1. Kos, V. N., C. A. Desjardins, A. Griggs, G. Cerqueira, A. Van Tonder, M. T. G. Holden, P. Godfrey, K. L. Palmer, K. Bodi, E. F. Mongodin, J. Wortman, M. Feldgarden, T. Lawley, S. R. Gill, B. J. Haas, B. Birren, and M. S. Gilmore. 2012. Comparative Genomics of Vancomycin-Resistant Staphylococcus aureus Strains and Their Positions within the Clade Most Commonly Associated with Methicillin-Resistant S. aureus Hospital-Acquired Infection in the United States. mBio 3.

2. Casjens, S. R., E. F. Mongodin, W.-G. Qiu, B. J. Luft, S. E. Schutzer, E. B. Gilcrease, W. M. Huang, M. Vujadinovic, J. K. Aron, L. C. Vargas, S. Freeman, D. Radune, J. F. Weidman, G. I. Dimitrov, H. M. Khouri, J. E. Sosa, R. A. Halpin, J. J. Dunn, and C. M. Fraser. 2012. Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids. PLoS ONE 7:e33280.

3. Schutzer, S. E., C. M. Fraser-Liggett, S. R. Casjens, W.-G. Qiu, J. J. Dunn, E. F. Mongodin, and B. J. Luft. 2011. Whole-genome sequences of thirteen isolates of Borrelia burgdorferi. Journal of bacteriology 193:1018-1020.

4. Haven, J., L. C. Vargas, E. F. Mongodin, V. Xue, Y. Hernandez, P. Pagan, C. M. Fraser-Liggett, S. E. Schutzer, B. J. Luft, S. R. Casjens, and W.-G. Qiu. 2011. Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme disease Bacterium. Genetics.

5. Han, A., J. M. Zenilman, J. H. Melendez, M. E. Shirtliff, A. Agostinho, G. James, P. S. Stewart, E. F. Mongodin, D. Rao, A. H. Rickard, and G. S. Lazarus. 2011. The importance of a multifaceted approach to characterizing the microbial flora of chronic wounds. Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society 19:532-541.

6. Casjens, S. R., E. F. Mongodin, W.-G. Qiu, J. J. Dunn, B. J. Luft, C. M. Fraser-Liggett, and S. E. Schutzer. 2011. Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates. Journal of bacteriology 193:6995-6996.

7. Casjens, S. R., C. M. Fraser-Liggett, E. F. Mongodin, W.-G. Qiu, J. J. Dunn, B. J. Luft, and S. E. Schutzer. 2011. Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate. Journal of bacteriology 193:1489-1490.

8. Cantarel, B. L., A. R. Erickson, N. C. Verberkmoes, B. K. Erickson, P. A. Carey, C. Pan, M. Shah, E. F. Mongodin, J. K. Jansson, C. M. Fraser-Liggett, and R. L. Hettich. 2011. Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments. PLoS ONE 6:e27173.

9. Purushe, J., D. E. Fouts, M. Morrison, B. A. White, R. I. Mackie, N. A. C. f. R. Bacteria, P. M. Coutinho, B. Henrissat, and K. E. Nelson. 2010. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microbial Ecology 60:721-729.

10. Morrison, M., S. C. Daugherty, W. C. Nelson, T. M. Davidsen, K. E. Nelson, and N. A. C. f. F. R. Bacteria. 2010. The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology. Microbial Ecology 59:212-213.

11. Li, L., W. W. L. Hsiao, R. Nandakumar, S. M. Barbuto, E. F. Mongodin, B. J. Paster, C. M. Fraser-Liggett, and A. F. Fouad. 2010. Analyzing endodontic infections by deep coverage pyrosequencing. Journal of dental research 89:980-984.

12. Bik, E. M., C. D. Long, G. C. Armitage, P. Loomer, J. B. Emerson, E. F. Mongodin, K. E. Nelson, S. R. Gill, C. M. Fraser-Liggett, and D. A. Relman. 2010. Bacterial diversity in the oral cavity of 10 healthy individuals. The ISME journal 4:962-974.

13. Wywial, E., J. Haven, S. R. Casjens, Y. A. Hernandez, S. Singh, E. F. Mongodin, C. M. Fraser-Liggett, B. J. Luft, S. E. Schutzer, and W.-G. Qiu. 2009. Fast, adaptive evolution at a bacterial host-resistance locus: the PFam54 gene array in Borrelia burgdorferi. Gene 445:26-37.

