• NIH, 2007-2010, Molecular Evolution of Microbial Pathogen Genomes

• 6,855,814 - Sequences of E. coli O157, granted Feb 2005.
• 6,706,522 - Plasmid DNA from Yersinia pestis, granted Mar 2004.
• 6,365,723 - Sequences of E. coli O157, granted Apr 2002.

• "progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement"

Darling AE, Mau B, Perna NT, PLOS One 5 (6): e11147 Jun 2010.  Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms.  The multiple genome alignments generated by the software provide a platform for comparative genomic and population genomic studies.

• "Reordering contigs of draft genomes using the Mauve Aligner"

Rissman AL, Mau B, Perna NT et al. Bioinformatics 25(16): 2071-2073 August 2009. Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel application of the Mauve aligner and viewer provides an automated reordering algorithm coupled with a powerful drill-down display allowing detailed exploration of results.

• "Phylogeny and virulence of naturally occuring type III secretion system-deficient pectobacterium strains"

Kim HS, Ma B, Perna NT, et al., Applied Enviornmental Microbiology 75 (13) 4539-4549 Jul 2009. The authors used three previously described DNA-based methods, 16S-23S intergenic transcribed spacer PCR-restriction fragment length polymorphism analysis, multilocus sequence analysis (MLSA), and pulsed-field gel electrophoresis, to examine isolates from diseased stems and tubers and found that MLSA provided the most reliable classification of isolates.

• "Text-mining of PubMed abstracts by natural language processing to create public knowledge base on molecular mechanisms of bacterial enteropathogens"

Zaremba S, Ramos-Santacruz M, Perna NT, et al., BMC Bioinformatics 10 article #177 Jun 2009. We have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity.

• Software:
• ASAP - A Systematic Annotation Package for Community Analysis of Genomes (organizes the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization)
• Mauve - Multiple Genome Alignment (A system for efficiently constructing multiple genome alignments in the presence of large scale evolutionary events such as rearrangement and inversion)
• GRIL - Genome Inversion and Rearrangement Locator (A tool that can be used to identify the location of rearrangements and inversions in the backbone of a set of DNA sequences)