Patrick Marks

scHLAcount computes allele-specific HLA expression from single-cell RNA-seq data, revealing cell-type and tumor-normal differences in allelic patterns.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

This paper introduces Linked-Reads as a method to comprehensively analyze genome variation, showing it can detect both small and large variants and reconstruct haplotypes more effectively than short-read sequencing.

The paper introduces Novel-X, a method using Linked-Read data to detect novel sequence insertions without whole-genome de novo assembly, outperforming short-read tools and enabling cost-effective large-scale screening.

This study evaluates Linked-Read sequencing for detecting structural variants, finding it can identify most known events with low sequencing depth and provides breakpoint resolution.

The paper presents extensive sequencing data from seven human genomes to serve as benchmark reference materials for improving sequencing technologies and variant calling.