Nicole Perna

Position title: Professor & Graduate Program Director


Phone: 608-890-0171

Systems-scale evolutionary genomics of agriculturally, biomedically and industrially significant bacteria

4434 Genetics/Biotech
Ph.D., University of New Hampshire, (1996), Postdoctoral Research: University of Wisconsin — Madison
Lab Website
Research Interests
We focus on systems-scale evolutionary genomics of agriculturally, biomedically and industrially significant bacteria.
Research Fields
Disease Biology, Computational, Systems & Synthetic Biology, Evolutionary & Population Genetics, Gene Expression, Genomics & Proteomics, Bacteria

Research Description:
Our research is directed at understanding the molecular evolution of complex traits like virulence and host range. Our work focuses on the Enterobacteriaceae, a bacterial family with members occupying diverse environmental niches including plant and animal hosts with lifestyles ranging from mutualism to pathogenesis. We use both computational and experimental approaches to study the rates, patterns, mechanisms and phenotypic consequences of genome-scale evolution.

Some of our current areas of research are:

1) Specialization in either plant or animal hosts

2) Recombination within and between species, populations and strains

3) Rates and patterns of genome rearrangement

4) Regulatory evolution and energy metabolism

5) Evolution of chemotaxis and signaling systems

We also develop tools and resources for genome analysis, including a multiple genome alignment and visualization system, and an interactive web-based genome database and analysis platform. Tools developed in our group are publicly distributed for use by the larger research community.

Representative Publications:
Search PubMed for more publications by Nicole Perna

R. Mau, J.D. Glasner, A. Darling and N.T. Perna. 2006. Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol. 7:R44.

B.D. Anderson, M.C. Gilson, A.A. Scott, B.S. Biehl, J.D. Glasner, G. Rajashekara, G.A. Splitter and N.T. Perna. 2006. CGHScan: Finding Variable Regions Using High-Density Microarray Comparative Genomic Hybridization Data. BMC Genomics . 7:91.

J.D. Glasner, M.C. Rusch, P. Liss, G. Plunkett III, E. L. Cabot, A. Darling, B.D. Anderson, P. Infield-Harm, M.C. Gilson and N.T. Perna. 2006. ASAP: A resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res. 1;34(Database issue):D41-5.

S. Yang, N.T. Perna, D.A. Cooksey, Y. Okinaka, S.E. Lindow, A.M. Ibekwe, N.T. Keen and C.-H. Yang. 2004. Genome-wide identification of plant up-regulated genes of Erwinia chrysanthemi 3937 using GFP based IVET Leaf Arrays. MPMI. 17:999-1008.

A. Darling, B. Mau, F.R. Blattner and N.T. Perna. 2004. Mauve, Muliple Genome Alignment. Genome Research. 14:1394-1403.