Selected studies describing the design and application of Functional Gene Arrays:
Gao, H., Z. K. Yang, T. J. Gentry, L. Wu, C. W. Schadt, and J. Zhou. 2007. Microarray-based
Analysis of Microbial Community RNAs by Whole Community RNA Amplification
(WCRA). Appl. Environ. Microbiol 73: 563-571 .
He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Wu WM, Gu B, Jardine P, Criddle
CS, and J-Z Zhou. 2007. GeoChip: A novel comprehensive microarray for investigating
biogeochemical and environmental processes. ISME Journal 1:67-77
Li, X., Z. He, and J. Zhou. 2005. Selection of optimal oligonucleotide probes for microarrays
using multiple criteria, global alignment and parameter estimation. Nucl. Acids Res. 33:61146123.
Liebich, J., C. W. Schadt, S. C. Chong, Z. L. He, S. K. Rhee, and J. Z. Zhou. 2006. Improvement
of oligonucleotide probe design criteria for functional gene microarrays in environmental
applications. Appl. Environ. Microbiol.72:1688-1691.
Schadt, C., and J. Zhou. 2006. Advances in Microarray-Based Technologies for Soil Microbial
Community Analyses pp189-203. in Soil Biology, vol. 8., Springer-Verlag.
Schadt, C. W., J. Liebich, S. C. Chong, T. J. Gentry, Z. L. He, H. B. Pan, and J. Z. Zhou. 2005.
Design and use of functional gene microarrays (FGAs) for the characterization of microbial
communities, pp331-355, in Microbial Imaging, vol. 34., Elsevier.
Wu, L., X. Liu, C. W. Schadt, and J. Zhou. 2006. Microarray-Based Analysis of Subnanogram
Quantities of Microbial Community DNAs by Using Whole-Community Genome
Amplification. Appl. Environ. Microbiol. 72:4931-4941.
Zhou, J-Z., S. Kang, C.W. Schadt, and C.T. Garten. 2008. Spatial scaling of functional
gene diversity across various microbial taxa. PNAS 105:7768-7773
Functional Gene Markers in Fungal Ecology:
Blackwood, C. B., M. P. Waldrop, D. R. Zak, and R. L. Sinsabaugh. 2007. Molecular analysis of
fungal communities and laccase genes in decomposing litter reveals differences among forest
types but no impact of nitrogen deposition. Environ. Microbiol. 9:1306–1316.
Edwards I.P., Upchurch R.A. and D.R. Zak. 2008. Isolation of Fungal Cellobiohydrolase I genes
from sporocarps and forest soils by PCR. Appl. Environ. Microbiol 74:3481-3489.
Luis, P., G. Walther, H. Kellner, F. Martin, and F. Buscot. 2004. Diversity of laccase genes from
basidiomycetes in a forest soil. Soil. Biol. Biochem. 36:1025–1036.
Lyons, J. I., S. Y. Newell, A. Buchan, and M. A. Moran. 2003. Diversity of ascomycete laccase
gene sequences in southeastern US salt marsh. Microb. Ecol. 45:270–281.
Reviews of Functional Genes in Microbial Ecology:
Philippot, L. and S. Hanlin. 2005. Finding the missing link between diversity and activity using
denitrifying bacteria as a model functional community. Curr. Opinion. Microbiol. 8:234-239.
Ward, B.B. 2005. Molecular approaches to marine microbial ecology and the marine nitrogen
cycle. Annual Review of Earth and Planetary Sciences 33: 301
Zher, J.P., B.D. Jenkins, S.M. Short and G.F. Steward. 2003. Minireview: Nitrogenase gene
diversity and microbial community stucture: A cross-system comparison. Environ. Microbiol.
5:539-554.