Moses H. Stamboulian

The paper uses metaproteomics to analyze human gut microbiome data, identifying generalist and specialist bacterial species and recovering ORFs missed by gene predictors.

The paper introduces HAPiID, a two-step method for faster and more effective peptide/protein identification in human gut metaproteomic data by using high abundance proteins as guides.

The paper develops a method to quantify metabolic interactions between microbial species while adjusting for phylogenetic relationships, revealing niche differentiation and habitat filtering in gut microbiomes.

The paper constructs a phylogenetic tree of human gut bacterial species using over 3000 genomes, including MAGs, and applies it to metagenomics and metaproteomics data analysis.

This study revisits the ortholog conjecture by analyzing function prediction accuracy using orthologs and paralogs across two species pairs, finding strong evidence against the conjecture.