14. Emami, K., E. Topakas, T. Nagy, J. Henshaw, K. A. Jackson, K. E. Nelson, E. F. Mongodin, J. W. Murray, R. J. Lewis, and H. J. Gilbert. 2009. Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system. The Journal of biological chemistry 284:1086-1096.

15. White, J. R., P. Escobar-Paramo, E. F. Mongodin, K. E. Nelson, and J. DiRuggiero. 2008. Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy. Appl Environ Microbiol 74:6447-6451.

16. van de Werken, H. J. G., M. R. A. Verhaart, A. L. VanFossen, K. Willquist, D. L. Lewis, J. D. Nichols, H. P. Goorissen, E. F. Mongodin, K. E. Nelson, E. W. J. van Niel, A. J. M. Stams, D. E. Ward, W. M. de Vos, J. van der Oost, R. M. Kelly, and S. W. M. Kengen. 2008. Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol 74:6720-6729.

17. Rasko, D. A., M. J. Rosovitz, G. S. A. Myers, E. F. Mongodin, W. F. Fricke, P. Gajer, J. Crabtree, M. Sebaihia, N. R. Thomson, R. Chaudhuri, I. R. Henderson, V. Sperandio, and J. Ravel. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of bacteriology 190:6881-6893.

18. Deboy, R. T., E. F. Mongodin, D. E. Fouts, L. E. Tailford, H. Khouri, J. B. Emerson, Y. Mohamoud, K. Watkins, B. Henrissat, H. J. Gilbert, and K. E. Nelson. 2008. Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. Journal of bacteriology 190:5455-5463.

19. Shapir, N., E. F. Mongodin, M. J. Sadowsky, S. C. Daugherty, K. E. Nelson, and L. P. Wackett. 2007. Evolution of catabolic pathways: Genomic insights into microbial s-triazine metabolism. Journal of bacteriology 189:674-682.

20. Ashby, M. N., J. Rine, E. F. Mongodin, K. E. Nelson, and D. Dimster-Denk. 2007. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol 73:4532-4542.

21. Pieper, R., C. L. Gatlin-Bunai, E. F. Mongodin, P. P. Parmar, S.-T. Huang, D. J. Clark, R. D. Fleischmann, S. R. Gill, and S. N. Peterson. 2006. Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin. Proteomics 6:4246-4258.

22. Mongodin, E. F., N. Shapir, S. C. Daugherty, R. T. Deboy, J. B. Emerson, A. Shvartzbeyn, D. Radune, J. Vamathevan, F. Riggs, V. Grinberg, H. Khouri, L. P. Wackett, K. E. Nelson, and M. J. Sadowsky. 2006. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS genetics 2:e214.

23. Gatlin, C. L., R. Pieper, S.-T. Huang, E. F. Mongodin, E. Gebregeorgis, P. P. Parmar, D. J. Clark, H. Alami, L. Papazisi, R. D. Fleischmann, S. R. Gill, and S. N. Peterson. 2006. Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus. Proteomics 6:1530-1549.

24. Diep, B. A., S. R. Gill, R. F. Chang, T. H. Phan, J. H. Chen, M. G. Davidson, F. Lin, J. Lin, H. A. Carleton, E. F. Mongodin, G. F. Sensabaugh, and F. Perdreau-Remington. 2006. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367:731-739.

25. Deboy, R. T., E. F. Mongodin, J. B. Emerson, and K. E. Nelson. 2006. Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. Journal of bacteriology 188:2364-2374.

26. Conners, S. B., E. F. Mongodin, M. R. Johnson, C. I. Montero, K. E. Nelson, and R. M. Kelly. 2006. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS microbiology reviews 30:872-905.

27. Centeno, M. S. J., C. I. P. D. Guerreiro, F. M. V. Dias, C. Morland, L. E. Tailford, A. Goyal, J. A. M. Prates, L. M. A. Ferreira, R. M. H. Caldeira, E. F. Mongodin, K. E. Nelson, H. J. Gilbert, and C. M. G. A. Fontes. 2006. Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus. FEMS microbiology letters 261:123-132.

28. Rasko, D. A., and E. F. Mongodin. 2005. The first decade of microbial genomics: what have we learned and where are we going next? Genome biology 6:341.

