Matthew B. Harms

Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis.

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

Enrichment of Repeat Expansions in FGF14 Associated with Amyotrophic Lateral Sclerosis

The paper identifies FGF14 GAA repeat expansions in ALS patients, showing enrichment compared to controls and suggesting a broader pathogenic role in motor neuron disease.

Polygenic Risk and Rare Variants in Endotypes of Idiopathic Pulmonary Fibrosis

This study identifies independent associations between IPF risk and rare variants, the MUC5B SNP, and polygenic scores, showing that telomere-associated common variants improve disease prediction and explain genetic heterogeneity in IPF.

Inferring compound heterozygosity from large-scale exome sequencing data

The paper develops a method to infer compound heterozygosity from exome sequencing data, achieving high accuracy in phasing rare variants for recessive disease diagnosis.

DYNATE: Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree

DYNATE identifies rare-variant association regions by dynamically aggregating genomic regions and controlling false discovery rate, finding a new ALS-associated gene.

Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS

Clinical testing panels for ALS: global distribution, consistency, and challenges

The paper evaluates the variability in ALS clinical genetic testing panels globally, finding inconsistent gene inclusion and potential diagnostic challenges.

Cell environment shapes TDP-43 function: implications in neuronal and muscle disease

The paper compares TDP-43's transcriptional and splicing effects in muscle and neuronal cells, showing tissue-specific roles in disease.

Precision genetic cellular models identify therapies protective against endoplasmic reticulum stress

The paper identifies compounds that correct aberrant molecular phenotypes in cellular models of glycosylation defects using a phenotypic screening approach.

Human loss-of-function variants suggest that partial LRRK2 inhibition is a safe therapeutic strategy for Parkinsons disease

The paper analyzes loss-of-function variants in LRRK2 across large genomic datasets to assess the safety of partial LRRK2 inhibition as a Parkinson's disease therapy.

Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes

The paper analyzes multi-nucleotide variants (MNVs) in 125,748 exomes and 15,708 genomes, identifying their distribution, mutational origins, and functional implications.

Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients

The paper identifies an enrichment of rare protein-truncating variants in ALS patients, highlighting novel genes like DNAJC7 and known ALS genes such as SOD1, NEK1, and FUS.

Regional collapsing of rare variation implicates specific genic regions in ALS

The paper applies two novel collapsing methods to ALS sequencing data to identify risk regions in known ALS genes and candidate genes.