Publictaions

Deng, Y., Z. He, J. Van Nostrand and J. Zhou (2008). Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics 9: 491. [pdf]

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. Applied and Environmental Microbiology 73: 563-71. [pdf]

Gentry, T. J., G. S. Wickham, C. W. Schadt, Z. He and J. Zhou (2006). Microarray applications in microbial ecology research. Microbial Ecology 52: 159-175. [pdf]

Hazen, T. C., E. A. Dubinsky, T. Z. DeSantis, G. L. Andersen, Y. M. Piceno, N. Singh, J. K. Jansson, A. Probst, S. E. Borglin, J. L. Fortney, W. T. Stringfellow, M. Bill, M. S. Conrad, L. M. Tom, K. L. Chavarria, T. R. Alusi, R. Lamendella, D. C. Joyner, C. Spier, J. Baelum, M. Auer, M. L. Zemla, R. Chakraborty, E. L. Sonnenthal, P. D'haeseleer, H.-Y. N. Holman, S. Osman, Z. Lu, J. D. Van Nostrand, Y. Deng, J. Zhou and O. U. Mason (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330: 204-208.

He, Z., J. D. Van Nostrand, Y. Deng and J. Zhou (2011). Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Frontiers of Environmental Science & Engineering in China (10.1007/s11783-011-0301-y, in press). [pdf]

He, Z., L. Wu, M. W. Fields and J. Zhou (2005a). Use of microarrays with different probe sizes for monitoring gene expression. Applied and Environmental Microbiology 71: 5154-5162. [pdf]

He, Z., L. Wu, X. Li, M. W. Fields and J. Zhou (2005b). Empirical establishment of oligonucleotide probe design criteria. Applied and Environmental Microbiology 71: 3753-60. [pdf]

He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, Z. Huang, W. Wu, B. Gu, P. Jardine, C. Criddle and J. Zhou (2007). GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. The ISME Journal 1: 67-77. [pdf]

He, Z. and J. Zhou (2008). Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Applied and Environmental Microbiology 74: 2957-66. [pdf]

He, Z., Y. Deng, J. D. Van Nostrand, Q. Tu, M. Xu, C. L. Hemme, X. Li, L. Wu, T. J. Gentry, Y. Yin, J. Liebich, T. C. Hazen and J. Zhou (2010a). GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. The ISME Journal 4: 1167-1179. [pdf]

He, Z., M. Xu, Y. Deng, S. Kang, L. Kellogg, L. Wu, J. D. Van Nostrand, S. E. Hobbie, P. B. Reich and J. Zhou (2010b). Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecology Letters 13: 564-575. [pdf]

He, Z. L., J. D. Van Nostrand, L. Y. Wu and J. Z. Zhou (2008). Development and application of functional gene arrays for microbial community analysis. Transactions of Nonferrous Metals Society of China 18: 1319-1327. [pdf]

Kimes, N. E., J. D. Van Nostrand, E. Weil, J. Zhou and P. J. Morris (2010). Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environmental Microbiology 12: 541-556. [pdf]

Leigh, M. B., V. H. Pellizari, O. Uhlik, R. Sutka, J. Rodrigues, N. E. Ostrom, J. Zhou and J. M. Tiedje (2007). Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). The ISME Journal 1: 134-48. [pdf]

Li, X., Z. He and J. Zhou (2005). Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Research 33: 6114-23. [pdf]

Liang, Y., G. Li, J. D. Van Nostrand, Z. He, L. Wu, Y. Deng, X. Zhang and J. Zhou (2009a). Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiology Ecology 70: 324-333. [pdf]

Liang, Y., J. D. V. Nostrand, J. Wang, X. Zhang, J. Zhou and G. Li (2009b). Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil. Chemosphere 75: 193-199. [pdf]

Liang, Y., Z. He, L. Wu, Y. Deng, G. Li and J. Zhou (2010a). Development of a common oligo reference standard (CORS) for microarray data normalization and comparison across different microbial communities. Applied and Environmental Microbiology 76: 1088¨C1094. [pdf]

Liang, Y., J. D. Van Nostrand, Y. Deng, Z. He, L. Wu, X. Zhang, G. Li and J. Zhou (2010b). Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. The ISME Journal (In press, doi:10.1038/ismej.2010.142). [pdf]

Liebich, J., C. W. Schadt, S. C. Chong, Z. He, S. K. Rhee and J. Zhou (2006). Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Applied and Environmental Microbiology 72: 1688-91.

