GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE336nnn/GSE336203/primaryOK200TranscriptomicsHomo sapiensExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE336203GEOGSEfalseERVmancer: A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and diseaseHuman endogenous retroviruses (HERVs), remnants of ancient infections, comprise ~8% of the human genome and influence development, immunity, and cancer. Studying them is limited by short-read sequencing, which cannot uniquely assign reads to repetitive elements. We present ERVmancer, a phylogeny-informed method that resolves mapping ambiguity and quantifies HERV expression from individual loci to entire clades. Benchmarking with matched long- and short-read data shows ERVmancer surpasses existing methods in sensitivity and specificity. Application recapitulates long-read observed HERV patterns in multiple sclerosis and reveals novel biology in breast cancer, including p53-mediated suppression of HERVH-LTR7, enabling scalable study of retroviral mechanisms.2026/07/23GSE336203GSM9829979GSM9829968GSM9829969GSM9829966GSM9829977GSM9829978GSM9829967GSM9829975GSM9829976GSM9829973GSM9829984GSM9829985GSM9829974GSM9829982GSM9829971GSM9829972GSM9829983GSM9829980GSM9829970GSM98299812131118573336203Homo sapiens