Kelsey N. Thompson

BAQLaVa improves viral profiling from metagenomes and metatranscriptomes, revealing reduced virome diversity in inflammatory bowel diseases and novel phage-host relationships.

MaAsLin 3 fits hurdle models separating microbial prevalence (augmented logistic) and abundance (median-adjusted log-linear) associations, improving precision over existing differential abundance tools and showing 77% of IBD associations are prevalence-driven.

Anpan quantifies strain-level associations in microbiomes, identifying genetic elements and phylogenetic effects linked to colorectal cancer, with improved accuracy over existing methods.

The paper evaluates metagenomic analysis methods in simulated and real environmental data, finding that newer marker-based methods perform better at lower taxonomic levels.

Marker genes for 26,970 species-level genome bins, 4,992 defined only by metagenome-assembled genomes, let MetaPhlAn 4 quantify uncharacterized species and beat MetaPhlAn 3, mOTUs and Bracken on synthetic benchmarks.