tissue typesPromoter-flanking regionAccessibility landscapeCancer Genome AtlasTranscriptional eventsTissue-specific phenomenonDNA sequencesGenome AtlasTissue typesImmune pathwaysPromoterTumor progressionAccessibility patternsLung adenocarcinomaNew toolKey dynamic featuresTumor typesPathwayRegulationImmune activitySequence