Dr. Nicole Perna


Principal Investigator

425G Henry Mall Room 4434
Madison, Wisconsin 53706

Phone: 608-890-0171
Email: This email address is being protected from spam bots, you need Javascript enabled to view it

Curriculum Vitae

Degrees and Training

Research Interests

  • Molecular Epidemiology
  • Bacterial Genomics
  • Molecular Evolution

Research Description

The family Enterobacteriaciae is phenotypically diverse ranging from commensals to pathogens of humans, mammals, birds, reptiles and plants. The species E. coli alone includes harmless intestinal flora as well as strains associated with diarrheal disease, urinary tract infections, neonatal septicemia and meningitis. Genome sequences are now available for several representatives of this group and provide a solid foundation for investigation of the genetic basis of organismal differences in complex traits like virulence. We use genome scale comparative analyses to identify the genetic elements that distinguish one complete genome from another and survey the distribution of these factors in the population as a whole. These data will provide unparalle led sensitivity for pathogen identification and also generate insight into the evolution of virulence and the emergence of novel pathogens from within established species. Analyses to date have revealed an extraordinary level of horizontal transfer among enterobacterial strains and species punctuating a conserved clonally diverging ancestral genomic framework. We are now expanding this research to investigate regulatory variation by global gene expression pattern monitoring.


