Bioinformatics Group

 

We Are:

A multidisciplinary team of microbiologists, epidemiologists, data scientists, and software developers develops custom analysis tools and pipelines capable of rapidly processing up to 2,000 bacterial genomes each month. Leveraging this capacity, they conduct genome-based outbreak surveillance at every level—from continents down to individual hospital wards—while prospectively and retrospectively linking genomic findings with epidemiological data. Their integrated approach delivers expertise, curated genomes, detailed reports, and interactive dashboards that empower data-driven decision-making.


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Our Database and Software:

  
 

Custom-designed to meet the challenge of near real-time processing.

 

 

 

 

 

 

 

 

An analysis pipeline: the MRSN Integrated Genome Handling Tool (MIGHT) automates quality control, taxonomic classification, de novo assembly, molecular typing, comprehensive predictions of resistant genotypes, and clustering by core genome MLST (cgMLST) prior to reference-based SNP analysis. MIGHT is a docker-based python multiprocessing pipeline incorporating state-of-the-art tools (e.g. kraken2, shovill, bakta, AMRfinder…) for microbial genomics.

 

A curated genome repository and database of genotypic markers: with >95,000 sequenced isolates. In sync with MIGHT, this standardizes and centralizes the storage of isolate metadata, sequencing reads, assemblies, QC metrics, antibiotic resistance genes prediction, molecular typing results (sequence-types and cgMLST clusters) and more.

 

A front-end query and reporting tool: to functionalize and visualize the genomic data in real-time. This Reactjs web application acts as a dashboard interface for the database enabling all users to perform complex queries (e.g. combinations of date, site, type, species ID, lineage, resistance genes, genetic relatedness to other genomes in the repository etc.). Results are visualized in interactive diagrams of genetic relatedness, metadata tables and exportable reports.

  
             
 

Our hardware:

  • High Performance Computing system with a combination of CPU and GPU servers.

  • Onsite and offsite storage servers.

  

 
 




   
 
 

Our work:

  • Global reach: retrospective surveillance in 10+ countries, tracking of international spread, detection of emerging lineages and antibiotic resistance genes. Reach back bioinformatic expertise for DoD partners around the globe.

  • Local impact: prospective, genome-based outbreak detection in support of infection control in 20+ US Military Treatment Facilities.