Xun Chen

GraffiTE analyzes transposable element insertion polymorphisms using genome-graphs, achieving high precision and recall across multiple species and sequencing technologies.

The paper refines the annotation of endogenous retrovirus LTRs in primates by identifying new subfamilies and their regulatory roles through phylogenetic analysis and functional validation.

The paper uses genome graphs to detect polymorphic mobile elements in active epigenomic states during influenza infection, revealing novel peaks and modifying quantitative trait loci estimates.

The paper shows ancestry-related differences in transcriptional response to influenza are driven by epigenetic variation and genetic control of enhancer activity.

ERVcaller detects and genotypes transposable element insertions using whole-genome sequencing data with high sensitivity and precision.