Vanessa Porter

Allele-specific chromatin modifications of HPV-associated extrachromosomal DNAs in cervical cancer

The paper identifies epigenetic differences between HPV-human hybrid and human-only ecDNAs in cervical cancer, showing allele-specific regulation and enhancer activity in hybrid ecDNAs.

Genomic structures and regulation patterns at HPV integration sites in cervical cancer

The paper uses long-read sequencing to analyze HPV integration sites in cervical cancer genomes, identifying structural and epigenetic impacts of integration.

Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes

This paper presents a long-read sequencing dataset of cancer samples, showing its ability to resolve structural variants, haplotypes, and methylation patterns in precision medicine.

The benefit of a complete reference genome for cancer structural variant analysis

This paper shows that using a complete reference genome improves the accuracy and reduces false positives in detecting structural variants in cancer genomes.

IMPALA: A Comprehensive Pipeline for Detecting and Elucidating Mechanisms of Allele Specific Expression in Cancer

IMPALA detects allele-specific expression in cancer samples and identifies potential regulatory mechanisms influencing ASE.