Nancy L. Parmalee

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

This paper introduces DAF-seq, a method for single-molecule and single-cell chromatin fiber sequencing, enabling precise analysis of protein occupancy and chromatin accessibility.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.