ASAP, a systematic annotation package for community analysis of genomes. - Jeremy D. Glasner; Paul Liss; Guy Plunkett III; Aaron E. Darling; Tejasvini Prasad; Michael Rusch; Alexis Byrnes; Michael K. Gilson; Bryan S. Biehl; Frederick R. Blattner; Nicole T. Perna (Nucleic Acids Res., 2003)

Multiple Alignment of Rearranged Genomes. - Aaron E. Darling; Bob Mau; Mark Craven; Nicole T. Perna (CSB, 2004)

Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes. - Bob Mau; Aaron E. Darling; Nicole T. Perna (Comparative Genomics, 2004)

GRIL: genome rearrangement and inversion locator. - Aaron E. Darling; Bob Mau; Frederick R. Blattner; Nicole T. Perna (Bioinform., 2004)

Procrastination Leads to Efficient Filtration for Local Multiple Alignment. - Aaron E. Darling; Todd J. Treangen; Louxin Zhang; Carla Kuiken; Xavier Messeguer; Nicole T. Perna (WABI, 2006)

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. - Jeremy D. Glasner; Michael Rusch; Paul Liss; Guy Plunkett III; Eric L. Cabot; Aaron E. Darling; Bradley D. Anderson; Paul Infield-Harm; Michael C. Gilson; Nicole T. Perna (Nucleic Acids Res., 2006)

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. - Jeremy D. Glasner; Guy Plunkett III; Bradley D. Anderson; David J. Baumler; Bryan S. Biehl; Valerie Burland; Eric L. Cabot; Aaron E. Darling; Bob Mau; Eric C. Neeno-Eckwall; David Pot; Yu Qiu; et al. (Nucleic Acids Res., 2008)

Reordering contigs of draft genomes using the Mauve Aligner. - Anna I. Rissman; Bob Mau; Bryan S. Biehl; Aaron E. Darling; Jeremy D. Glasner; Nicole T. Perna (Bioinform., 2009)

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. - Sam Zaremba; Mila Ramos-Santacruz; Thomas Hampton; Panna Shetty; Joel Fedorko; Jon Whitmore; John M. Greene; Nicole T. Perna; Jeremy D. Glasner; Guy Plunkett III; Matthew Shaker; David Pot (BMC Bioinform., 2009)

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays. - Yann S. Dufour; Gary E. Wesenberg; Andrew J. Tritt; Jeremy D. Glasner; Nicole T. Perna; Julie C. Mitchell; Timothy J. Donohue (Nucleic Acids Res., 2010)

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. - John P. Hamilton; Eric C. Neeno-Eckwall; Bishwo N. Adhikari; Nicole T. Perna; Ned Tisserat; Jan Leach; C. André Lévesque; C. Robin Buell (Database J. Biol. Databases Curation, 2011)

The evolution of metabolic networks of E. coli. - David J. Baumler; Roman G. Peplinski; Jennifer L. Reed; Jeremy D. Glasner; Nicole T. Perna (BMC Syst. Biol., 2011)

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. - David J. Baumler; Bing Ma; Jennifer L. Reed; Nicole T. Perna (BMC Syst. Biol., 2013)