Pathogen Genomics Lab


The lab is interested in all things pathogen genomics. We use Next-Generation Sequencing approaches, specifically on Oxford Nanopore and Illumina platforms, to generate high-quality genomic data from a variety of different viruses and parasites. Our goal is to use these data to understand the natural history and transmission dynamics of these important pathogens. Ultimately, we want to incorporate pathogen genomics and genomic epidemiology into routine public health practice both locally and globally.


  • RNA Virus Genomic Epidemiology - Like many of our colleagues, we have spent the last ~18 months responding to the COVID-19 pandemic and have spent much of our time working on the genomic epidemiology of SARS-CoV-2. 
  • Genomics of Disease Control/Elimination - Helminth infections are diseases of poverty and are a massive cause of human morbidity around the world. For many parasitic nematodes there are active large-scale disease control and/or elimination programs in place. We are interested in incorporating genomic epidemiology approaches to better understand parasite transmission in light of control/elimination programs. Specifically, we are focused on filarial worms and hook worms.
  • Training and Methods Development - Public health and global health must be a collaborative endeavor, therefore It is a core function of our lab to be able to train our colleagues in all aspect of work. Whether it is teaching folks how to key out mosquitoes, do library preparation, or build a custom Nextstrain pipeline, we pride ourselves on knowing our systems well enough to teach them to others. If we can be anything, we want to be good collaborators!

To know more about the research of the Pathogen Genomics Lab contact:  

Dr. Joseph Fauver at

Lab Team

Joseph R. Fauver, PhD - Assistant Professor, UNMC College of Public Health, Department of Epidemiology and Pathogen Genomics Lab Director


Kaylee Herzog, PhD - Post Doctoral, UNMC College of Public Health, Department of Epidemiology and Pathogen Genomics Lab Research Assistant