Ziad Khan

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

SniffCell assigns somatic variants to cell types using DNA methylation from bulk long-read sequencing, revealing cell-type-specific mutations in human tissues.

This paper evaluates Illumina Constellation sequencing for rare disease research, showing it can detect structural variants and haplotype phasing with low DNA input and existing infrastructure.

This paper introduces a qPCR-based assay to assess rRNA depletion efficiency in RNA-Seq libraries pre-sequencing, showing strong correlation with post-sequencing rRNA rates.

The paper sequences the rat Y chromosome and reveals a short pseudoautosomal region with high recombination rate and unique evolutionary features.

Celeste provides a scalable cloud infrastructure for population-scale sequencing projects, including a variant-calling pipeline optimized for clinical variant detection.

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

xAtlas is a scalable variant caller for NGS data that provides faster and accurate SNV and indel detection compared to existing methods.

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.