Institute for Environmental Genomics
Institute for Environmental Genomics
Institute for Environmental Genomics

In press
1.Deng Y, Z He, J Xion g, H Yu, MY Xu, SE Hobbie, PB Reich, CW Schadt, A Kent, E Pendall, M Wallenstein, and J Zhou. Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities. Glob Change Biol. doi: 10.1111/gcb.13098. In press..(To request article, click here)
2.Ding J, Y Zhang, MM Wang, X Sun, J Cong, Y Deng, H Lu, T Yuan, JD Van Nostrand, D Li, J Zhou and Y Yang. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests. Mol Ecol. DOI: 10.1111/mec.13384. In press.(To request article, click here)
3.Tu, Q, X Zhou, Z He, K Xue, L Wu, P Reich, S Hobbie, J Zhou. The Diversity and Co-occurrence Patterns of N-2-Fixing Communities in a CO2-Enriched Grassland Ecosystem. Microbial Ecol. DOI:10.1007/s00248-015-0659-7. [pdf].
4.Van Nostrand, JD, A Zhou, and J Zhou. StressChip for monitoring microbial stress response in the environment. In: (FJ De Bruijn, ed) Environmental Control of Gene Expression and Adaptation in Bacteria. Wiley-Blackwell. In press, Expect pub data, Apr. 2016.
5.Van Nostrand, JD, H Yin, Z He and J Zhou. Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip. In: (FM Martin and S Uroz, eds) Methods in Molecular Biology - Microbial Environmental Genomics. Springer Press. In press, expected pub date, Jan. 2016.
6.Wang Y, R Zhang, Q Zheng, Y Deng, JD Van Nostrand, J Zhou, and N Jiao. Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis. ICES Journal of Marine Science. In press doi:10.1093/icesjms/fsv187.
7.Weiss, S., W. Van Treuren, C. Lozupone, K. Faust, J. Friedman, Y. Deng, L. C. Xia, Z. Z. Xu, L. Ursell, E. J. Alm, A. Birmingham, J. Cram, J. A. Fuhrman, J. Raes, F. Sun, J.-Z. Zhou, and R. Knight. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J, in press.
8.Xue K, M Yuan, Z Shi, Y Qin, Y Deng, L Cheng, L Wu, Z He, J Van Nostrand, R Bracho, S Natali, E Schuur, C Luo, K Konstantinidis, Q Wang, J Cole, J Tiedje, Y Luo, and J Zhou. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nat Clim Change. In press..
9.Zhang, Z., Y. Li, B. Xie, X. Chen, Q. Yao, X. Zhang, M. L. Kempher, M, J.-Z. Zhou, A. Oren, and Q. Qin. Nascent genomic evolution and allopatric speciation of Myroides profundi D25 in its transition from land to ocean. mBIO, in press.
1.Huang C, Z Lia, F Chena, Q Liua, Y Zhao, L Gao, C Chena, J Zhou, and A Wang. 2016. Efficient regulation of elemental sulfur recovery through optimizing working height of upflow anaerobic sludge blanket reactor during denitrifying sulfide removal process. Bioresource Technol. 200:1019-1023. [pdf].
2.Xu, X., Z. Shi, D. Li, A. Rey, H. Ruan, J. M. Craine, J. Liang, J.-Z. Zhou, and Y. Luo. 2016. Soil properties control decomposition of soil organic carbon: Results from data-assimilation analysis. Geoderma. 262:235-242.(To request article, click here)
1.Azarbad, H. A., M. Niklinska, R. Laskowski, N. van Straalen, C. van Gestel, J.-Z. Zhou, Z. He, C. Wen, and W. Roling. 2015. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiology Ecology, 91:1-11,
1.Hemme, CL, SJ Green, L Ris hishwar, O Prakash, A Pettenato, R Chakraborty, AM Deutchbauer, JD Van Nostrand, L Wu, Z He, IK Jordan, TC Hazen, AP Arkin, JE Kostka, and J-Z Zhou. 2016. Lateral Gene Transfer in a Heavy Metal-Contaminated Groundwater Microbial Community. mBio. 7:e02234-15. [pdf].
1.Cai, M., Y. Nie, C. Chi, Y. Tang, Y. Li, X. Wang, Z. Liu, Y. Yang, J.-Z. Zhou, and X. L. Wu. 2015. Crude oil as a microbial seed bank with unexpected functional potentials. Sci. Reports, 5:16057, doi:10.1038/srep16057. [pdf].
2.Cong J, Y Yang, X Liu, H Lu, X Liu, J Zhou, D Li, H Yin, J Ding, and Y Zhang. 2015. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession. Scientific Reports. 5:10007. [pdf].
3.Dai, J, H Wei, C Tian, FH Damron, J Zhou, and D Qiu. 2015. An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis. BMC Microbiol 15:34, doi:10.1186/s12866-015-0357-0. [pdf].
4.Deng, J, Y Gu, J Zhang, K Xue, Y Qin, M Yuan, H Yin, Z He, L Wu, EAG Schuur, JM Tiedje, and J Zhou. 2015. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Mol Ecol. 24:222-234.(To request article, click here)
5.Deng, Y, P Zhang, Y Qin, Q Tu, Y Yand, Z He, CW Schadt, and J Zhou. 2015. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environ Microbiol. doi:10.1111/1462-2920.12981.(To request article, click here)
6.Ding, J., Y. Zhang, Y. Deng, C. Yang, T. Yuan, J. D Van Nostrand, D. Li, J.-Z. Zhou, and Yunfeng Yang. 2015. Integrated metagenomics and network analysis of soil microbial community of the forest timberline. Sci Rep, 5:doi10.1038/srep07994. [pdf].
7.Dopheide, A, G Lear, Z He, J Zhou, GD Lewis. 2015. Functional gene composition, diversity and redundancy in microbial stream biofilm communities. PLOS One, 10(4): e0123179. [pdf].
8.Hemme CL, Q Tu, Z Shi, Y Qin, W Gao, Y Deng, JD Van Nostrand, L Wu, Z He, PSG Chain, S Green Tringe, MW Fields, E Rubin, JM. Tiedje, TC Hazen, A Arkin, J Zhou. 2015. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front in Microbiol,
9.Huang C, Z Li, F Chen, Q Liu, Y Zhao, J Zhou, and A Wang. 2015. Microbial community structure and function in response to the shift of sulfide/nitrate loading ratio during the denitrifying sulfide removal process. Bioresource Technol. 197:227-234.(To request article, click here)
10.Huang, C, Y Zhao, Z Lia, Y Yuan, C Chen, W Tan, S Gao, L Gao, J Zhou, A Wang. 2015. Enhanced elementary sulfur recovery with sequential sulfate-reducing, denitrifying sulfide-oxidizing processes in a cylindrical-type anaerobic baffled reactor. Bioresource Tech. 192:478-785.
11.Leigh, M. B., W.M. Wu, E. Cardenas, O. Uhlik, S. Carroll, T. Gentry, T. L. Marsh, J.-Z. Zhou, P. Jardine, C. S. Criddle, J. M. Tiedje. 2015. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing. Front. Environ. Sci. Engineer. 9(3):453-464.(To request article, click here)
12.Li X, PL Bond, JD Van Nostrand, J Zhou and L Huang. 2015. From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization. Sci Reports. 5:12978, DOI: 10.1038/srep12978. [pdf].
13.Liang Y, Y Jiang, F Wang, C Wen, Y Deng, K Xue, Y Qin, Y Yang, L Wu, J Zhou and B Sun. 2015. Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. ISME J. doi: 10.1038/ismej.2015.78. [pdf].
14.Liang, J, D Li, Z Shi, JM Tiedje, J Zhou, EAG Schuur, KT Konstantinidis, and Y Luo. 2015. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation. Soil Biol Biochem. 80:127-135.
15.Liang, Y, Wu L, Clark IM, Xue K, Yang Y, Van Nostrand JD, Deng Y, He Z, McGrath S, Storkey J, Hirsch PR, Sun B, Zhou J. 2015. Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity. mBio 6(2):e00240-15. doi:10.1128/mBio.00240-15. [pdf].
16.Liang, Y, X Zhang, J Zhou, and G Li. 2015. Long-term oil contamination increases deterministic assembly processes in soil microbes. Ecol Applications. 25:1235-1243.
17.Lin, J, J Chen, J He, J Chen, Q Yan, J Zhou, and P Xie. 2015. Effects of microcystin-LR on bacterial and fungal functional genes profile in rat gut. Toxicon. 96:50-56.
18.Liu, S., Wang, K. Xue, B. Sun, Y. Zhang, Z. He, J. D. Van Nostrand, J.-Z. Zhou and Y. Yang. 2015. The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry. Env. Microbiol. 17:566-576.(To request article, click here)
19.Ma, J, Y Deng, T Yuan, J Zhou, and PJJ Alvarez. 2015. Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycle. Environ Poll. 198:154-160.(To request article, click here)
20.MacDonald, CA, MJ Crawley, DJ Wright, J Kuczynski, L Robinson, R knight, WA Al-Soud, SJ Sorenson, Y Deng, J Zhou, and BK Singh. 2015. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment. Environ Microbiol. 17:841-854.(To request article, click here)
21.Michaletz ST, M D Weiser, J Zhou, M Kaspari, BR Helliker, and BJ Enquist. 2015. Plant Thermoregulation: Energetics, Trait–Environment Interactions, and Carbon Economics. Trends in Ecol Evol. 30:714-724.(To request article, click here)
22.Myung J, Z Wang, T Yuan, P Zhang, JD Van Nostrand, J Zhou, and CS Criddle. 2015. Production of nitrous oxide from nitrite in stable Type II methanotrophic enrichments. Environ Sci Technol. 49:10969-10975.(To request article, click here)
23.Penton, CR, D St. Louis, A Pham, JR Cole, L Wu, Y Luo, EAG Schuur, J Zhou and JM Tiedje. 2015. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Front. Microbiol. 6:746. Doi:10.3389/fmicb.2015.00746 Front. Microbiol. 6:746. Doi:10.3389/fmicb.2015.00746 Front. Microbiol. 6:746. Doi:10.3389/fmicb.2015.00746. [pdf].
24.Qu Y, X Zhang, Q Ma, J Deng, Y Deng, JD Van Nostrand, L Wu, Z He, Y Qin, J Zhou, and J Zhou. 2015. Microbial community dynamics and activity link to indigo production from indole in bioaugmented activated sludge systems. PLoS ONE, 10(9): e0138455. [pdf].
25.Qu, Y, Q Ma, J Deng, W Shen, X Zhang, Z He, JD Van Nostrand, J Zhou, and J Zhou. 2015. Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems. Environ Sci Technol 49:4627-4635.(To request article, click here)
26.Saxena, G., E. M. Marzinelli, N. N. Naing, Z. He, Y. Liang, Y. Piceno, S. Mitra, H. Ping, U. M. Joshi, S.Reuben, K. C. Mynampati, S. Mishra, S. Umashankar, .J.-Z. Zhou, G. Andersen, S. Kjelleberg, and S. Swarup. 2015. Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environ. Sci & Tech., 49:1462-1472.
27.Sheng, Z, JD Van Nostrand, J Zhou, and Y Liu. 2015. The effects of silver nanoparticles on intact wastewater biofilms. Front. Microbiol. 6:680. doi: 10.3389/fmicb.2015.00680. [pdf].
28.Shi S, E Nuccio, DJ Herman, R Rijkers, K Estera, J Li, U Nunes da Rocha, Z He, J Pett-Ridge, EL Brodie, J Zhou, and M Firestone. 2015. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 6(4):e00746-15. [pdf].
29.Shi Y, P Grogan, H Sun, J Xiong, Y Yang, J Zhou, H Chu. 2015. Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities. Soil Biol Biochem. 86:126-1347.
30.Smith MB, AM Rocha, CS Smillie, SW Olesen, C Paradis, L Wu, JH Campbell, JL Fortney, TL Mehlhorn, KA Lowe, JE Earles, J Phillips, SM Techtmann, DC Joyner, DA Elias, KL Bailey, RA Hurt Jr, SP Preheim, MC Sanders, J Yang, MA Mueller, S Brooks, DB Watson, P Zhang, Z He, EA Dubinsky, PD Adams, AP Arkin, MW Fields, J Zhou, EJ Alm, TC Hazen. 2015. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 6: e00326-15. [pdf].
