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We develop and deploy a range of bioinformatics software pipelines to DoD high-performance computing assets for annotating whole genome function, developing unique DNA fingerprints for pathogens, and comparing genomes. Research topics include, creating diagnostic platforms for detecting and strain typing pathogens, understanding bacterial secretion systems and host-pathogen interactions, investigating the human microbiome, predicting orthology, revealing thermodynamic forces underlying viral evolution, and analyzing genotype-phenotype associations.

Research Projects

Comparative Genomics Comparative Genomics

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

Genotype-Phenotype Analysis Genotype-Phenotype Analysis

We develop algorithms for inferring disease risks from genomic data and apply them to better undertand human susceptibility to traumatic events and sleep deprivation.

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.