Danielle G. Lemay

TaxaHFE reduces microbiome dataset features by collapsing them into higher taxonomic levels, improving model performance and interpretability.

The paper evaluates how sequencing parameters affect gene detection in human fecal metagenomes using DIAMOND, finding that read length, e-value thresholds, and custom databases improve detection accuracy.

SAMSA2 is a metatranscriptome analysis pipeline designed for supercomputing clusters, offering faster and more flexible analysis of large RNA-seq datasets.