James T. Bennett

This study benchmarks nine short-read sequencing chemistries across seven sequencers using donor-specific assemblies to measure sequencing errors against sample-matched references, revealing platform-specific error profiles and highlighting the importance of donor-specific references for unbiased comparison.

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

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.

The paper identifies somatic BRAF variants as a cause of PIK3CA-negative lymphatic malformations, expanding the genetic understanding of vascular malformations.

This paper introduces targeted long-read sequencing to identify complex structural variants and disease-causing mutations missed by conventional methods, improving diagnostic accuracy in genetic disorders.