Michael Shaffer

This study uses multi-omics to analyze Salmonella's metabolic strategies in mice on different diets over time, identifying phase-specific gene expression linked to infection stages and therapeutic targets.

This study investigates how gut microbiome carbon and sulfur metabolisms support Salmonella during infection by analyzing multi-omics data from infected mice.

The paper curates a database of gut microbial genes linked to trimethylamine-induced cardiovascular disease and validates its predictive power using fecal metatranscriptome and metaproteome data.

kb_DRAM integrates DRAM tools into KBase for microbial and viral genome annotation and metabolic modeling through a user-friendly interface.

SCNIC generates correlation networks and identifies modules of correlated features in compositional data, increasing statistical power and revealing microbial relationships.

ORT links genome-scale metabolic models with reactive transport codes to improve ecosystem models using metagenomic data.