31.Su, J. Q., L.J. Ding, K. Xue, H. Y. Yao, J. Quensen, S. Bai, W. X. Wei, J.S. Wu, J.-Z. Zhou, J. M. Tiedje, and Y.G. Zhu. 2015. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol. Ecol., 24:136-150.
32.Trivedi, P., I.J. Rochester, C. Trivedi, J.D. Van Nostrand, J.-Z. Zhou, S. Karunaratne, I.C. Anderson, B.K. Singh. 2015. Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities. Soil Biol Biochem. 91: 169-181.
33.Tu, Q., M. Yuan, Z. He, Y. Deng, K. Xue, L. Wu, S. Hobbie, P. Reich, and J.-Z. Zhou. 2015. Fungal Communities Respond to Long-Term CO2 Elevation by Community Reassembly. Appl. Environ. Microbiol. 81:5445-2454.
34.Wang, F, Y Liang, Y Jiang, Y Yang, K Xue, J Xiong, J Zhou, and B Sun. 2015. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling. Sci Rep. 5:14345. [pdf].
35.Wang, M., S. Liu, F. Wang, B. Sun, J.-Z. Zhou., and Y. Yang. 2015. Microbial responses to southward and northward Cambisol soil transplant. MicrobiologyOpen , 4:931-940. [pdf].
36.Wang, X, JD Van Nostrand, Y Deng, X Lu, C Wang, J Zhou and X Han. 2015. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiol Ecol. 91(12). doi: 10.1093/femsec/fiv133. [pdf].
37.Wei, STS, MA Fernandez-Martinez, Y Chan, JD Van Nostrand, A de los Rios-Murillo, JMY Chiu, AM Ganeshram, SC Cary, J Zhou, and SB Pointing. 2015. Diverse metabolic and stress-tolerance pathways in chasmoendolithic and soil communities of Miers Valley, McMurdo Dry Valleys, Antarctica. Polar Biol. 38:433-443.
38.Wood SA, M Almaraz, MA Bradford, KL McGuire, S Naeem, C Neill, CA Palm, KL Tully, and JZ Zhou. 2015. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Frontiers in Microbiology, 6:90. doi: 10.3389/fmicb.2015.00090. [pdf].
39.Wood SA, MA Bradford, JA Gilbert, KL McGuire, CA Palm, KL Tully, JZ Zhou, and S Naeem. 2015. Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. J. Applied Ecol. 52:744-752. [pdf].
40.Wu L, C Wen, Y Qin, H Yin, Q Tu, JD Van Nostrand, T Yuan, M Yuan, Y Deng, and J Zhou. 2015. Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiol. 15:125. DOI 10.1186/s12866-015-0450-4. [pdf].
41.Xiong, J., Z. He, S. Shi, A. Kent, Y. Deng, L. Wu, J. D. Van Nostrand, and J.-Z. Zhou. 2015. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C-4 agroecosystem. Sci Rep, 5, 9316. [pdf].
42.Xu M, Z He, Q Zhang, J Liu, J Guo, G Sun, and J Zhou. 2015. Responses of aromatic-degrading microbial communities to elevated nitrate in sediments. Environ Sci Technol 49:12422–12431.(To request article, click here)
43.Xu, T., Y. Li, Z. Shi, C.L. Hemme, Y. Li, Y. Zhu, J.D. Van Nostrand, Z. He, and J. Zhou. 2015. Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase. Appl. Environ. Microbiol. 81:4423–4431. [pdf].
44.Xue K, JD Van Nostrand, J Vangronsveld, N Witters, JO Janssen, J Kumpiene, G Siebielec, R Galazka, L Giagnoni, M Arenella, JZ Zhou, G Renella. 2015. Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil. Chemosphere 138:469-477.(To request article, click here)
45.Yan, Q., Y. Bi, Y. Den, Z. He, L. Wu, Z. Shi, J. Li, X. Wang, Z. Hu, Y. Yu and J.-Z. Zhou. 2015. Impacts of the world’s largest dam (Three-Gorges Dam) on microbial functions as revealed by comparative metagenomics. Sci Reports, 5:8605. doi:10.1038/srep08605. [pdf].
46.Yang, C., Y. Li, B.Y. Zhou, Y. Zhou, W. Zheng, Y. Tian, J.D. Van Nostrand, L. Wu, Z. He, J.-Z. Zhou, and T. Zheng. 2015. Illumina sequencing-based analysis of bacterial community dynamics during Akashiwo sanguine bloom in Xiamen sea, China. Sci Rep, 5: doi:10.1038/srep08476. [pdf].
47.Yin H, J Niu, Y Ren, J Cong, X Zhang, F Fan, Y Xiao, X Zhang, J Deng, M Xie, Z He, J Zhou, Y Liang, and X Liu. 2015. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination. Sci Rep. 5:14266. [pdf].
48.Yue H, M Wang, S Wang, JA Gilbert, X Sun, L. Wu, Q. Lin, Y. Hu, X. Li, Z. He, J.-Z. Zhou, and Y. Yang. 2015. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME J, 9:2012-2020. [pdf].
49.Zhang P, JD Van Nostrand, Z He, R Chakraborty, Y Deng, D Curtis, M Fields, TC Hazen, AP Arkin, and J Zhou. 2015. A slow-release substrate stimulates groundwater microbial communities for long-term in-situ Cr(VI) reduction. Eviron Sci Technol. 49:12922-12931.(To request article, click here)
50.Zhang P, WM Wu, JD Van Nostranda, Y Deng, Z He, T Gihring, G Zhang, CW Schadt, D Watson, P Jardine, CS Criddle, S Brooks, TL Marsh, JM Tiedje, AP Arkin, and J Zhou. 2015. Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reduction. Appl Environ Microbiol. 81:4164-4172.
51.Zhang Y, J Cong, H Lu, G Li, Y Xue, Y Deng, H Li, J Zhou and D Li. 2015. Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China. Microbial Biotech. 8:739-746.
52.Zhang Y, Z Tian, M Liu, ZJ Shi, L Hale, J Zhou, and M Yang. 2015. High concentrations of the antibiotic spiramycin in wastewater lead to high abundance of ammonia-oxidizing archaea in nitrifying populations. Environ Sci Technol. 49:9124-9132.
53.Zhang Z, H Wang, J Zhou, H Li, Z He, JD Van Nostrand, Z Wang, and X Xu. 2015. Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilization. Hydrobiolia. 743:221-235.
54.Zhang, Y, J Cong, H Lu, G Li, Y Xue, Y Deng, H Li, J Zhou and D Li. 2015. Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China. Microbial Biotech. 8:739-746. [pdf].
55.Zhou A, KL Hillesland, Z He, W Schackwitz, Q Tu, GM Zane, Q Ma, Y Qu, DA Stahl, JD Wall, TC Hazen, MW Fields, AP Arkin, and J Zhou. 2015. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J, 9:2360-2372.
56.Zhou, J., Z. He, Y. Yang, Y. Deng, S.G. Tringe and L. Alvarez-Cohen. 2015. High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats. mBio, 6:1e02288-14. [pdf].
1.Antony-Babu, A, A Deveau, J Van Nostrand, J Zhou, F Le Tacon, C Robin, P Frey-Klett, and S Uroz. 2014. Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles. Environ Microbiol. 16(9):2831-2847.(To request article, click here)
2.Bartley, L, T Xu, C Zhang, H Nguyen, and J Zhou. 2014. Switchgrass biomass content, synthesis, and biochemical conversion to biofuels. In: H Luo, Y Wu, and C Kole (eds) Compendiou of Bioenergy Plants: Switchgrass. CRC Press.(To request article, click here)
3.Chen Y, N Qin, J Guo, G Qian, D Fang, D Shi, M Xu, F Yang, Z He, JD Van Nostrand, T Yuan, Y Deng, J Zhou and Ln Li. 2014. Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis. BMC Genomics 15:753. [pdf].
4.Chen, Y., J. S. Pettis, M. Corona, W. Chen, C. Li, M. Spivak, P. K. Visscher, G. DeGrandi-Hoffman, H. Boncristiani, Y. Zhao, D. van Engelsdorp, K. Delaplane, L. Solter, F. Drummond, M. Kramer, W. I. Lipkin , G. Palacios, M. C. Hamilton, B. Smith, S. Huang, H. Zheng, J. Li , X. Zhang, A. Zhou, L. Wu, J.-Z. Zhou, M.-L. Lee, E. W. Teixeira, Z. Li, J,D. Evans. 2014. Israeli acute paralysis virus: epidemiology, pathogenesis and implications for honey bee health. PLoS Pathogens, 10(7):e1004261. [pdf].
5.Chu, H., S. Wang, H. Yue, Q. Lin, Y. Hu, X. Li, J.-Z. Zhou and Y. Yang. 2014. Contrasting soil microbial community structures in two major landscapes of the Tibetan alpine meadow. Microbiology Open, 3(5):585-594.(To request article, click here)
6.Deng, Y and Z He. 2014. Microarray data analysis. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
7.Diaz, M. R., J. D. Van Nordstrand, G.P. Eberli, A. M. Piggot, J.-Z. Zhou, and J. S. Klaus. 2014. Functional Gene Diversity of Oolitic Sands from Great Bahama Bank. Geobiology, 12: 231-249.(To request article, click here)
8.Gao, Y. S. Wang, D. Xu, H. Yu, L. Wu, Q. Lin, Y. Hu, X. Li, Z. He, Y. Deng, J.-Z. Zhou, and Y. Yang. 2014. GeoChip as a Metagenomics Tool to Analyze the Microbial Gene Diversity along an Elevation Gradient. Genomics Data, 2:132-134. [pdf].
9.He, Z and J Zhou. 2014. Microarrays for microbial community analysis at a glance. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
10.He, Z.; J. Xiong, A. D Kent, Y. Deng, K. Xue, G. Wang, L. Wu, J. D Van Nostrand, and J. Zhou.. 2014. Distinct responses of soil microbial communities to elevated CO2 and O-3 in a soybean agro-ecosystem. ISME J 8:714-726. [pdf].
11.Hillesland, KL, S Lim, JJ Flowers, S Turkarslan, N Pinel, GM Zane, N Elliott, Y Qin, L Wu, NS Baliga, J Zhou, JD Wall and DA Stahl. 2014. Erosion of functional independence early in the evolution of a microbial mutualism. Proc Nat Acad Sci USA. 111(4):14822-14827.(To request article, click here)
12.Hu X, Q Liu, Z Li, Z He, Y Gong, Y Cao, and Y Yang. 2014. Metabolic and phylogenetic profile of bacterial community in Guishan Coastal Water (Pearl River Estuary), South China Sea. South China Sea. J. Ocean Univ. China. 13:857-864.(To request article, click here)
13.Jia, X., X. Zhou, Y. Luo, K Xue, X. Xue, X. Xu, Y. Yang, L. Wu, and J.-Z. Zhou. 2014. Effects of substrate addition on soil respiratory carbon release under long-term warming and clipping in a tallgrass prairie. PLosOne, doi: 10.1371/journal.pone.0114203. [pdf].
14.Kappell Anthony D., Wei Yin, Newton Ryan J., Van Nostrand Joy D., Zhou Jizhong, McLellan Sandra L., Hristova Krassimira R.. 2014. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico coastal microbial communities after the Deepwater Horizon oil spill. Front. Microbiol., 5:1-13. [pdf].
15.Kuramae, E.E., J. Z. Zhou, G. A. Kowalchuk, and J. A. van Veen. 2014. Soil-borne microbial functional structure across different land uses. Scientific World J. vol. 2014, Article ID 216071, 8 pages, doi:10.1155/2014/216071. [pdf].
16.Levy, O., B. A. Ball, B. Bond-Lamberty, K. S. Cheruvelil, A. O. Finley, N. Lottig, S. W. Punyasena, J. Xiao, J.-Z. Zhou, L. B. Buckley, C. T. Filstrup, T. Keitt, J. R. Kellner12, Alan K. Knapp, A. D. Richardson, C. Stow, D. Tcheng, M. Toomey, R. Vargas, J. W. Voordeckers, T. Wagner, and J. W. Williams.. 2014. Approaches to advance scientific understanding of macrosystems ecology. Front. Ecol. Environ. 12: 15–23.(To request article, click here)
17.Li Y, J He, Z He, Y Zhou, M Yuan, X Xu, F Sun, C Liu, J Li, W Xie, Y Deng, Y Qin, JD Van Nostrand, L Xiao, L Wu, J-Z Zhou, W Shi, and X Zhou. 2014. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J. 8:1879-1891. [pdf].
