About MAAGE
The Midwest Alliance for Applied Genomic Epidemiology is a collaborative initiative dedicated to protecting our public health through innovative genomic surveillance tools to enhance disease prevention and response.
Our Mission
The Midwest Alliance for Applied Genomic Epidemiology is a collaboration of Argonne National Laboratory, the Illinois Department of Public Health, and the University of Illinois. Our mission is to develop a comprehensive genomic surveillance and epidemiology platform, empowering state and local public health agencies to detect and monitor the spread of infectious diseases with enhanced sensitivity.
We are committed to providing educational resources to equip the public health and healthcare communities with the knowledge and skills necessary to integrate this platform into their daily operations.
Our Leadership
Thomas Brettin
Strategic Program Manager
Argonne National Laboratory
Becky Smith
Associate Professor of Pathology
University of Illinois Urbana-Champaign
Charles Williams
Chief of Testing
Illinois Department of Public Health
Key Features
Comprehensive Genomic Surveillance Platform
A unified and scalable system to support genomic surveillance and epidemiological analysis for pathogens of public health importance. Extends BV-BRC infrastructure with customized workflows to meet public health needs.
Scalable Data Management and Integration
Framework to collect, process, analyze, integrate, share, and publish genomic and other omics data from multiple sources. Supports harmonized ingestion of sequencing data from IDPH's Chicago and Springfield laboratories and other statewide partners. Supports private data for internal analysis, case investigations, and cross-team collaboration.
Advanced Genomic Epidemiological Analysis
High-resolution pathogen analysis, including variant and lineage identification, SNP and cgMLST/HierCC clustering, phylogenetics, transmission reconstruction, and AMR detection. Advanced, evolving analytic workflows that integrate multi-omics data and continuously adapt to new surveillance methods and public health needs.
Integrated Outbreak Investigation Tools
Combines genomic data with demographic, clinical, and geospatial metadata to support real-time outbreak detection and disease control. Enables visualization of transmission patterns, cluster evolution, and geographic spread.
Public Dashboards & Community Engagement
Interactive dashboards offering statewide pathogen trends and sequencing insights. Improves data transparency, communication, and public engagement.
Education, Training & Workforce Development
Bioinformatics and genomic epidemiology training modules for public health practitioners. Workshops, outreach programs, and expert engagement to build statewide capacity.
Funding
This project has been funded in whole or in part by...
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