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We have deployed a range of bioinformatics software pipelines to DoD high-performance computing assets for whole genome function annotation, the development of unique DNA fingerprints for pathogens, and comparative genomics. Research topics include creating diagnostic platforms for pathogen detection and strain typing, understanding bacterial secretion systems active in host-pathogen interactions, orthology detection, and the fundamental thermodynamic forces underlying viral evolution.

Research Projects

Comparative Genomics Comparative Genomics

We develop effective, high-throughput computational approaches to enable comparative genomics studies based on orthology.

Host-Pathogen Interactions Host-Pathogen Interactions

We identify virulence factors associated with bacterial secretion systems via bioinformatics and in vitro and in vivo experimentation.

Pathogen Diagnostics Pathogen Diagnostics

We design customized and platform-specific diagnostic probe sets to identify known and new pathogen species and strains.

Respiratory Microbiome Respiratory Microbiome

We investigate how alterations in the respiratory microbiome of Service members affect their health and factors associated with chronic and acute respiratory disease.

Sequencing and Annotation Sequencing and Annotation

We develop high-throughput computational solutions for annotating, analyzing, managing, and storing genome-scale sequencing data.

Viral Evolution Viral Evolution

Using sequencing data and mathematical models, we study the capacity of viral pathogens to create escape mutants that evade the host immune system.