18.Li, X., J. Rui, J. Xiong, J. Li, Z. He, J.-Z. Zhou, A. C. Yannarell, and R. I. Mackie. 2014. Functional Potential of Soil Microbial Communities in the Maize Rhizosphere. PlosOne, DOI: 10.1371/journal.pone.0112609, 9(11):e112609. [pdf].
19.Li, Y., T. Xu, T. J. Tschaplinski, N. L. Engle, Y. Yang, D. E. Graham, Z. He, and J.-Z. Zhou. . 2014. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation. Biotechnol Biofuels., 7:25. [pdf].
20.Liang Y, H Zhao, X Zhang, J Zhou, and G Li. . 2014. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites. Sci Tot Environ. 487:272-278.. [pdf].
21.Liang, B., H. Cheng, J. D. Van Nostrand, J. Ma, H. Yu, D. Kong, W. Liu, N. Ren, L. Wu, A. Wang, D. Lee, and J.-Z. Zhou.. 2014. Microbial Community Structure and Function of Nitrobenzene Reduction Biocathode in Response to Carbon Source Switchover. Water Res., 54:137-48 . [pdf].
22.Luo, C., L. M. Rodriguez-R, E. R. Johnston, L. Wu, L. Cheng, K. Xue, Q. Tu, Y. Deng, Z. He, J. Z. Shi, M. M. Yuan, S. A. Rebecca, D. Li, Y. Luo, E. A.G. Schuur, P. Chain, J. M. Tiedje, J.-Z. Zhou, and K. T. Konstantinidis. 2014. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Appl. Environ. Microbiol. 80: 1777-1786. [pdf].
23.Paula, F. S., J. L. M. Rodrigues, J.-Z. Zhou, L. Wu, R. C. Mueller, B. S. Mirza, B. J. M. Bohannan, Klaus Nüsslein, Y. Deng, J. M. Tiedje, and V. H. Pellizari. 2014. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Mol. Ecol. 23:2988-2999.(To request article, click here)
24.Probst, AJ, PY Lum, B John, EA Dubinsky, YM Piceno, LM Tom, GL Andersen, Z He and TZ DeSantis. 2014. Microarray of 16S rRNA gene probes for quantifying population differences across microbiome samples. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
25.Qin, Q.L., B. Xie, X. Zhang, X. Chen, B. Chen, J.-Z. Zhou, A. Oren, and Y. Zhang. 2014. A proposed genus boundary for the prokaryotes based on genomic insights.. J. Bacteriol. 196: 2210-2215. [pdf].
26.Singh, B., C. Quince, C. A. Macdonald, A. Khachane, W. A. Al-Soud, N. Thomas, S. J Sørensen, Z. He, D. White, A.Sinclair, B. Crooks J.-Z. Zhou and C. D. Campbell. 2014. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ. Microbiol. 16(8):2408-2402.(To request article, click here)
27.Sun, Y., Shen, Y. X., Liang, P., Zhou, J., Yang, Y., & Huang, X. 2014. Linkages between microbial functional potential and wastewater constituents in large-scale membrane bioreactors for municipal wastewater treatment. Water Res. 56, 162-171.(To request article, click here)
28.Tu, Q, Y Deng, J Zhou, and Z He. 2014. Development and evaluation of functional gene arrays with GeoChip as an example. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
29.Tu, Q., H. Yu, Z. He, Y. Deng, L. Wu, J. D. Van Nostrand, A. Zhou, J. Voordeckers, Y.-J. Lee, Y. Qin, C. Hemme, Z. Shi, K. Xue, T. Yuan, A. Wang, and J.-Z. Zhou. 2014. GeoChip 4: a functional gene arrays-based high throughput environmental technology for microbial community analysis. Mol. Ecol. Resource 14(5):914-928.(To request article, click here)
30.Tu, Q., Z. He, and J.-Z. Zhou. 2014. Strain/Species identification in metagenomes using genome-specific markers. Nucl. Acid Res., 42: E67-E67 (Editor's pick by Genomeweb) .(To request article, click here)
31.Tu, Q., Z. He, Y. Li, Y. Chen, Y. Deng, L. Lin, C. L. Hemme, T. Yuan, J. D. Van Nostrand, L. Wu, X. Zhou, W. Shi, L. Li, J. Xu, and J.-Z. Zhou. 2014. Development of HuMiChip for Functional Profiling of Human Microbiomes. PLoS One, 9:e90546. [pdf].
32.Van Nostrand J and J Zhou. 2014. Applications of functional gene microarrays for profiling microbial communities. In, V Garcia-Canas, A Cifuentes, and C Simo, eds, Comprehensive Analytical Chemistry: Applications of Advanced Omics Technologies: From Genes to Metabolites, Elsevier, Amsterdam, The Netherlands.
33.Van Nostrand, JD and J Zhou. 2014. GeoChip applications in bioremediation studies. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
34.Varrone*, C., J. D. Van Nostrand*, W. Liu, B. Y. Zhou, Z. Wang, F. Liu, Z. He, L. Wu, J.-Z. Zhou, and A. Wang.. 2014. Metagenomic-based analysis of biofilm communities for electrohydrogenesis: From wastewater to hydrogen. Intl. J. of Hydrogen Energy: 39: 222-4233 (*Equal contribution). [pdf].
35.Vigneron, A, P Cruaud, P Pignet, J-C Caprais, N Callac, M Ciobanu, A Godfroy, EG Roussel, BA Cragg, RJ Parkes, JD Van Nostrand, Z He, J Zhou, and L Toffin. 2014. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin. PLOS One, 9(8): e104427. [pdf].
36.Wakelin, Steven, Emily Gerard, Amanda Black, Kelly Hamonts, Leo Condron, Tong Yuan, Joy van Nostrand, Jizhong Zhou, and Maureen O'Callaghan. 2014. Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu. Environmental Pollution, 190, 1-9.(To request article, click here)
37.Wang, C, X Wang, D Liu, H Wu, X Lu, Y Fang, W Cheng, W Luo, P Jiang, J Shi, H Yin, J Zhou, X Han and E Bai. 2014. Aridity threshold in controlling ecosystem nitrogen cycling in arid and semi-arid grasslands. Nature Comm. 5:4799. [pdf].
38.Wang, F. J.-Z. Zhou, and B. Sun. 2014. Structure of functional ecological networks of soil microbial communities for nitrogen transforming and its response to cropping in major soils in Eastern China. Chinese Science Bulletin, 59: 387-396 (In Chinese).
39.Wang, X., X. Yu, X. Wen, Y. Yang, and J.-Z. Zhou. 2014. Microbial community functional structures in wastewater treatment plants as characterized by GeoChip. PLoS One, 9: e93422. doi:10.1371/journal.pone.0093422. [pdf].
40.Xia, Y., X. Wang, X. Wen, K. Ding, J.-Z. Zhou, Y. Yang, and Y. Zhang. 2014. Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors. Appl. Microbiol. Biotechnol. 98(16):7233-7242.(To request article, click here)
41.Xu Tao, Yongchao Li, Zhili He, Jizhong Zhou. 2014. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis in Clostridium cellulolyticum. Mol Microbiol 91(4), 694–705.(To request article, click here)
42.Xu, M., Q. Zhang, C. Xia, Y. Zhong, G. Sun, J. Guo, T. Yuan, J.-Z. Zhou, and Z. He. 2014. Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments. ISME J. 8:1932-1944. [pdf].
43.Xu, T., Li, Y., Van Nostrand, J. D., He, Z., & Zhou, J. 2014. Cas9-Based Tools for Targeted Genome Editing and Transcriptional Control. Appl. Environ. Microbiol. doi: 10.1128/AEM-03786-13. [pdf].
44.Xu, X, C Chen, A Wang, H Yu, X Zhou, H Guo, Y Yuan, D Lee, J Zhou, N Ren. 2014. Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input. J Haz Mat 278:250-257. [pdf].
45.Xue, K Z He, JD Van Nostrand, and J Zhou. 2014. GeoChip analysis of soil microbial community responses to global change. In: Z He (ed) Microarrays: Current Technology, Innovations and Applications, Caister Academic Press,
46.Xue, K., J. D. Van Nostrand, Z. He and J.-Z. Zhou. 2014. Functional Molecular Analysis of Microbial Nitrogen Cycle by Microarray-based GeoChip: Insights for Climate Change, Agriculture and Other Ecological Studies. In: D. Marco (ed) Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications. Caister Academic, Poole, UK. (out Sept. 2014)
47.Yang F, Ning K, X. Chang, X. Yuan, Q. Tu, Y. Tong, Y. Deng, C. L. Hemme, J. Van Nostrand, X. Cui, Z. He, Z. Chen, D. Guo, J. Yu, Y. Zhang, J.-Z. Zhou, and J. Xu. 2014. Saliva microbiota carry caries-specific functional gene signatures. PLoS One, 9(2):e76458. [pdf].
48.Yang, Y., Y. Gao, Q. Lin, D. Xu, H. Yu, L. Wu, Y. Hu, X. Li, Z. He, Y. Deng, S. Wang and J.-Z. Zhou.. 2014. The microbial gene diversity along an elevation gradient of the Tibetan grassland. ISME J, 8: 430-440. [pdf].
49.Yin, H, X Zhang, X Li, Z He, Y Liang, X Guo, Q Hu, Y Xiao, J Cong, L Ma, J Niu, and X Liu. 2014. Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans. BMC Microbiology 2014, 14:179. [pdf].
50.Yu, H, C Chen, J Ma, W Liu, J Zhou, D Lee, N Ren, A Wang. 2014. GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process. J Environ Sci. 26:1375-1382.(To request article, click here)
51.Yuan, Y, C Chen, B Liang, C Huang, Y Zhao, X Xu, W Tan, X Zhou, S Gao, D Sun, D Lee, J Zhou, and A Wang. 2014. Fine-tuning key parameters of an integrated reactor system for the simultaneous removal of COD, sulfate and ammonium and elemental sulfur reclamation. J Haz Mat. 269:56-67. [pdf].
52.Zhang Y, J Cong, H Lu, C Yang, Y Yang, JZ Zhou, and D. Li. 2014. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types. PLoS One, 9: e93773. doi:10.1371/journal.pone.0093773. [pdf].
53.Zhang Y, J Cong, H Lu, G Li, Y Qu, X Su, J Zhou, and D Li. 2014. Community structure and elevational diversity patterns of soil Acidobacteria. J Environ Sci. 26(8):1717-1724.(To request article, click here)
54.Zhao J, J Zuo, X Wang, J Lin, Y Yang, J Zhou, H Chu, and P Li. 2014. GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant. Water Res. 67:345-354.(To request article, click here)
55.Zhao M, F. Wang, S. Liu, K. Xue, Y. Liang, S. Bai, Z. He, J.D. van Nostrand, J.-Z. Zhou, and Y. Yang, B Sun. 2014. GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping. Genomics Data, 2:166-169. [pdf].
56.Zhao, M., K. Xue, F. Wang, S. Liu, S. Bai, B. Sun, J.-Z. Zhou and Y. Yang. 2014. Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping. ISME J. 8(10):2045-2055. [pdf].
57.Zhou, Jizhong, Ye Deng, Ping Zhang, Kai Xue, Yuting Liang, Joy D. Van Nostrand, Yunfeng Yang, Zhili He, Liyou Wu, David A. Stahl, Terry C. Hazen, James M. Tiedje, and Adam P. Arkin. 2014. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem . Proc. Nat. Acad. Sci. USA, 111: E836-E845. [pdf].
58.Zimmerman N, J Izard, C Klatt, and JZ Zhou and E. Aronson. . 2014. The Unseen World: environmental microbial sequencing and identification methods for ecologists. Front Ecol Environ, 12: 224-231.(To request article, click here)
1.Bai S, Li J, He Z, Van Nostrand JD, Tian Y, Lin G, Zhou J, Zheng T. 2013. GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Appl Microbiol Biotechnol. 97(15):7035-7048.(To request article, click here)
2.Bartley, Laura E., Matthew L. Peck, Sung-Ryul Kim, Berit Ebert, Chithra Manisseri, Dawn M. Chiniquy, Robert Sykes et al. 2013. Overexpression of a BAHD acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification. Plant physiology, 161(4), 1615-1633.(To request article, click here)
3.Chan, Yuki; Joy D. Van Nostrand, Jizhong Zhou, Stephen B. Pointing, and Roberta L. Farrell. 2013. Functional ecology of an Antarctic Dry Valley. PNAS. 110:8990-8995. [pdf].
