Elizabeth A. Worthey

nf_xpatial provides a standardized Nextflow pipeline for preprocessing and clustering Xenium spatial transcriptomics data, enabling reproducible analysis and parameter comparison.

The paper identifies germline and somatic genetic variants and molecular signatures in placental chorangiomas from monochorionic twins, linking them to hypoxia, angiogenesis, and oxidative stress.

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

The paper introduces a Nextflow-based pipeline for analyzing Oxford Nanopore single-cell RNA sequencing data, enabling gene and transcript-level quantification with portability and reproducibility.

The paper evaluates variant prioritization methods for rare disease diagnosis using data from the Rare Genomes Project, finding that top models identify causal variants in most solved families and uncover potential candidates in unsolved ones.

QuaC automates and standardizes QC for genome and exome sequencing data by integrating tools, setting thresholds, and generating comprehensive reports.

AMELIE 3 automatically reanalyzes undiagnosed Mendelian disease patients using new literature, achieving 80% diagnostic yield with 0.5-1 alerts per patient per year.

Genome sequencing for early-onset dementia identified genetic variants in 50% of patients, including pathogenic variants and moderate penetrance alleles, supporting an oligogenic model.

VarSight uses binary classification algorithms to prioritize clinically reported variants in rare disease patients, outperforming existing methods in identifying pathogenic variants.

This paper identifies pathogenic structural variants in rare disease patients using whole genome sequencing and reports their clinical relevance.

The paper develops a method to detect diploid-triploid mixoploidy using whole genome sequencing data and validates it with clinical cytogenetic testing.