Publications Relevant to PhyloTrac

Environmental Sequencing


  1. 1.Woese C, Fox G: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977, 74:5088-5090.

  2. 2.Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM: The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 2007, 35(Database issue):D169-172.


  1. 3.DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006, 72(7):5069-5072.


  1. 4.Curtis TP, Sloan WT, Scannell JW: Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 2002, 99(16):10494-10499.

  2. 5.Hill TCJ, Walsh KA, Harris JA, Moffett BF: Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 2003, 43(1):1-11.

  3. 6.Gans J, Wolinsky M, Dunbar J: Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 2005, 309(5739):1387-1390.

  4. 7.Dunbar, J., S. M. Barns, L. O. Ticknor, and C. R. Kuske: Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 2002, 68:3035-45




PhyloChip Analysis


  1. 1.DeSantis TZ, Stone CE, Murray SR, Moberg JP, Andersen GL: Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol Lett 2005, 245(2):271-278.

  2. 2.Brodie EL, DeSantis TZ, Parker JP, Zubietta IX, Piceno YM, Andersen GL: Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A 2007, 104(1):299-304.

  3. 3.Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK et al: Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 2006, 72(9):6288-6298.

  4. 4.Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP et al: Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol 2007, 45(6):1954-1962.

  5. 5.DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL: High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 2007, 53(3):371-383.

  6. 6.Wilson, K. H., W. J. Wilson, J. L. Radosevich, T. Z. DeSantis, V. S. Viswanathan, T. A. Kuczmarski, and G. L. Andersen: High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 2002, 68:2535-41.