4.Deng, Y., Yang Y., He Z., Zhou J.. 2013. Molecular ecological network of microbial communities. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference ( Springer-Verlag Berlin Heidelberg, 2013. 2013-03-06 15:51:49 UTC.
5.Eisenlord, Sarah D., Zachary Freedman, Donald R. Zak, Kai Xue, Zhili He, and Jizhong Zhou. 2013. Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition. Appl. Environ. Microbiol. 79, no. 4 (2013): 1191-1199. [pdf].
6.Freedman, Z., S. D. Eisenlord, K. Xue, D. R. Zak, and J.-Z. Zhou.. 2013. Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil Biol. Biochem., 66:130-138.(To request article, click here)
7.He Z., Van Nostrand J., Zhou J. . 2013. GeoChip-based metagenomics technologies for analyzing microbial community functional structure and activities. . In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference ( Springer-Verlag Berlin Heidelberg, 2013. 2013-03-06 15:48:27 UTC.
8.Jiang, H-L, Q He, Z He, CL Hemme, L Wu, and J Zhou. 2013. Continuous Cellulosic Bioethanol Fermentation by Cyclic Fed-Batch Cocultivation. Appl. Environ. Microbiol. 79(5), 1580-1589. [pdf].
9.Kang*, S., J.D. Van Nostrand*, H.L. Gough, Z. He, T.C. Hazen, D.A. Stahl, J. Zhou. 2013. Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments. FEMS Microbiol. Ecol. 86(2):200-214. *Authors contributed equally to this work.(To request article, click here)
10.Lee, Y.-J., J. D. van Nostrand, Q. Tu, Z. Lu, L. Cheng, T. Yuan, Y. Deng, M. Q. Carter, Z. He, L. Wu, F. Yang, J. Xu, and J.-Z. Zhou.. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J., 7: 1974-84. [pdf].
11.Li, D., C. Schadel, R., M.L. Haddix, E.A. Paul, R. Conant, J.W. Li, J.Z. Zhou, and Y.Q. Luo. . 2013. Differential responses of soil organic carbon fractions to warming: Results from an analysis with data assimilation. Soil Biol. & BioChem., 67: 24-30.(To request article, click here)
12.Li, D., X. Zhou, L. Wu, J.-Z. Zhou, and Y. Luo.. 2013. Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie. Glob Change Biol, 19;3553–3564.(To request article, click here)
13.Li, M.; J. Mathieu, Y. Yang, Yu; S. Fiorenza, Y. Deng, Z. He, J.-Z. Zhou, P. Alvarez.. 2013. Widespread distribution of soluble di-iron monooxygenase (SDIMO) genes in Arctic groundwater impacted by 1,4-dioxane. Environ. Sci & Technol., 47:9950-9958.(To request article, click here)
14.Li, Xinyu, Ye Deng, Qi Li, Caiyan Lu, Jingjing Wang, Huiwen Zhang, Jianguo Zhu, Jizhong Zhou, and Zhili He. 2013. Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone. The ISME journal. 7(3):660-671. [pdf].
15.Lin, Lu, Yuetong Ji, Qichao Tu, Ranran Huang, Lin Teng, Xiaowei Zeng, Houhui Song et al. 2013. Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in Thermoanaerobacter. Biotechnology for biofuels, 6(1), 103.(To request article, click here)
16.Lu, Zhenmei, Zhili He, Victoria A. Parisi, Sanghoon Kang, Ye Deng, Joy D. Van Nostrand, Jason R. Masoner, Isabelle M. Cozzarelli, Joseph M. Suflita, and Jizhong Zhou. 2013. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ Sci Technol, 46(11), 5824-5833.(To request article, click here)
17.Penton, C.R., D. St. Louis, Y. Luo, J. Cole, L. Wu, J.-Z. Zhou, T. Schuur, J.-M. Tiedje.. 2013. Fungal diversity in permafrost and tallgrass prairie soils under experimental warming. Environ. Microbiol., 79: 7063-7072.(To request article, click here)
18.Qiu, Dongru, Hehong Wei, Qichao Tu, Yunfeng Yang, Ming Xie, Jingrong Chen, Mark H. Pinkerton, Yili Liang, Zhili He, and Jizhong Zhou. 2013. Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1. Appl. Environ. Microbiol. 79(17), 5250-5257. [pdf].
19.Somenahally, Anil C., Jennifer J. Mosher, Tong Yuan, Mircea Podar, Tommy J. Phelps, Steven D. Brown, Zamin K. Yang et al. 2013. Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities. PloS one, 8(12), e83909.. [pdf].
20.Sul, Woo Jun, Stella Asuming-Brempong, Qiong Wang, Dieter M. Tourlousse, C. Ryan Penton, Ye Deng, Jorge LM Rodrigues et al. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biology and Biochemistry. 65:33-38.(To request article, click here)
21.Tu Q, He Z, Deng Y, Zhou J. 2013. Strain/Species-specific probe design for microbial identification microarrays. Appl Environ Microbiol. 79(16):5085-8. doi: 10.1128/AEM.01124-13. [pdf].
22.Van Nostrand, J. D, Terry J. Gentry, and J.-Z. Zhou. 2013. Microarray-Based Microbial Identification and Characterization. In Y.-W. Tang and C. W. Stratton (eds) Advanced Techniques in Diagnostic Microbiology, 2nd ed., Springer, New York, NY (Invited).
23.Wakelin, Steven A., Barbara IP Barratt, Emily Gerard, Adrienne L. Gregg, Eoin L. Brodie, Gary L. Andersen, Todd Z. DeSantis et al. 2013. Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biol Biochem. 57:675-682.(To request article, click here)
24.Xu, Chenggang, Ranran Huang, Lin Teng, Dongmei Wang, Christopher L. Hemme, Ilya Borovok, Qiang He et al. 2013. Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. Biotechnology for biofuels, 6(1), 73.(To request article, click here)
25.Xu, Meiying; Zhili He, Ye Deng, Liyou Wu, Joy D van Nostrand, Sarah E Hobbie, Peter B Reich and Jizhong Zhou. 2013. Elevated CO2 influences microbial carbon and nitrogen cycling. BMC Microbiology 2013, 13:124. [pdf].
26.Xu. M, Y. Fang, J. Liu, X. Chen, G. Sun, J. Guo, Z. Hua, Q. Tu, L. Wu, J.-Z. Zhou, X. Liu.. 2013. Draft genome sequence of Shewanella decolorationis S12, adye-degrading bacterium isolated from a water treatment plant. Genome Announce. 1(6):e00993-13. doi:10.1128/genomeA.00993-13. [pdf].
27.Xue, K, L Wu, Y Deng, Z He, J Van Nostrand, PG Robertson, TM Schmidt and J Zhou. 2013. Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands. Appl. Environ. Microbiol. 79(4):1284-1294. [pdf].
28.Yang, Y., J. Chen, D. Qiu, and J.-Z. Zhou.. 2013. Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction. BMC Microbiol, 13:267. DOI: 10.1186/1471-2180-13-267. [pdf].
29.Yang, Y., M. Xu, Z. He, J. Guo, G. Sun, J.-Z. Zhou. 2013. Microbial electricity generation enhances decabromodiphenyl ether (BDE-209) degradation . PLoS One, 8:e70686. doi: 10.1371/journal.pone.0070686. [pdf].
30.Yang, Y.F., L. W. Wu, Q. Lin, M.Y. Yuan, D.P Xu, H. Yu, Y.G. Hu, J.C. Duan, X.Z. Li, Z.L. He, K. Xue, S.P. Wang, and J.-Z. Zhou.. 2013. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Glob Change Biol, 19: 637–648.(To request article, click here)
31.Zhang Y, J Xie, M Liu, Z Tian, Z He, JD Van Nostrand, L Ren, J Zhou, M Yang. 2013. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems. Water Res. 47(16):6298-6308.(To request article, click here)
32.Zhang Y, Zhenmei Lu, Shanshan Liu, Yunfeng Yang, Zhili He, Zuohua Ren, Jizhong Zhou, and Diqiang Li. 2013. Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau. BMC microbiology, 13(1), 72. [pdf].
33.Zhang Z, X Zhao, Y Liang, G Li, and J Zhou. 2013. Microbial functional genes reveal selection of microbial community by PAHs in polluted soils. Environmental Chemistry Letters, 11(1), 11-17.(To request article, click here)
34.Zhao FJ, Eleanor Harris, Yan Jia, Jincai Ma, Liyou Wu, Wenju Liu, Steve P. McGrath, Jizhong Zhou, and Yong-Guan Zhu. 2013. Arsenic Methylation in Soils and Its Relationship with Microbial arsM Abundance and Diversity, and As Speciation in Rice. Environ Sci Technol. 47(13):7147-1754.(To request article, click here)
35.Zhou A, E Baidoo, Z He, A Mukhopadhyay, JK Baumohl, P Benke, MP Joachimiak, M Xie, R Song, AP Arkin, TC Hazen, Jay D Keasling, Judy D Wall, David A Stahl and Jizhong Zhou. 2013. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The ISME Journal. 7:1790-1802. [pdf].
36.Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, Zhou J.. 2013. StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Environ Sci Technol. 2013 Sep 3;47(17):9841-9.(To request article, click here)
37.Zhou J, Liu W, Deng Y, Jiang Y, Xue K, He, Van Nostrand JD, Wu L, Yang Y, and Wang A. 2013. Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community. mBio 4(2):e00584-12. [pdf].
38.Zhou JZ, Jiang Y, Deng Y, Shi Z, Zhou BY, Xue K, Wu L, He Z, Yang Y. 2013. Random sampling process leads to overestimation of beta diversity of microbial communities. mBio 4(3):e00324-13. doi:10.1128/mBio.00324-13. [pdf].
1.Beazley MJ, Robert J. Martinez, Suja Rajan, Jessica Powell, Yvette M. Piceno, Lauren M. Tom, Gary L. Andersen, Terry C. Hazen, Joy D. Van Nostrand, Jizhong Zhou, Behzad Mortazavi, Patricia A. Sobecky. 2012. Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill. PLoS ONE 7(7): e41305. [pdf].
2.Carter, Michelle Q; Kai Xue, Maria T. Brandl, Feifei Liu, Liyou Wu, Jacqueline W. Louie,Robert E. Mandrell, Jizhong Zhou. 2012. Functional Metagenomics of Escherichia coli O157:H7 Interactions with Spinach Indigenous Microorganisms during Biofilm Formation. PLoS ONE 7(9): e44186. [pdf].
3.Clark, M. E., Z. He, A. M. Redding, M.P. Joachimiak, J.D. Keasling, J.-Z. Zhou, A.P. Arkin, A. Mukhopadhyay, and M. W. Fields. 2012. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics 13:138. [pdf].
4.Dassa, B., Ilya Borovok, R. Lamed, B. Henrissat, P. Coutinho, C. L. Hemme, Y. Huang, J.-Z. Zhou and E. A. Bayer. 2012. Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics. 13:210. [pdf].
5.Deng, Y., Z. He, M. Xu, Y. Qin, J. D. Van Nostrand, L. Wu, B. A. Roe, G. Wiley, S. E. Hobbie, P. B. Reich, and J.-Z, Zhou. 2012. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities. Appl. Environ. Microbiol., 78:2991-2995. [pdf].
6.Deng, Ye, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, and Jizhong Zhou. 2012. Molecular ecological network analyses. BMC bioinformatics, 13(1), 113. [pdf].
7.Ding, Guo-Chun, Holger Heuer, Zhili He, Jianping Xie, Jizhong Zhou, and Kornelia Smalla. 2012. More functional genes and convergent overall functional patterns detected by geochip in phenanthrene-spiked soils. FEMS microbiology ecology 82, no. 1 (2012): 148-156.(To request article, click here)
8.He, Z., Y. Deng, and J.-Z. Zhou. 2012. Development of functional gene microarrays for microbial community analysis. Curr.Opin. Microbiol., 23: 49-55.(To request article, click here)
9.He, Z., Y. Piceno, Y. Deng, M. Xu, Z. Lu, T. DeSantis, G. Andersen, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2012. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J, 6: 259-272. [pdf].