  1. Anderson, B.D., M.C. Gilson, A.A. Scott, B.S. Biehl, J.D. Glasner, G. Rajashekara, G.A. Splitter, and N.T. Perna, CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data. BMC Genomics, 2006. 7: p. 91.
  2. Glasner, J.D., M. Rusch, P. Liss, G. Plunkett, 3rd, E.L. Cabot, A. Darling, B.D. Anderson, P. Infield-Harm, M.C. Gilson, and N.T. Perna, ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res, 2006. 34(Database issue): p. D41-5.
  3. Mau, B., J.D. Glasner, A.E. Darling, and N.T. Perna, Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol, 2006. 7(5): p. R44.
  4. Riley, M., T. Abe, M.B. Arnaud, M.K. Berlyn, F.R. Blattner, R.R. Chaudhuri, J.D. Glasner, T. Horiuchi, I.M. Keseler, T. Kosuge, H. Mori, N.T. Perna, G. Plunkett, 3rd, K.E. Rudd, M.H. Serres, G.H. Thomas, N.R. Thomson, D. Wishart, and B.L. Wanner, Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res, 2006. 34(1): p. 1-9.
  5. Bartholomay, L.C., W.L. Cho, T.A. Rocheleau, J.P. Boyle, E.T. Beck, J.F. Fuchs, P. Liss, M. Rusch, K.M. Butler, R.C. Wu, S.P. Lin, H.Y. Kuo, I.Y. Tsao, C.Y. Huang, T.T. Liu, K.J. Hsiao, S.F. Tsai, U.C. Yang, A.J. Nappi, N.T. Perna, C.C. Chen, and B.M. Christensen, Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus. Infect Immun, 2004. 72(7): p. 4114-26.
  6. Darling, A.C., B. Mau, F.R. Blattner, and N.T. Perna, Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res, 2004. 14(7): p. 1394-403.
  7. Darling, A.E., B. Mau, F.R. Blattner, and N.T. Perna, GRIL: genome rearrangement and inversion locator. Bioinformatics, 2004. 20(1): p. 122-4.
  8. Kudva, I.T., R.W. Griffin, M. Murray, M. John, N.T. Perna, T.J. Barrett, and S.B. Calderwood, Insertions, deletions, and single-nucleotide polymorphisms at rare restriction enzyme sites enhance discriminatory power of polymorphic amplified typing sequences, a novel strain typing system for Escherichia coli O157:H7. J Clin Microbiol, 2004. 42(6): p. 2388-97.
  9. Yang, S., N.T. Perna, D.A. Cooksey, Y. Okinaka, S.E. Lindow, A.M. Ibekwe, N.T. Keen, and C.H. Yang, Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol Plant Microbe Interact, 2004. 17(9): p. 999-1008.
  10. Glasner, J.D., P. Liss, G. Plunkett, 3rd, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F.R. Blattner, and N.T. Perna, ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res, 2003. 31(1): p. 147-51.
  11. Lathem, W.W., T. Bergsbaken, S.E. Witowski, N.T. Perna, and R.A. Welch, Acquisition of stcE, a C1 esterase inhibitor-specific metalloprotease, during the evolution of Escherichia coli O157:H7. J Infect Dis, 2003. 187(12): p. 1907-14.
  12. Wei, J., M.B. Goldberg, V. Burland, M.M. Venkatesan, W. Deng, G. Fournier, G.F. Mayhew, G. Plunkett, 3rd, D.J. Rose, A. Darling, B. Mau, N.T. Perna, S.M. Payne, L.J. Runyen-Janecky, S. Zhou, D.C. Schwartz, and F.R. Blattner, Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun, 2003. 71(5): p. 2775-86.
  13. Deng, W., V. Burland, G. Plunkett, 3rd, A. Boutin, G.F. Mayhew, P. Liss, N.T. Perna, D.J. Rose, B. Mau, S. Zhou, D.C. Schwartz, J.D. Fetherston, L.E. Lindler, R.R. Brubaker, G.V. Plano, S.C. Straley, K.A. McDonough, M.L. Nilles, J.S. Matson, F.R. Blattner, and R.D. Perry, Genome sequence of Yersinia pestis KIM. J Bacteriol, 2002. 184(16): p. 4601-11.
  14. Heimer, S.R., R.A. Welch, N.T. Perna, G. Posfai, P.S. Evans, J.B. Kaper, F.R. Blattner, and H.L. Mobley, Urease of enterohemorrhagic Escherichia coli: evidence for regulation by fur and a trans-acting factor. Infect Immun, 2002. 70(2): p. 1027-31.
  15. Kudva, I.T., P.S. Evans, N.T. Perna, T.J. Barrett, F.M. Ausubel, F.R. Blattner, and S.B. Calderwood, Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol, 2002. 184(7): p. 1873-9.
  16. Kudva, I.T., P.S. Evans, N.T. Perna, T.J. Barrett, G.J. DeCastro, F.M. Ausubel, F.R. Blattner, and S.B. Calderwood, Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing. J Clin Microbiol, 2002. 40(4): p. 1152-9.
  17. Okinaka, Y., C.H. Yang, N.T. Perna, and N.T. Keen, Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol Plant Microbe Interact, 2002. 15(7): p. 619-29.
  18. Taylor, D.E., M. Rooker, M. Keelan, L.K. Ng, I. Martin, N.T. Perna, N.T. Burland, and F.R. Blattner, Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates. J Bacteriol, 2002. 184(17): p. 4690-8.
  19. Torres, A.G., J.A. Giron, N.T. Perna, V. Burland, F.R. Blattner, F. Avelino-Flores, and J.B. Kaper, Identification and characterization of lpfABCC'DE, a fimbrial operon of enterohemorrhagic Escherichia coli O157:H7. Infect Immun, 2002. 70(10): p. 5416-27.
  20. Torres, A.G., N.T. Perna, V. Burland, A. Ruknudin, F.R. Blattner, and J.B. Kaper, Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli. Mol Microbiol, 2002. 45(4): p. 951-66.
  21. Welch, R.A., V. Burland, G. Plunkett, 3rd, P. Redford, P. Roesch, D. Rasko, E.L. Buckles, S.R. Liou, A. Boutin, J. Hackett, D. Stroud, G.F. Mayhew, D.J. Rose, S. Zhou, D.C. Schwartz, N.T. Perna, H.L. Mobley, M.S. Donnenberg, and F.R. Blattner, Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A, 2002. 99(26): p. 17020-4.
  22. Yang, C.H., M. Gavilanes-Ruiz, Y. Okinaka, R. Vedel, I. Berthuy, M. Boccara, J.W. Chen, N.T. Perna, and N.T. Keen, hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol Plant Microbe Interact, 2002. 15(5): p. 472-80.
  23. Zhou, S., W. Deng, T.S. Anantharaman, A. Lim, E.T. Dimalanta, J. Wang, T. Wu, T. Chunhong, R. Creighton, A. Kile, E. Kvikstad, M. Bechner, G. Yen, A. Garic-Stankovic, J. Severin, D. Forrest, R. Runnheim, C. Churas, C. Lamers, N.T. Perna, V. Burland, F.R. Blattner, B. Mishra, and D.C. Schwartz, A whole-genome shotgun optical map of Yersinia pestis strain KIM. Appl Environ Microbiol, 2002. 68(12): p. 6321-31.
  24. Lim, A., E.T. Dimalanta, K.D. Potamousis, G. Yen, J. Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N.T. Perna, G. Plunkett, 3rd, V. Burland, B. Mau, J. Hackett, F.R. Blattner, T.S. Anantharaman, B. Mishra, and D.C. Schwartz, Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome Res, 2001. 11(9): p. 1584-93.
  25. Perna, N.T., G. Plunkett, 3rd, V. Burland, B. Mau, J.D. Glasner, D.J. Rose, G.F. Mayhew, P.S. Evans, J. Gregor, H.A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E.J. Grotbeck, N.W. Davis, A. Lim, E.T. Dimalanta, K.D. Potamousis, J. Apodaca, T.S. Anantharaman, J. Lin, G. Yen, D.C. Schwartz, R.A. Welch, and F.R. Blattner, Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature, 2001. 409(6819): p. 529-33.
  26. Ffrench-Constant, R.H., N. Waterfield, V. Burland, N.T. Perna, P.J. Daborn, D. Bowen, and F.R. Blattner, A genomic sample sequence of the entomopathogenic bacterium Photorhabdus luminescens W14: potential implications for virulence. Appl Environ Microbiol, 2000. 66(8): p. 3310-29.
  27. Burland, V., Y. Shao, N.T. Perna, G. Plunkett, H.J. Sofia, and F.R. Blattner, The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res, 1998. 26(18): p. 4196-204.
  28. Perna, N.T., G.F. Mayhew, G. Posfai, S. Elliott, M.S. Donnenberg, J.B. Kaper, and F.R. Blattner, Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7. Infect Immun, 1998. 66(8): p. 3810-7.
  29. Blattner, F.R., G. Plunkett, 3rd, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew, J. Gregor, N.W. Davis, H.A. Kirkpatrick, M.A. Goeden, D.J. Rose, B. Mau, and Y. Shao, The complete genome sequence of Escherichia coli K-12. Science, 1997. 277(5331): p. 1453-74.
  30. Perna, N.T. and T.D. Kocher, Mitochondrial DNA: molecular fossils in the nucleus. Curr Biol, 1996. 6(2): p. 128-9.
  31. Perna, N.T. and T.D. Kocher, Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol, 1995. 41(3): p. 353-8.
  32. Perna, N.T., M.A. Batzer, P.L. Deininger, and M. Stoneking, Alu insertion polymorphism: a new type of marker for human population studies. Hum Biol, 1992. 64(5): p. 641-8.


Last Updated ( Tuesday, 31 July 2007 )
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