Kathleen H. Burns

This paper shows that olaparib treatment increases transposable element activity in BRCA1-deficient triple-negative breast cancer cells, leading to genomic instability and immune responses.

This study identifies ZC3H18 mutations that stabilize endogenous retroviral RNA, linking ERV RNA accumulation to oncogenesis in zebrafish and human cell lines.

The paper identifies LINE-1 retrotransposition as a cause of MET exon 14 skipping in cancer, leading to actionable mutations.

The paper develops TiMEstamp to identify LINE-1 chimeric insertions in the human genome, revealing new chimeras and mechanisms like trans-splicing.

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

The paper investigates how L1 retrotransposition intermediates can recombine with DNA breaks or other L1 insertions to form chromosomal rearrangements, showing dependence on ORF2p and BRCA1.

The paper identifies a subgroup of mCRPC characterized by LINE1 repeat DNA elements flanking the AR gene, which drive AR overexpression and confer resistance to androgen signaling inhibitors.

This study uses whole-genome sequencing to show that LINE-1 retrotransposition directly causes chromosomal rearrangements and instability in cancer genomes.

This study shows that vitamin C increases young LINE-1 element expression in mouse ESCs through H3K9me3 demethylation by KDM4A/C, without increasing somatic insertion rates.

The paper identifies polymorphic mobile element insertions (pMEIs) as contributors to gene expression and alternative splicing variations across 48 human tissues using GTEx data.

TypeTE improves Alu insertion genotype accuracy from 83% to 92% in the 1000 Genomes dataset by reassembling and re-mapping sequencing data.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

SQuIRE quantifies interspersed repeat elements in RNA-seq data by integrating alignment, annotation, and expression analysis tools.

The paper identifies distinct nuclear and cytoplasmic intermediates of LINE-1 retrotransposition using mass spectrometry and affinity purification.

The paper establishes the landscape of human cell-specific microRNA expression using small RNA-seq data from diverse cell types and tissues, identifying novel microRNA loci and patterns correlated with super-enhancer activity.