10.He, Z.L., J. D. Van Nostrand, and J.-Z. Zhou. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr.Opin. Microbiol. 23:460-466.(To request article, click here)
11.Huang, W., and J.-Z. Zhou. 2012. When single cell technology meets omics, the new toolbox of analytical biotechnology is emerging. Curr.Opin. Microbiol., 23:1.(To request article, click here)
12.Liang, Y., J. D. Van Nostrand, L. A. N’Guessan, A. D. Peacock, Y. Deng, P. E. Long, C. T. Resch, L. Wu, Z. He, G. Li, T. C. Hazen, D. R. Lovley, and J.-Z. Zhou. 2012. Microbial Functional Gene Diversity with a Shift of Subsurface Redox Condition during in situ Uranium Reduction. Appl. Environ. Microbiol., 78:2966-2972. [pdf].
13.Liang, Yili, Haichun Gao, Xue Guo, Jingrong Chen, Guanzhou Qiu, Zhili He, Jizhong Zhou, and Xueduan Liu. 2012. Transcriptome analysis of pellicle formation of Shewanella oneidensis. Archives of microbiology, 194(6), 473-482. [pdf].
14.Liu, W.Z., A. Wang, Aijie, D. Sun, Dan, N. Ren, Nanqi, Y. Zhang, J.-Z. Zhou. 2012. Characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (MEC). J. Biotechnol. 157: 628-632.(To request article, click here)
15.Lomax, C., W. Liu, L. Wu, K. Xue, J. Xiong, J.-Z. Zhou, S. P. McGrath, A. A.Meharg, A. J.Miller, and F-J. Zhao. 2012. Methylated arsenic species in plants originate from soil microorganisms. New Phytologist, 193:665-672. [pdf].
16.Lu, Z.-M., Y. Deng, J. D. Van Nostrand, Z. He, J. Voordeckers, A. Zhou, Y.-J. Lee, O. Mason, E. Dubinsky, K. Chavarria, L. Tom, J. Fortney, R. Lamendella, J. K. Jansson, P. D’haeseleer, T. C. Hazen, and J.-Z. Zhou. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J., 6: 451-460. (Highlighted by Science for Environment Policy,, the European Commission's environmental news service for policy makers, titled Microbes degrade oil from Deepwater Horizon spill). [pdf]. [suppl].
17.Lu, Z.M., Z. He, V. A. Parisi, S. Kang, Y. Deng, J. D. Van Nostrand, J. R. Masoner, I. M. Cozzarelli, J. M. Suflita, and J.-Z. Zhou. . 2012. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ. Sci. Technol., 46: 5824-5833.(To request article, click here)
18.Mason, Olivia U., Terry C. Hazen, Sharon Borglin, Patrick SG Chain, Eric A. Dubinsky, Julian L. Fortney, James Han et al. 2012. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME journal 6, no. 9 (2012): 1715-1727. [pdf].
19.Rajeev, Lara; Kristina L. Hillesland, Grant M. Zane, Aifen Zhou, Marcin P. Joachimiak, Zhili He, Jizhong Zhou, Adam P. Arkin, Judy D. Wall and David A. Stahl. 2012. Deletion of the Desulfovibrio vulgaris Carbon Monoxide Sensor Invokes Global Changes in Transcription. J Bacteriol. 194(21):5783-93. [pdf].
20.Reith, Frank, Joel Brugger, Carla M. Zammit, Adrienne L. Gregg, Katherine C. Goldfarb, Gary L. Andersen, Todd Z. DeSantis et al. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. The ISME Journal, 6(11), 2107-2118. [pdf].
21.Trivedi, P., Z. He, J. D. Van Nostrand, Gene Albrigo, J.-Z. Zhou, and N. Wang. 2012. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J, 6: 363-383. [pdf].
22.Van Nostrand, Joy D., Zhili He, Jizhong Zhou. 2012. Use of functional gene arrays for elucidating in situ biodegradation. Frontiers in Microbiology. doi: 10.3389/fmicb.2012.00339. 3:339. [pdf].
23.Walker, Christopher B., Alyssa M. Redding-Johanson, Edward E. Baidoo, Lara Rajeev, Zhili He, Erik L. Hendrickson, Marcin P. Joachimiak et al. 2012. Functional responses of methanogenic archaea to syntrophic growth. The ISME journal. [pdf].
24.Wang, H., Z. He, Z. Lu, J. Zhou, J.D. Van Nostrand, X. Xu, and Z. Zhang. 2012. Genetic linkage of soil carbon pools and microbial functions in subtropical freshwater wetlands in response to experimental warming. Appl. Environ. Microbiol. 78(21), 7652-7661. [pdf].
25.Wang, Y., H. Zheng, F. Chen, J. Zeng, S. Chen, J.-Z. Zhou, and Z. Ouyang. 2012. Methane metabolic microbial community in soils of slash pine plantation and Masson pine plantation. Acta Ecologica Sinica, 32:2-7.
26.Wawrik, B., M. Mendivelso, V.A. Parisi, J.M. Suflita, I.A. Davidova, C.R. Marks, J.D. Van Nostrand, Y. Liang, J.-Z. Zhou, B.J. Huizinga, D. Str?poc, and A.V. Callaghan. 2012. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microb. Ecol. 81:26-42. DOI: 10.1111/j.1574-6941.2011.01272.x. [pdf].
27.Wawrik, B., W. Boling, J. Van Nostrand, J.P. Xie, J.-Z. Zhou,D. A. Bronk. 2012. Assimilatory Nitrate Utilization by Bacteria on the West Florida Shelf as Determined by Stable Isotope Probing and Functional Microarray Analysis. FEMS Microbiology Ecology. 79:400-411.(To request article, click here)
28.Xie, J, L Wu, JD Van Nostrand, Z He, Z Lu, H Yu, J Xiong, X Liu, and J Zhou. 2012. Improvements on environmental DNA extraction and purification procedures for matagenomic analysis. J Cent South Univ. 19:3055-3063.(To request article, click here)
29.Xiong, J, Z He, J. Van Nostrand, G Luo, S Tu, J Zhou, and G Wang. 2012. Assessing the Microbial Community and Functional Genes in a Vertical Soil Profile with Long-Term Arsenic Contamination. PloS one, 7(11), e50507. [pdf].
30.Xu, X., S. Niu, R. A. Sherry, X. Zhou, J.-Z. Zhou, Y. Luo. 2012. Interannual variability in responses of belowground NPP and NPP partitioning to long-term warming and clipping in a tallgrass prairie. Global Change Biol. 18(5):1648-1656.(To request article, click here)
31.Xu, Xia, Rebecca A. Sherry, Shuli Niu, Jizhong Zhou, and Yiqi Luo. 2012. Long-term experimental warming decreased labile soil organic carbon in a tallgrass prairie. Plant and soil, 361(1-2), 307-315.(To request article, click here)
32.Xu, Xia, Yiqi Luo, and Jizhong Zhou. 2012. Carbon quality and the temperature sensitivity of soil organic carbon decomposition in a tallgrass prairie. Soil Biology and Biochemistry, 50:142-148.(To request article, click here)
33.Yergeau, E., S. Bokhorst, S. Kang, J.-Z. Zhou, C. W. Greer, R. Aerts, G. A. Kowalchuk. 2012. Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J, 6: 692-702. [pdf].
34.Zhou AF, YI Chen, GM Zane, ZH He, CL Hemme, MP Joachimiak, J Baumohl, Q He, MW Fields, AP Arkin, J. D. Wall, T. C. Hazen, and J.-Z. Zhou. 2012. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol, 78(4):1168-1177. [pdf].
35.Zhou JZ, K. Xue, J.-P. Xie, Y. Deng, L.Y. Wu, X.L. Cheng, S.F .Fei, S.P. Deng, Z.-H. He, J.D. van Nostrand, and Y.Q. Luo . 2012. Microbial Mediation of Carbon Cycle Feedbacks to Climate Warming. Nature Climate Change 2 106-110. doi:10.1038/nclimate1331.(To request article, click here)
1.He, Z., D. J. Van Nostrand, Y. Deng, and Z.-J. Zhou. 2011. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front. Environ. Sci. Engin. China 5: 1-20. [pdf].
2.He. Q, Christopher L. Hemme, Helong Jiang, Zhili He, Jizhong Zhou. 2011. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresource Technology 102 (2011) 9586–9592. [pdf].
3.Hemme, CL, Matthew W. Fields, Qiang He, Ye Deng, Lu Lin, Qichao Tu, Housna Mouttaki, Aifen Zhou, Xueyang Feng, Zheng Zuo, Bradley D. Ramsay, Zhili He, Liyou Wu, Joy Van Nostrand, Jian Xu, Yinjie J. Tang, Juergen Wiegel, Tommy J. Phelps, and Jizhong Zhou. 2011. Correlation of Genomic and Physiological Traits of Thermoanaerobacter Species with Biofuel Yields. Appl. Environ. Microbiol, 77:7998-8008. [pdf].
4.Li, B., W.G. Cao, J.-Z. Zhou, and F. Luo. 2011. Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions. BMC Systems Biology 5:73. [pdf].
5.Liang, Y.T. J. D. van Nostrand, Y. Deng, Z.H. He, L.Y. Wu, X. Zhang, G.H. Li and J.-Z. Zhou. 2011. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. The ISME J. 5, 403-413. [pdf]. [suppl].
6.Lin, L., H. Song, Q. Tu, Y. Qin, A. Zhou, W. Liu, Z. He, J.-Z. Zhou, and J. Xu. 2011. The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria. PLoS Genetics, 7(10): e1002318. [pdf].
7.Liu, A.H., L. Wu, Z.L. He, and J.-Z. Zhou. 2011. Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection. Anal Bioanal Chem, 401:2003–2011. [pdf].
8.Sundararajan, A., J. Kurowski, T. Yan, D. M. Klingman, M.P. Joachimiak, J.-Z. Zhou, B. Naranjo, J. A. Gralnick, and M. W. Fields. 2011. Shewanella oneidensis MR-1 Sensory Box Protein Involved in Aerobic and Anoxic Growth. Appl. Environ. Microbiol 77: 4647-4656. [pdf].
9.Van Nostrand, J. D., S. Kang, Y. Deng, Y. Liang, Z. He, and J.-Z. Zhou. 2011. Monitoring Microbial Activity with GeoChip. In: Microbial Metal and Metalloid Metabolism: Advances and Applications. In: J.F. Stolz and R.S. Oremland (eds). Microbial Metal and Metalloid Metabolism: Advances and Applications.ASM Press, Washington DC, (Invited book chapter).(To request article, click here)
10.Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2011. Microarray analysis of environmental samples. In: Environmental Microbiology: Current Technology and Water Applications. Horizon Scientific, Norwich, UK. (Invited book chapter).
11.Van Nostrand, J.D. and J. Zhou. 2011. Application of functional gene arrays (GeoChips) in monitoring carbon cycling. In: N. Jiao, F. Azam, and S. Sander (eds) Biological Carbon Pump (booklet). AAAS. pp 64-65.(To request article, click here)
12.Van Nostrand, J.D., L.Y. Wu*,W.-M. Wu, Z.J. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carroll, Z.-H. He, B.H. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J.M. Tiedje, T. C. Hazen, and J.Z. Zhou. 2011. Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer. Appl. Environ. Microbiol, 77:3860-3869. [pdf]. [suppl].
13.Van Nostrand, J.D., Z.L. He, and J.Z. Zhou. 2011. Metagenomics analysis of below-ground microbial communities using microarrays. In: D. Marco (ed) Metagenomics: Current Innovations and Future Trends, Caister Academic. pp 265-288..
14.Van Nostrand,J.D., Z. He, and J.-Z. Zhou. 2011. New developments and applications of microarrays for microbial community analysis in natural and impacted ecosystems. Pp. 37-45. In: M. Moo-Young (ed) Comprehensive Biotechnology, 2e. Elsevier, Amsterdam, The Netherlands..
15.Van Nostrand,J.D., Z. He, and J.-Z. Zhou. 2011. GeoChip: A high throughput metagenomics technology for dissecting microbial community functional structure. In: F.J. de Bruijn (ed) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. John Wiley & Sons, New Jersey, 509-520.