29. Mongodin, E. F., K. E. Nelson, S. Daugherty, R. T. Deboy, J. Wister, H. Khouri, J. Weidman, D. A. Walsh, R. T. Papke, G. Sanchez Perez, A. K. Sharma, C. L. Nesbø, D. MacLeod, E. Bapteste, W. F. Doolittle, R. L. Charlebois, B. Legault, and F. Rodriguez-Valera. 2005. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America 102:18147-18152.

30. Mongodin, E. F., I. R. Hance, R. T. Deboy, S. R. Gill, S. C. Daugherty, R. Huber, C. M. Fraser, K. Stetter, and K. E. Nelson. 2005. Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species. Journal of bacteriology 187:4935-4944.

31. Mongodin, E. F., J. B. Emerson, and K. E. Nelson. 2005. Microbial metagenomics. Genome biology 6:347.

32. Haft, D. H., J. Selengut, E. F. Mongodin, and K. E. Nelson. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS computational biology 1:e60.

33. Gill, S. R., D. E. Fouts, G. L. Archer, E. F. Mongodin, R. T. Deboy, J. Ravel, I. T. Paulsen, J. F. Kolonay, L. Brinkac, M. Beanan, R. J. Dodson, S. C. Daugherty, R. Madupu, S. V. Angiuoli, A. S. Durkin, D. H. Haft, J. Vamathevan, H. Khouri, T. Utterback, C. Lee, G. Dimitrov, L. Jiang, H. Qin, J. Weidman, K. Tran, K. Kang, I. R. Hance, K. E. Nelson, and C. M. Fraser. 2005. Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. Journal of bacteriology 187:2426-2438.

34. Fouts, D. E., E. F. Mongodin, R. E. Mandrell, W. G. Miller, D. A. Rasko, J. Ravel, L. M. Brinkac, R. T. Deboy, C. T. Parker, S. C. Daugherty, R. J. Dodson, A. S. Durkin, R. Madupu, S. A. Sullivan, J. U. Shetty, M. A. Ayodeji, A. Shvartsbeyn, M. C. Schatz, J. H. Badger, C. M. Fraser, and K. E. Nelson. 2005. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS biology 3:e15.

35. Nelson, K. E., D. E. Fouts, E. F. Mongodin, J. Ravel, R. T. Deboy, J. F. Kolonay, D. A. Rasko, S. V. Angiuoli, S. R. Gill, I. T. Paulsen, J. Peterson, O. White, W. C. Nelson, W. Nierman, M. J. Beanan, L. M. Brinkac, S. C. Daugherty, R. J. Dodson, A. S. Durkin, R. Madupu, D. H. Haft, J. Selengut, S. van Aken, H. Khouri, N. Fedorova, H. Forberger, B. Tran, S. Kathariou, L. D. Wonderling, G. A. Uhlich, D. O. Bayles, J. B. Luchansky, and C. M. Fraser. 2004. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids research 32:2386-2395.

36. Mongodin, E. F., J. Finan, M. W. Climo, A. Rosato, S. R. Gill, and G. L. Archer. 2003. Microarray transcription analysis of clinical Staphylococcus aureus isolates resistant to vancomycin. Journal of bacteriology 185:4638-4643.

37. Mongodin, E. F., O. Bajolet, J. Cutrona, N. Bonnet, F. Dupuit, E. Puchelle, and S. de Bentzmann. 2002. Fibronectin-binding proteins of Staphylococcus aureus are involved in adherence to human airway epithelium. Infection and immunity 70:620-630.

38. Mongodin, E. F., O. Bajolet, J. Hinnrasky, E. Puchelle, and S. de Bentzmann. 2000. Cell wall-associated protein A as a tool for immunolocalization of Staphylococcus aureus in infected human airway epithelium. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 48:523-534.

39. Dupuit, F., D. Gaillard, J. Hinnrasky, E. F. Mongodin, S. de Bentzmann, E. Copreni, and E. Puchelle. 2000. Differentiated and functional human airway epithelium regeneration in tracheal xenografts. American journal of physiology. Lung cellular and molecular physiology 278:L165-176.

40. Le Prigent, K., D. Lagadic-Gossmann, E. F. Mongodin, and D. Feuvray. 1997. HCO3(-)-dependent alkalinizing transporter in adult rat ventricular myocytes: characterization and modulation. The American journal of physiology 273:H2596-2603.