Phillip A. Richmond

The paper identifies 61,243 phenologs between human diseases and model organism phenotypes, using a hypergeometric method to rank candidate genes and validate their predictive power.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

This study identifies heterozygous gain-of-function STAT6 variants in two patients with severe allergic disease and shows JAK inhibitors reduce the enhanced STAT6 responses.

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

FlexTyper enables reverse mapping of short reads to extract genomic insights without reference-guided alignment, demonstrating utility in genotyping, ancestry detection, and pathogen identification.

GeneBreaker simulates rare genetic disease cases to benchmark variant calling and prioritization tools, aiding in the diagnosis of Mendelian disorders.

This study identifies a 4bp non-coding deletion in the FOXG1 locus at 14q12 as a candidate for isolated strabismus, showing its potential role in regulating FOXG1 expression.

metPropagate uses metabolomics data to prioritize candidate genes for neurometabolic diseases, achieving high accuracy in identifying causative genes for both known and novel IEMs.

This study uses multi-omic profiling of blood samples from ALD patients to identify molecular markers predictive of cerebral demyelination, but finds no statistically significant markers due to high inter-individual variation.

ExpansionHunter Denovo detects known and novel repeat expansions in short-read sequencing data without requiring predefined repeat catalogs.

This paper identifies and corrects technical biases on sex chromosomes in sequencing data using a new tool called XYalign.