16.Wang, A.J., L.F. Gao, N.Q. Ren, J.F. Xu, C. Liu, G.-L Cao, H. Yu, W.Z. Liu, C. L. Hemme, Z.H. He, and J.-Z. Zhou. 2011. Isolation and Characterization of Shigella flexneri G3, Capable of Effective Cellulosic Saccharification under Mesophilic Conditions. Appl. Environ. Microbiol, 77: 517-523. [pdf]. [suppl].
17.Wang, J., J. D. Van Nostrand, L. Wu, Z. He, G. Li, and J.-Z. Zhou. 2011. Microarray-Based Evaluation of Whole-Community Genome DNA Amplification Methods. Appl. Environ. Microbiol, 77: 4241-4245. [pdf]. [suppl].
18.Wu, WM, J. Carley, D. Watson , B.H. Gu, S. Brooks, S. S. Kelly, K. Kemner, J. D. van Nostrand , L. Wu, M. Xu, J.-Z. Zhou, J. Luo, E. Cardenas, C. Hwang, M. W. Fields, T. L. Marsh, J. M. Tiedje, S. J. Green, J. E. Kostka, P. K. Kitanidis, P. M. Jardine, C. S. Criddle. 2011. Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Acta Scientiae Circumstaniae. 3: 449-459. (Chinese).
19.Xie, J.P. Z.H. He, X.X. Liu, X.D. Liu, J. D. Van Nostrand, Y. Deng, L.Y. Wu, J.-Z. Zhou, and G.-Z. Qiu. 2011. GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage. Appl. Environ. Microbiol, 77: 991-999. [pdf]. [suppl].
20.Xie, J.P., H.C., Jiang, X.X. Liu, X.D. Liu, J.-Z. Zhou, and G.Z. Qiu. 2011. 16s rDNA based microbial diversity analysis of eleven acid mine drainages obtained from three Chinese copper mines . Journal of Central South University of Technology, 18: 1930-1939.(To request article, click here)
21.Zhou J, Ye Deng, Feng Luo, Zhili He, and Yunfeng Yang. 2011. Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2. mBio 2(4):e00122-11. [pdf]. [suppl].
22.Zhou, J-.Z. *, L.-Y. Wu*, Y. Deng, X.-Y. Zhi, Y.-H. Jiang, Q.-C. Tu, J.-P. Xie, J. D. Van Nostrand, Z.-H. He, and Y.-F. Yang. 2011. Reproducibility and Quantitation of Amplicon Sequencing-Based Detection. The ISME J. 5: 1303-1313. [pdf]. [suppl].
23.Zhou, J., Q. He, C. L. Hemme, A. Mukhopadhyay, K. Hillesland, A. Zhou, Z. He, J. D. Van Nostrand, T. C. Hazen, D. A. Stahl, J. D. Wall, and A. P. Arkin. 2011. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nature Review in Microbiology. 9:452-466. [pdf]. [suppl].
1.Andersen, G. L., Z. He, T.Z. DeSantis, E. L. Brodie, J.-Z. Zhou. 2010. The Use of Microarrays in Microbial Ecology. In: Environmental Molecular Microbiology (Liu, WT; Jansson, JK, eds), pp. 87-109, Caister Academic Press, Wymondham, UK.
2.Cardenas, E., W.-M. Wu, M. B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P. K. Kitanidis, P. M. Jardine, J.-Z. Zhou, C. S. Criddle, T. L. Marsh, and J. M. Tiedje. 2010. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach. Appl. Environ. Microbiol,76: 6778-6786. [pdf]. [suppl].
3.Epelde, L., J. M. Becerril, G. A. Kowalchuk, Y. Deng, J.-Z. Zhou, and C. Garbisu. 2010. Impact of Metal Pollution and Thlaspi caerulescens Growth on Soil Microbial Communities. Appl. Environ. Microbiol. 76(23): 7843-7853. [pdf].
4.Gao, H., S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K. H. Nealson, J. K. Fredrickson, J. M. Tiedje, M. Romine4 and J.-Z. 2010. Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microbiol Biotech. 3(4): 455-466.(To request article, click here)
5.Gao, H., X. Wang, Z.K. Yang, J. Chen, Y. Liang, H. Chen, T. Palzkill, and J.-Z. Zhou. 2010. Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS ONE, e15295, DOI: 10.1371/journal.pone.0015295. [pdf]. [suppl].
6.Gao, Weimin; Terry J. Gentry; Tonia L. Mehlhorn; Susan L. Carroll; Philip M. Jardine; Jizhong Zhou. 2010. Characterization of Co(III) EDTA-Reducing Bacteria in Metal- and Radionuclide-Contaminated Groundwater. Geomicrobiology Journal, 27:93–100. [pdf].
7.Gihring, T.M., C.Q. Schadt, G.-L. Zhang, Z.Yang, S.Carroll, K.Lowe, T.-L. Mehlhorn, P. Jardine, D. Watson, S.C. Brooks, W.Wu, J.E. Kostka, W. Overholt, S.J. Green, J.-Z. Zhou, P. Zhang, J.D. Van Nostrand.. 2010. Changes in Microbial Community Structure and Activity during Amendment with Long-Term Electron Donor Sources for Bioreduction of Groundwater Contaminants. Geochimica et Cosmochimica Acta. 74: A329-A329 (abstract). [pdf].
8.Hazen, T. C., E. Dubinsky, T. DeSantis, G. Andersen, Y. Piceno, N. Singh, J. Jansson, A. Probst, S. Borglin, J. Fortney, W. Stringfellow, M. Bill, M. Conrad, L. Tom, K. Chavarria, T. Alusi, R. Lamendella, D. Joyner, C. Spier, J. Baelum, M. Auer, M. Zemla, R. Chakraborty, E. Sonnenthal, P. D'haeseleer, H.-Y. Holman, S. Osman, Z.M. Lu, J. van Nostrand, Y. Deng, J.Z. Zhou, and O. U. Mason. 2010. Deep-sea oil plume enriches Indigenous oil-degrading bacteria. Science, 330: 204-208. [pdf]. [suppl].
9.He, Q., Z. He, D. C. Joyner, M. Joachimiak, M. N. Price, Z. K. Yang, H.-C. B. Yen, C. L. Hemme, R. Chakraborty, W. Chen, M. M. Fields, D. A. Stahl, J. D. Keasling, M. Keller, A. P. Arkin, T. C. Hazen, J. D. Wall, and J.-Z. Zhou. 2010. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris. The ISME J, 4: 1386-1397. [pdf]. [suppl].
10.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. Leibich, T.C. Hazen, and J. Zhou. 2010. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J. 4: 1167-1179. [pdf]. [suppl].
11.He, Z.H., A.F. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, K. Huang, E. J. Alm, M. W. Fields, J. Wall, D. Stahl, T. C. Hazen, J. D. Keasling, A. P. Arkin, and J.-Z. Zhou. 2010. Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation. Appl. Environ. Microbiol, 76(5):1574-86. [pdf]. [suppl].
12.He, Z.H., M. Xu, D. Ye, S. Kang, L. Kellogg, L.Y. Wu, J. D. Van Nostrand, S. E. Hobbie, P. B. Reich, and J.-Z. Zhou. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol. Lett, 13:564-575. [pdf]. [suppl].
13.Hemme, C. L., H. Mouttaki, Y.-J. Lee, L. Goodwin, S. Lucas, A. Copeland, A. Lapidus, T. G. d. Rio, H. Tice, E. Saunders, T. Brettin, J. C. Detter, C. S. Han, S. Pitluck, M. L. Land, L. J. Hauser, N. Krypides, N. Mikhailova, Z. He, L. Wu, J. D. V. Nostrand, B. Henrissat, Q. He, P. A. Lawson, R. S. Tanner, L. R. Lynd, J. Wiegel, M. W. Fields, A. P. Arkin, C. W. Schadt, B. S. Stevenson, M. J. McInerney, Y. Yang, H. Dong, Denfeng Xing, Nanqi Ren, Aijie Wang, R. L. Huhnke, J. R. Mielenz, S.-Y. Ding, M. E. Himmel, S. Taghavi, D. v. d. Lelie, E. M. Rubin, and J.-Z. Zhou. 2010. Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production. Journal of Bacteriology, 192: 6494-6496. [pdf].
14.Hemme, C. L., Y. Deng, T. J. Gentry, M. W. Fields, L. Wu, Z. Fang, S. Barua, K. Barry, S. Green-Tringe, D. B. Watson, Z. He, T. C. Hazen, J. M. Tiedje, E. M. Rubin and J.-Z Zhou. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. The ISME J, 4:660–672.. [pdf]. [suppl].
15.Huang, Y., W.M. Zong, X. Yan, R.F. Wang, C.L. Hemme, J.-Z. Zhou, Z.H. Zhou. 2010. Succession of the Bacterial Community and Dynamics of Hydrogen Producers in a Hydrogen-Producing Bioreactor. Appl. Environ. Microbiol, 76: 3387-3390. [pdf]. [suppl].
16.Kimes, N. E., J. D.Van Nostrand, E.Weil, J.-Z. 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. Environ. Microbiol. 12:541-556. [pdf].
17.Li B, F Luo, JZ Wang, FA Feltus, J Zhou. 2010. Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins. The 2010 International Conference on Bioinformatics & Computational Biology (BioComp 2010), 166-172, Los Vegas, July 2010. [pdf].
18.Liang, Y., H. Gao, J. Chen, Y. Dong, L. Wu, Z. He, X. Liu, G. Qiu, and J.-Z. Zhou. 2010. Pellicle formation in Shewanella oneidensis. BMC Microbiol. 10: 291, DOI: 10.1186/1471-2180-10-291. [pdf].
19.Liang. Y.T., Z. H. He, L. Y. Wu, Y. Deng, G.H. Li, and J.-Z. Zhou. 2010. Development of a Common Oligonucleotide Reference Standard for Microarray Data Normalization and Comparison across Different Microbial Communities. Appl. Environ. Microbiol, 76(4):1088-94. doi:10.1128/AEM.02749-09. [pdf].
20.Lin L., H.H. Song, Y.T. Ji, Z.H. He, Y.T. Pu, J.-Z. Zhou, and J. Xu. 2010. Ultrasound-mediated DNA transformation in thermophilic Gram-positive anaerobes. PLoS One 5: issue 9, e12582. [pdf]. [suppl].
21.Liu, W.Z., A.J. Wang, Sh. Cheng, B. E. Logan, H. Yu, Y. Deng, J. D. van Nostrand, L.Y. Wu, Z.H. He and J.-Z. Zhou. 2010. Geochip-based Functional Gene analysis of anodophilic communities in microbial electrolysis cellS under Different Operational modes. Environ. Sci. & Technol., 44: 7729-7735. [pdf]. [suppl].
22.Mason OU, Nakagawa T, Rosner M, Van Nostrand JD, Zhou J, et al. 2010. First Investigation of the Microbiology of the Deepest Layer of Ocean Crust. PLoS ONE 5(11): e15399. [pdf]. [suppl].
23.Parnell JJ, Rompato G, Latta LC IV, Pfrender ME, Van Nostrand JD, He J, Zhou J, Andersen G, Champine P, Ganesan B, Weimer BC. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoS ONE 5(9): e12919. [pdf]. [suppl].
24.Reeve, J., C. W. Schadt, L. Carpenter-Boggs, S.H. Kang, J.-Z. Zhou, and J. P. Reganold. 2010. Effects of soil type and farm management on soil ecological functional genes and microbial activities. The ISME J. 4: 1099-1107. [pdf]. [suppl].
25.Reganold, J.P., P.K. Andrews, J.R. Reeve, L. Carpenter-Boggs, C.W. Schadt, J.R. Alldredge, C.F. Ross, N.M. Davies, and J.-Z. Zhou. 2010. Fruit and soil quality of organic and conventional strawberry agroecosystems. PLoS ONE 5: e12346. [pdf]. [suppl].
26.Van Nostrand, J. D, L. Wu, Z. He, and J.-Z. Zhou. 2010. GeoChips for analysis of microbial functional communities. In: J. R. van der Meer (ed) Handbook of Hydrocarbon and Lipid Microbiology, vol 4, Experimental Protocols and Appendices. Springer, New York, pp 4039-4050. (Invited book chapter). [pdf].
