Nicole Perna

Professor of Genetics

3426 Genetics-Biotechnology Center,  608.890.0171




PhD (1996), University of New Hampshire

Postdoctoral fellow, University of Wisconsin-Madison

Research Interests

Studying genome evolution and structure in plant and animal bacterial pathogens.

Lab Website


Our research is aimed at building a systems-scale understanding of how complex traits evolve in bacteria.  We develop and apply genome-scale technologies and resources to probe how bacteria interact with each other, their hosts, and the environment. We study these processes primarily in enterobacteria, where depth of knowledge about a single model organism, Escherichia coli K-12, can be integrated with breadth of genomic data representing approximately half a billion years of evolutionary divergence.

Representative Publications  (Google Scholar | PUBMED)

  • Baumler, D. J., Ma, B., Reed, J. L. & Perna, N. T. Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. BMC systems biology 7, 46, doi:10.1186/1752-0509-7-46 (2013).
  • Baumler, D. J., Peplinski, R. G., Reed, J. L., Glasner, J. D. & Perna, N. T. The evolution of metabolic networks of E. coli. BMC systems biology 5, 182, doi:10.1186/1752-0509-5-182 (2011).
  • Rodriguez-Palenzuela, P. et al. Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts. Environ Microbiol 12, 1604-1620, doi:10.1111/j.1462-2920.2010.02207.x (2010).
  • Rissman, A. I. et al. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics (Oxford, England) 25, 2071-2073, doi:10.1093/bioinformatics/btp356 (2009).