Liu, W., A. Wang, S. Cheng, B. E. Logan, H. Yu, Y. Deng, J. D. V. Nostrand, L. Wu, Z. He and J. Zhou (2010). Geochip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environmental Science & Technology 44: 7729-7735. [pdf]

Mason, O. U., C. A. Di Meo-Savoie, J. D. Van Nostrand, J. Zhou, M. R. Fisk and S. J. Giovannoni (2009). Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. The ISME Journal 3: 231-42. [pdf]

Parnell, J. J., G. Rompato, L. C. I. V. Latta, M. E. Pfrender, J. D. Van Nostrand, Z. He, J. Zhou, G. Andersen, P. Champine, B. Ganesan and B. C. Weimer (2010). Functional biogeography as evidence of gene transfer in hypersaline microbial communities. PLoS ONE 5: e12919. [pdf]

Rhee, S.-K., X. Liu, L. Wu, S. C. Chong, X. Wan and J. Zhou (2004). Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Applied and Environmental Microbiology 70: 4303-4317. [pdf]

Rodriguez-Martinez, E. M., E. X. Perez, C. W. Schadt, J. Zhou and A. A. Massol-Deya (2006). Microbial diversity and bioremediation of a hydrocarbon-contaminated aquifer (Vega Baja, Puerto Rico). International Journal of Environmental Research and Public Health 3: 292-300. [pdf]

Tas, N., M. H. van Eekert, G. Schraa, J. Zhou, W. M. de Vos and H. Smidt (2009). Tracking functional guilds: Dehalococcoides spp. in European river basins contaminated with hexachlorobenzene. Applied and Environmental Microbiology 75: 4696-704. [pdf]

Tiquia, S. M., L. Wu, S. C. Chong, S. Passovets, D. Xu, Y. Xu and J. Zhou (2004). Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36: 664-70, 672, 674-5. [pdf]

Van Nostrand, J. D., W.-M. Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J. M. Tiedje, T. C. Hazen and J. Zhou (2009). GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environmental Microbiology 11: 2611-2626. [pdf]

Waldron, P. J., L. Wu, J. D. V. Nostrand, C. W. Schadt, Z. He, D. B. Watson, P. M. Jardine, A. V. Palumbo, T. C. Hazen and J. Zhou (2009). Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environmental Science & Technology 43: 3529-3534. [pdf]

Wang, F., H. Zhou, J. Meng, X. Peng, L. Jiang, P. Sun, C. Zhang, J. D. Van Nostrand, Y. Deng, Z. He, L. Wu, J. Zhou and X. Xiao (2009). GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proceedings of the National Academy of Sciences of the United States of America 106: 4840-4845. [pdf]

Wu, L., D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje and J. Zhou (2001). Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology 67: 5780-5790. [pdf]

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. Applied and Environmental Microbiology 72: 4931-41.

Wu, L., L. Kellogg, A. H. Devol, J. M. Tiedje and J. Zhou (2008). Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Applied and Environmental Microbiology 74: 4516-29. [pdf]

Xie, J., Z. He, X. Liu, X. Liu, J. D. Van Nostrand, Y. Deng, L. Wu, G. Qiu and J. Zhou (2010). GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Applied and Environmental Microbiology (doi:10.1128/AEM.01798-10, in press). [pdf]

Xiong, J., L. Wu, S. Tu, J. D. Van Nostrand, Z. He, J. Zhou and G. Wang (2010). Microbial communities and functional genes associated with soil arsenic contamination and rhizosphere of the arsenic hyper-accumulating plant Pteris vittata L. Applied and Environmental Microbiology 76: 7277¨C7284. [pdf]

Xu, M., W.-M. Wu, L. Wu, Z. He, J. D. Van Nostrand, Y. Deng, J. Luo, J. Carley, M. Ginder-Vogel, T. J. Gentry, B. Gu, D. Watson, P. M. Jardine, T. L. Marsh, J. M. Tiedje, T. Hazen, C. S. Criddle and J. Zhou (2010). Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. The ISME Journal 4: 1060-1070.

Yergeau, E., S. Kang, Z. He, J. Zhou and G. A. Kowalchuk (2007). Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal 1(2): 163-79. [pdf]

Zhang, Y., X. Zhang, X. Liu, Y. Xiao, L. Qu, L. Wu and J. Zhou (2007). Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. FEMS Microbiology Letters 266: 144-151. [pdf]

Zhou, J. (2003). Microarrays for bacterial detection and microbial community analysis. Current Opinion in Microbiology 6: 288-294. [pdf]

Zhou, J., S. Kang, C. W. Schadt and C. T. Garten (2008). Spatial scaling of functional gene diversity across various microbial taxa. Proceedings of the National Academy of Sciences of the United States of America 105: 7768-7773. [pdf]

Zhou, J., Z. He, J. D. Van Nostrand, L. Wu and Y. Deng (2010). Applying GeoChip analysis to disparate microbial communities. Microbe 5: 60-65. [pdf]