27.Van Nostrand, J. D, Y. Liang, Z. He, G. Li, and J.-Z. Zhou. 2010. GeoChip: A high throughput genomic tool for linking community structure to functions. In: K. N. Timmis (ed) Handbook of Hydrocarbon and Lipid Microbiology, vol 3, Consequences of microbial interactions with hydrocarbons, oils, and lipids. Springer, New York, . pp 2677-2685. (Invited book chapter) . [pdf].
28.Van Nostrand, J. D., Z. He, and J.-Z. Zhou. 2010. Analysis of microbial communities by functional gene Arrays. In: L. Barton, M. Mandl and A. Loy (eds) Geomicrobiology: Molecular and Environmental Perspective. Springer, New York, Pp 109-126. [pdf].
29.Wang, A.J., W.Z., Liu WZ, N. Q. Ren, J.-Z. Zhou, and A.A. Cheng. 2010. Key factors affecting microbial anode potential in a microbial electrolysis cell for H-2 production. International Journal of Hydrogen Energy. 35: 13481-13487.(To request article, click here)
30.Wu, M.-M.,, J. Carley, S. J. Green, J. Luo, S. D. Kelly, J. D. van Nostrand, K. Lowe, T. Mehlhorn, S. Carroll, B. Boonchayanant1, F.E. Löfller, D. Watson, K.M. Kemner, J.-Z. Zhou, P. K. Kitanidis, J. E. Kostka, P. M. Jardine, and C. S. Criddle. 2010. Effects of nitrate on the stability of uranium in a bioreduced region of the subsurface. Environ. Sci. Technol. 44: 5104-5111. [pdf]. [suppl].
31.Xiong, J.B., L.Y. Wu, S.X. Tu, J. D. van Nostrand, Z.H. He, J.-Z. Zhou, and G.J. Wang. 2010. Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the Rhizosphere of the Arsenic-Hyperaccumulating Plant Pteris vittata L. Appl. Environ. Microbiol, 76: 7277-7284. [pdf]. [suppl].
32.Xu M, WM Wu, L Wu, Z He, JD Van Nostrand, Y Deng, J Luo, J Carley, M Ginder-Vogel, TJ Gentry, B Gu, D Watson, PM Jardine, TL Marsh, JM Tiedje, T Hazen, CS Criddle and J Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. The ISME Journal. 4: 1060-1070. [pdf]. [suppl].
33.Yang, Y., L. A. McCue, A. B. Parsons, C. X. Guan, S. Feng and J.-Z. Zhou. 2010. The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control. BMC Microbiology: 2010 10:264. DOI: 10.1186/1471-2180-10-264. [pdf].
34.Zhou AF, ZH He, AM Redding, A Mukhopadhyay, CL Hemme, M. P. Joachimiak, K. S. Bender, J. D. Keasling, D. A. Stahl, M. W Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J.-Z. Zhou. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol, 12: 2645-2657. [pdf]. [suppl].
35.Zhou JZ, Y. Deng, F. Luo, Z.-H. He, Q. Tu, and X.Y. Zhi. 2010. Functional Molecular Ecological Networks. mBio 1(4):e00169-10. doi:10.1128/mBio.00169-10. [pdf]. [suppl].
36.Zhou, J.-Z., Z. He, J. D. Van Nostrand, L.Y. Wu, and Y. Deng. 2010. Applying GeoChip Analysis to Disparate Microbial Communities. Microbes, 5:60-65. (Invited review). [pdf].
1.Brajesh K. Singh, Colin D. Campbell, Soren J. Sorenson, Jizhong Zhou. 2009. Soil genomics. Nat. Microbiol. Rev., 7: 10 , DOI: 10.1038/nrmicro2119-c1|ISSN 1740-1526. [pdf].
2.Feng, X.Y., H. Mouttaki, L. Lin, R. Huang, B. Wu, C. L. Hemme, Z.H. He, B.Zhang, L. Hicks, J. Xu, J.Z. Zhou, and Y. J. Tang. 2009. Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp Strain X514 via Isotopomer-Assisted Metabolite Analysis. Appl. Environ. Microbiol, 75: 5001-5008. [pdf]. [suppl].
3.Gao, H., Z.K Yang, S. Barua, S. B. Reed, M. F. Romine, K. H. Nealson, J. K. Fredrickson, J. M. Tiedje, and J.-Z. Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. The ISME J., 3: 966-976. [pdf]. [suppl].
4.Gentry, TJ, Z He, J Zhou. 2009. Detection and Characterization of Uncultivated Microorganisms Using Microarrays. In: Epstein SS (ed) Uncultured Microorganisms (Micorbiology Monographs) Vol. 10. pp 179-202, Springer-Verlag Berlin Heidelberg (invited chapter). [pdf].
5.He Qiang, Peter M. Lokken, Si Chen, Jizhong Zhou. 2009. Characterization of the Impact of Acetate and Lactate on Ethanolic Fermentation by Thermoanaerobacter ethanolicus. Bioresource Technology, 100: 5955-5965 . [pdf]. [suppl].
6.Hwang, C., W.-M.Wu, T.J. Gentry, J. Carley, S.L. Carroll, D. Watson, P.M. Jardine, J. CZ. Zhou, C.S. Criddle, and M.W. Fields. 2009. Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. The ISME J, 3: 47-64. [pdf]. [suppl].
7.Liang YL, He ZL, Gao HC, Qiu GZ, Zhou JZ, Liu XD. 2009. Characterization of cytochrome mutants for pellicle formation in Shewanella onedensis MR-1. TRANSACTIONS OF NONFERROUS METALS SOCIETY OF CHINA,19(3):700-706. [pdf].
8.Liang, Y., J. Wang, J. D. Van Nostrand, J.-Z. Zhou, X. Zhang, G. Li. 2009. Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil. Chemosphere, 75: 193-199. [pdf].
9.Liang, YT; Li, GH; Van Nostrand, JD, et al.. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS MICROBIOLOGY ECOLOGY, 70(2):324-333.. [pdf]. [suppl].
10.Liebich, J, T Wachtmeister, J Zhou and P Burauel. 2009. Degradation of Diffuse Pesticide Contaminants: Screening for Microbial Potential Using a Functional Gene Microarray. VADOSE ZONE JOURNA, 8 : 703-710. [pdf].
11.Luo, Wensui; Shelly D. Kelly, Kenneth M. Kemner, David Watson, Jizhong Zhou, Philip M. Jardine, and Baohua Gu. 2009. Sequestering Uranium and Technetium through Co-precipitation with Aluminum in a Contaminated Acidic Environment. Environ Sci & Technol., 43: 7516-7522. [pdf]. [suppl].
12.Mason, O. U., C. A DiMeo-Savoie, J. D. Van Nostrand, J.-Z. Zhou, M. R. Fisk, and S. J. Giovannoni. 2009. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J, 3: 231-242. [pdf]. [suppl].
13.Ning, J., J. Liebich, M. Kastner, J.-Z Zhou, A. Schaffer, P. and Burauel. 2009. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl. Microbiol. Biotechnol., 82: 983-993. [pdf].
14.Tas, N., M. H.A. van Eekert, G. Schraa, J.-Z. Zhou, W. M. de Vos, and H. Smidt. 2009. Tracking Functional Guilds: "Dehalococcoides" spp. in European River Basins Contaminated with Hexachlorobenzene . Appl. Environ. Microbiol. 75: 4696-4704. [pdf]. [suppl].
15.Van Nostrand, J. D, W.-M. Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C. Criddle, P. Jardine, J. M. Tiedje, T. C. Hazen, J.-Z. Zhou. 2009. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol., 11: 2611-2626. [pdf]. [suppl].
16.Waldron, P. J., J. D.Van Nostrand, D. B. Watson, Z. He, L. Wu, P. M. Jardine, T. C. Hazen, and J.-Z. Zhou. 2009. Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels. Environ. Sci. Technol., 43: 3529-3534. [pdf]. [suppl].
17.Walker C, S. S. Stolyar, D. Chivian, N. Pinel, J. A. Gabster, P. S. Dehal, Z. He,Z.K. Yang, H. B. Yen, J.-Z. Zhou, J. D. Wall, T. C. Hazen, A. P. Arkin, D. A.Stahl. 2009. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environ Microbiol., 11: 2244-2252. [pdf]. [suppl].
18.Walker, C. B., Z.L. He, Z. K. Yang, J. A. Ringbauer, Jr., J.-Z. Zhou, G. Voordouw, J. D. Wall, A. P. Arkin, T.C. Hazen, S. Stolyar, and D. A. Stahl. 2009. The Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris. J. Bacteriol. 191: 5793-5801. [pdf].
19.Wang, A.J., W. Z., Liu, S.A. Cheng, D.F. Xing, J.-Z. Zhou, and B. E. Logan. 2009. Source of methane and methods to control its formation in single chamber microbial electrolysis cells. International Journal of Hydrogen Energy, 34: 3653-3658.(To request article, click here)
20.Wang, F., H. Zhou, J. Meng, X.T. Peng, L. Jiang, P. Sun, C. Zhang, J.D.VanNostrand , Y. Deng, Z. He, L. Wu, J.-Z. Zhou, X. Xiao. 2009. GeoChip-based Analysis of Metabolic Diversity of Microbial Communities at the Juan de Fuca Ridge Hydrothermal Vent. Proc Nat. Acad. Sci, 106: 4840-4845. [pdf]. [suppl].
21.Yang Y. , D. P. Harris, F. Luo, W. Xiong, M. Joachimiak, L. Wu, P. Dehal. J.Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin, and J.-Z. Zhou. 2009. Snapshot of Iron Response in Shewanella oneidensis by Gene Network Reconstruction. BMC Genomics, BMC Genomics 2009, 10:131 doi:10.1186/1471-2164-10-131. [pdf]. [suppl].
22.Zhou, J.-Z. 2009. Predictive Microbial Ecology. Microbial Biotechnology, 2, 154-156. [pdf].
1.Cardenas, Eric, Wei-Min Wu, Mary Beth Leigh, Jack Carley, Sue Carroll, Terry Gentry, Jian Luo, David Watson, Baohua Gu, Matthew Ginder-Vogel, Peter K. Kitanidis, Philip M. Jardine, J.-Z. Zhou, Craig S. Criddle, Terence L. Marsh and James M. Tiedje. 2008. Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Appl. Environ. Microbiol, 74: 3718-3729. [pdf].
2.Deng, Y., Z. He, J. D. Van Nostrand, J.-Z. Zhou. 2008. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics, 9:491doi:10.1186/1471-2164-9-491. [pdf]. [suppl].
3.Gao, Haichun, Donna Pattison, Tingfen Yan, Dawn M. Klingeman, Xiaohu Wang, Joseph Petrosino, Lisa Hemphill, Xiufeng Wan, Adam B. Leaphart, George Weinstock, Timothy Palzkill, and Jizhong Zhou. 2008. Generation and Validation of a Shewanella oneidensis MR-1 Clone Set for Protein Expression and Phage Display. PLoS One Biology, 3(8):e2983. [pdf]. [suppl].
4.Gao, Haichun, Xiaohu Wang, Zamin K. Yang, Timothy Palzkill, and J.-Z. Zhou. 2008. Probing regulon of ArcA in Shewanella oneidensis MR-I by integrated genomic analyses. BMC Genomics 2008, 9(Suppl 1):S11. [pdf]. [suppl].
5.He, Z, J. D.Van Nostrand, L. 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 (Invited review). [pdf].
6.He, Z., and J.-Z. Zhou. 2008. Selection of oligonucleotide probes for microarrays. In: Molecular Microbial Ecology Manual 2nd, pp1880-1891. Springer Netherlands. (Invited review).
7.He, Zhili, and J.-Z. Zhou. 2008. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl. Environ. Microbiol. 74: 2957-2966. [pdf]. [suppl].
8.Pereira, Patricia M., Qiang He, Filipa M. A. Valente, Antonio V. Xavier, J.-Z. Zhou, Ines A. C. Pereira & Ricardo O. Louro. 2008. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 93:347-362. [pdf].
9.Pereira, Patricia M. Qiang He, Antonio V. Xavier, J.-Z. Zhou, Ines A. C. Pereira and Ricardo O. Louro. 2008. Transcriptional Response of Desulfovibrio vulgaris Hildenborough to Oxidative Stress Mimicking Environmental Conditions. Archives of Microbiology, 189: 451-461. [pdf]. [suppl].
