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Frank DN (2008) XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data. BMC Bioinformatics 9: 420. pubmed


Frank DN (2009)  BARCRAWL and BARTAB:  Software for design and implementation of barcoded primers for highly multiplexed DNA sequencing.  BMC Bioinformatics. 10:362.


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1. Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, et al. (2003) Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clin Microbiol 41: 295-303.

2. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, et al. (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102: 11070-11075.

3. McManus CJ, Kelley ST (2005) Molecular survey of aeroplane bacterial contamination. J Appl Microbiol 99: 502-508.

4. Papineau D, Walker JJ, Mojzsis SJ, Pace NR (2005) Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol 71: 4822-4832.

5. Spear JR, Walker JJ, McCollom TM, Pace NR (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci U S A 102: 2555-2560.

6. Spear JR, Walker JJ, Pace NR (2005) Hydrogen and primary productivity:  Inference of biogeochemistry from phylogeny in a geothermal ecosystem. In: Inskeep WP, McDermott TR, editors. Geothermal Biology and Geochemistry in Yellowstone National Park. Bozeman, MT: Thermal Biology Institute, Montana State University. pp. 113-128.

7. Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434: 1011-1014.

8. Baumgartner LK, Reid RP, Dupraz C, Decho AW, Buckley DH, et al. (2006) Sulfate reducing bacteria in microbial mats:  changing paradigms, new discoveries. Sedimentary Geology 185: 131-145.

9. Dalby AB, Frank DN, St Amand AL, Bendele AM, Pace NR (2006) Culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal microbiota. Appl Environ Microbiol 72: 6707-6715.

10. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, et al. (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 72: 3685-3695.

11. Rawls JF, Mahowald MA, Ley RE, Gordon JI (2006) Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433.

12. Salmassi TM, Walker JJ, Newman DK, Leadbetter JR, Pace NR, et al. (2006) Community and cultivation analysis of arsenite oxidizing biofilms at Hot Creek. Environ Microbiol 8: 50-59.

13. Spear JR, Walker JJ, Pace NR (2006) Microbial ecology and energetics in yellowstone hotsprings. Yellowstone Science 14: 17-24.

14. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.

15. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104: 13780-13785.

16. Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, et al. (2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 104: 20529-20533.

17. Lee L, Tin S, Kelley ST (2007) Culture-independent analysis of bacterial diversity in a child-care facility. BMC Microbiol 7: 27.

18. Spear JR, Barton HA, Robertson CE, Francis CA, Pace NR (2007) Microbial community biofabrics in a geothermal mine adit. Appl Environ Microbiol 73: 6172-6180.

19. Walker JJ, Pace NR (2007) Phylogenetic Composition of Rocky Mountain Endolithic Microbial Ecosystems. Appl Environ Microbiol.

20. Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, et al. (2008) Eucaryotic Diversity in a Hypersaline Microbial Mat. Appl Environ Microbiol 74: 329-332.

21. Frank DN (2008) XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data. BMC Bioinformatics 9: 420.

22. Frank DN, Pace NR (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 24: 4-10.

23. Isenbarger TA, Finney M, Rios-Velazquez C, Handelsman J, Ruvkun G (2008) Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microbiol 74: 840-849.

24. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, et al. (2008) Evolution of mammals and their gut microbes. Science 320: 1647-1651.

25. Peterson DA, Frank DN, Pace NR, Gordon JI (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 3: 417-427.

26. Sahl JW, Schmidt R, Swanner ED, Mandernack KW, Templeton AS, et al. (2008) Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado. Appl Environ Microbiol 74: 143-152.

27. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213-223.

28. Baumgartner LK, Spear JR, Buckley DH, Pace NR, Reid RP, et al. (2009) Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas. Environ Microbiol 11: 2710-2719.

29. Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, et al. (2009) Opportunistic pathogens enriched in showerhead biofilms. Proc Natl Acad Sci U S A 106: 16393-16399.

30. Frank DN (2009) BARCRAWL and BARTAB:  Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics. 10:362.

31. Frank DN, Wilson SS, St. Amand AL, Pace NR (2009) Culture-independent microbiological analysis of Foley urinary catheter biofilms. PLoS One. 4(11):e7811.

32. Frank DN, Wysocki A, Specht-Glick DD, Rooney A, Feldman RA, et al. (2009) Microbial diversity in chronic open wounds. Wound Repair Regen 17: 163-172.

33. Perkins SD, Mayfield J, Fraser V, Angenent LT (2009) Potentially pathogenic bacteria in shower water and air of a stem cell transplant unit. Appl Environ Microbiol 75: 5363-5372.

34. Robertson CE, Spear JR, Harris JK, Pace NR (2009) Diversity and stratification of archaea in a hypersaline microbial mat. Appl Environ Microbiol 75: 1801-1810.