The Bahl Lab

The Applied Molecular Epidemiology Research Group is led by Justin Bahl, Professor in the Departments of Infectious Diseases, Epidemiology and Biostatistics, and the Institute of Bioinformatics at the University of Georgia. He is the Scientific Director of the Georgia Pathogen Genomics Center of Excellence, a CDC-supported initiative advancing genomic surveillance and pandemic preparedness. His research integrates genomic epidemiology, phylodynamics, and integrated pathogen surveillance to improve pandemic preparedness and outbreak intelligence. He has published more than 100 peer-reviewed papers, secured over $30 million in research funding, and leads collaborations supported by NIH, CDC, NSF, and Horizon Europe.

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Our team studies how viruses emerge, spread, evolve, and persist among human, animal, and environmental systems. We combine pathogen genomics, evolutionary biology, artificial intelligence, ecological intelligence, and public health data to develop next-generation surveillance systems that improve outbreak detection, pandemic preparedness, and response.

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We are especially interested in the conditions that create opportunities for spillover, epidemic emergence, and sustained transmission. Rather than treating outbreaks as isolated events, we study them as outcomes of interacting biological, ecological, agricultural, social, and environmental processes. This integrated systems perspective provides a framework for unifying pathogen genomics with veterinary medicine, public health, wildlife ecology, environmental surveillance, and global health systems.

 

A central goal of our research is to connect pathogen evolution with the ecological and epidemiological contexts in which transmission occurs. Using comparative genomics, phylogenetics, phylodynamics, spatial modeling, and machine learning, we investigate how viral populations diversify, adapt, move between hosts, and establish new transmission pathways. Our work focuses primarily on RNA viruses and other emerging pathogens of public health importance, including influenza viruses, respiratory viruses, coronaviruses, and zoonotic pathogens circulating at the interface of wildlife, domestic animals, and humans.
 

Building on long-standing partnerships with public health, diagnostic, veterinary, wildlife health, and academic partners, we are advancing AI-enabled and globally connected surveillance systems that integrate diverse data streams, identify early warning signals, and support faster, more coordinated responses to emerging infectious disease threats.

 

Collaboration is fundamental. The lab brings together expertise in molecular biology, epidemiology, evolutionary biology, ecology, bioinformatics, data science, veterinary medicine, and public health to build analytical frameworks that are scientifically rigorous, operationally useful, and adaptable across pathogens, host systems, and geographic contexts. Our work is grounded in team science and designed to generate both fundamental insight into pathogen evolution and practical tools for disease prevention and control.

 

Our long-term vision is to build predictive pandemic intelligence systems that connect pathogen genomics, ecological surveillance, and public health decision-making across human, animal, and environmental health systems. By building bridges among disease surveillance, pathogen genomics, and pandemic preparedness, the aim to transform how emerging infectious disease threats are detected, understood, and controlled.

 

Research in the lab has been generously supported by the NIH-NIAID, the Centers for Disease Control and Prevention, the National Science Foundation, and the Horizon Europe program. Through this support, we have built a collaborative and interdisciplinary research program committed to scientific excellence, public health impact, and the training of the next generation of infectious disease scientists.