Caitlin M. A. Simopoulos

scEPS integrates GWAS and single-cell data to identify disease-associated cell neighborhoods by testing gene expression variance explained in disease contexts.

This study maps metaproteomic responses of human gut microbiota to 312 drugs, identifying 47 compounds that significantly alter microbial protein profiles and reveal functional state shifts.

The paper introduces PhyloFunc, a new functional beta-diversity metric for metaproteomic data that incorporates phylogenetic relationships to better capture functional dissimilarities between microbial communities.

This study quantifies protein-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics and network analysis, revealing high redundancy and environmental influences on functional organization.

MetaProClust-MS1 rapidly clusters metaproteomes using short MS1 profiles, showing robust microbiome shifts and correlated cluster topologies compared to traditional tandem mass spectrometry.

pepFunk improves functional analysis of metaproteomic gut microbiome data by focusing on peptides rather than proteins, identifying more enriched KEGG pathways.