10.Rodrigues, D. F., N. Ivannova, Z. He, M. Huebner, J.-Z. Zhou and J. M. Tiedje. 2008. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics 2008, 9:547doi:10.1186/1471-2164-9-547. [pdf]. [suppl].
11.Wang, X., H. Gao, Y. Shen, G.M. Weinstock, J.g Zhou, and T. Palzkill. 2008. A high-throughput percentage-of-binding strategy to measure binding energies in DNAprotein interactions: application to genome-scale site discovery. Nucl. Acids Res., 36: 4863-4871. [pdf]. [suppl].
12.Wu, Liyou*, Laurie Kellogg, Allan H. Devol, Anothy V. Palumbo, James M. Tiedje, and Jizhong Zhou*. 2008. Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments From the Gulf of Mexico. Appl. Environ. Microbiol, 74: 4516-4529. *equal contribution. [pdf]. [suppl].
13.Wu, Liyou, Xueduan Liu, Matthew W. Fields, Dorothea K. Thompson, Christopher E. Bagwell, James M. Tiedje, Terry C. Hazen, and J.-Z. Zhou. 2008. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness. The ISME J, 2:642-655. [pdf]. [suppl].
14.Yang, Y.F., Mengxia Zhu, Liyou Wu, and Jizhong Zhou. 2008. Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference. BMC Genomics, 9(Suppl 2):S5doi:10.1186/1471-2164-9-S2-S5. [pdf].
15.Yang, Yunfeng, Daniel P. Harris, Feng Luo, Liyou Wu, Andrea B. Parsons, Anthony V. Palumbo and J.-Z. Zhou. 2008. Characterization of the Shewanella oneidensis Fur Gene: Roles in Iron and Acid Tolerance Response. BMC Genomics 9(Suppl 1):S11. [pdf]. [suppl].
16.Yin, H., L. Cao, M. Xie, Q. Chen, G. Qiu, J.-Z. Zhou, L. Wu, D. Wang, X. Liu. 2008. Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China. Syst. & Appl. Microbiol. 31: 302-311. [pdf].
17.Yin, HQ, Cao, LH, Qiu, GZ, Wang, DZ, Kellogg, L, Zhou, J.-Z., Liu, XX, Dai ZM, Ding JN, Liu, XD. 2008. Molecular diversity of 16S rRNA and gyrB genes in copper mines. Archives of Microbiology, 189: 101-110. [pdf].
18.Zhou, J.-Z*, Sanghoon Kang*, Christopher W. Schadt, and Charles T. Garten, Jr. 2008. Spatial Scaling of Functional Gene Diversity across Various Microbial Taxa. Proc Nat. Acad. Sci, 105: 7768-7773. *equal contribution. [pdf]. [suppl].
1.Amos, B. K, Youlboong Sung, Kelly E. Fletcher, Terry J. Gentry, Jizhong Zhou, and Frank E. Loffler. 2007. Detection and quantification of Geobacter lovleyi strain SZ: Implications for Bioremediation at tetrachloroethene- and uranium-impacted sites. Appl. Environ. Microbiol. 73: 6898-6904. [pdf]. [suppl].
2.Bender, Kelly S., Huei-Che Bill Yen, Christopher L. Hemme, Zamin Yang, Zhili He, Qiang He, Jizhong Zhou, Katherine H. Huang, Eric J. Alm, Terry C. Hazen, Adam P. Arkin, and Judy D. Wall1. 2007. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibfio vulgatis hildenborough. Appl. Environ. Microbiol. 73: 5389-5400. [pdf].
3.Bretschger, O, Anna Obraztsova, Carter A. Sturm, In Seop Chang, Yuri A. Gorby, Samantha B. Reed, David E. Culley, Catherine L. Reardon, Soumitra Barua, Margaret F. Romine, Jizhong Zhou, Alex S. Beliaev, Rachida Bouhenni, Daad Saffarini, Florian Mansfeld, Byung-Hong Kim, James K. Fredrickson, and Kenneth H. Nealson. 2007. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl. Environ. Microbiol., 73:7003-7012. [pdf]. [suppl].
4.Butler, J. E., Qiang He, Kelly P. Nevin, Zhili He, Jizhong Zhou, Derek R. Lovley. 2007. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics 2007, 8:180. [pdf]. [suppl].
5.Caffrey, S, Hyung-Soo Park, Johanna Voordouw, Zhili He, Jizhong Zhou, and Gerrit Voordouw. 2007. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 189: 6159-6167. [pdf]. [suppl].
6.Gao, H., Z. K. Yang, T. J. Gentry, L.Wu, C. W. Schadt, and J.-Z. Zhou. 2007. Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl. Environ. Microbiol. 73: 563-571. (The 8th of the top 20 papers most requested in 2007 (January to March) by AEM). [pdf].
7.Garten, CT, Sanghoon Kang, Deanne J. Brice, Christopher W. Schadt, and Jizhong Zhou. 2007. Variability in soil properties at different spatial scales (1 m-1 km) in a deciduous forest ecosystem. Soil Biol & Biochem. 39: 2621-2627. [pdf].
8.Gentry, T., C. Schadt, and J. Zhou. 2007. Functional gene array for microbial community analysis. The 3rd edition of the ASM Manual of Environmental Microbiology, (Invited), ASM Press, Washington DC..
9.He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, W.M. Wu, B. Gu, P. Jardine, C. Criddle, and J.Z. Zhou. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. The ISME Journal, 1: 67-77 (News Relase by Nature Press Office: ( [pdf]. [suppl].
10.Huang, Z., C. Zhang, B.P. Hedlund, J. Wiegel, J.Z. Zhou. 2007. Molecular phylogeny of uncultivated Crenarchaeota in Great Basin hot springs of moderately elevated temperature. Geomicrobiology J. 24:535-542. [pdf].
11.Leigh, M.B., Pellizari, V.H., Uhlik, O., Sutka, R., Rodrigues, J., Ostrom, N.E., Zhou, J.Z. and Tiedje, JM. 2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). The ISME J, 1: 134-148. [pdf].
12.Luo*, F., D. Yang*, J. Zhong*, Haichun Gao, Latifur Khan, Dorothea K. Thompson and Jizhong Zhou. 2007. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics, 8:299. *Equal contribution. [pdf]. [suppl].
13.Luo, Feng; Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou and Richard H. Scheuermann. 2007. Modular Organization of Protein Interaction Networks. Bioinformatics 2007 23(2):207-214; doi:10.1093. [pdf].
14.Luo, Wensui, Wei-Min Wu, Tingfen Yan, Craig S. Criddle, Philip M. Jardine, Jizhong Zhou, and Baohua Gu. 2007. Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition. Appl. Microbiol. Biotechnol. 77:713-721. [pdf].
15.Mukhopadhyay, Aindrila, Redding, Alyssa M., Joachimiak, Marcin P., Arkin, Adam P., Borglin, Sharon E., Dehal, Paramvir S., Chakraborty, Romy, Geller, Jil T.,Hazen, Terry C., He, Qiang, Joyner, Dominique C.,Martin, Vincent J. J., Wall, Judy D., Yang, Zamin Koo, Zhou, Jizhong and Keasling, Jay D. (2007). 2007. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgatis Hildenborough. J. Bacteriol., 189(16):5996-6010. [pdf]. [suppl].
16.Stolyar, S., Qiang He, Marcin P. Joachimiak, Zhili He, Zamin Koo Yang, Sharon E. Borglin, Dominique C. Joyner, Katherine Huang, Eric Alm, Terry C. Hazen, Jizhong Zhou, Judy D. Wall, Adam P. Arkin, and David A. Stahl. 2007. Response of Desulfovibrio vulgaris to alkaline stress. J. Bacteriol.,189(24):8944-8952. [pdf]. [suppl].
17.Van Nostrand, J. D, T.V. Khijniak, T.J. Gentry, M.T. Novak, A.G. Sowder, J.Z. Zhou, P.M. Bertsch and P.J. Morris. 2007. Isolation and characterization of four gram-positive nickel-tolerant microorganisms from contaminated sediments. Microb. Ecol. 53: 670-682. [pdf].
18.Wagner, M., Hauke Smidt, Alexander Loy, and Jizhong Zhou. 2007. Unravelling microbial communities with DNA-microarrays: Challenges and future directions. Microb Ecol 53:498-506. [pdf].
19.Wu, Wei-Min, Jack Carley, Jian Luo, Matthew A Ginder-Vogel, Erick Cardenas, Mary Beth Leigh, Chaichi Hwang, Shelly D. Kelly, Chaungmin Ruan, Liyou Wu, Joy Van Nostrand, Terry Gentry , Kenneth Lowe, Tonia Mehlhorn, Sue Carroll, Matthew W. Fields, Baohua Gu, David Watson, Kenneth M. Kemner, Terence Marsh, James Tiedje, Jizhong Zhou, Scott Fendorf, Peter K. Kitanidis, Philip M. Jardine, and Craig S. Criddle. 2007. In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environ.Sci.Technol.2007,41,5716-5723. [pdf]. [suppl].
20.Yang Y, Wan MX, Shi WY, Peng H, Qiu GZ, Zhou JZ, Liu XD. 2007. Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China. AQUATIC MICROBIAL ECOLOGY 47: 141-151. [pdf].
21.Yergeau, E., Kang, S., He, Z., Zhou, J., and Kowalchuk, G.A. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME J. 1: 163-179. [pdf]. [suppl].
22.Yin HQ, Cao LH, Qiu GZ, Wang DZ, Kellogg L, Zhou JZ, Dai ZM, Liu XD. 2007. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems. J. Microbiol. Methods, 70: 165-178. [pdf].
23.Zhang YG, Zhang XQ, Liu XD, Xiao Y, Qu LJ, Wu LY, Zhou JZ. 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].
24.Zhou XC, and J.-Z. Zhou. 2007. Antibody-microarrays on hybrid polymeric thin film-coated slides for multiple-protein Immunoassays. In: Rampal, JB (ed), Microarrays: Volume 2: Applications and Data Analysis, Vol. 382, Methods in Molecular Biology, The Humana Press Inc, New Jersey, USA Pp. 257-270. (Invited).
1.Bagwell, C. E., X. Liu, L. Wu, and J.-Z. Zhou. 2006. Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer. FEMS Microbiology Ecology, 55:424-431. [pdf].
2.Brown, S.D, M. Martin, K. Huang, E. Alm, Y. Yang, A. Arkin, J.-Z. Zhou, and D. K. Thompson. 2006. Cellular Response of Shewanella oneidensis to Strontium Stress. Appl. Environ. Microbiol., 72: 890-900. [pdf]. [suppl].
3.Brown, S.D., M. R. Thompson, N. C. VerBerkmoes, K. Chourey, M. Shah, J.-Z. Zhou, R. L. Hettich, and D. K. Thompson. 2006. Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress. Molecular and Cellular Proteomics., 5: 1054-1071. [pdf]. [suppl].
4.Chhabra, S.R., He, Q., Huang, K.H, Gaucher, S.P. , Alm, E.J., He, Z., Hadi, M.Z., Hazen, T.C., Wall, J.D., Zhou, J-Z., Arkin, A.P. and A.K. Singh. 2006. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 188: 1817-1828. [pdf]. [suppl].
5.Cho, C. M., T. Yan, X. Liu, L. Wu, J.-Z. Zhou, and L. Y. Stein. 2006. Transcriptome of a Nitrosomonas europaea mutant with a disrupted nitrite reductase gene (nirK). Appl. Environ. Microbiol. 70:4450-4454. [pdf]. [suppl].
6.Chourey, K., M. Thompson, J. Morrell-Falvey, N. C. VerBerkmoes, S. D. Brown, M. Shah, J. Zhou, M. Doktycz, R. L. Hettich, and D. K. Thompson. 2006. Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 72: 6331-6344. [pdf]. [suppl].
7.Clark, M.E., Q. He, Z. He, K.H. Huang, E.J. Alm, X. Wan, T.C. Hazen, A.P. Arkin, J.D. Wall, J.-Z. Zhou, and M.W. Fields. 2006. Temporal transcriptomic analysis as Desulfovibrio vulgaris hildenborough transitions into stationary phase during electron donor depletion. Appl. Environ. Microbiol. 72: 5578-5588. [pdf]. [suppl].
8.Fields, M.F., C.E. Bagwell, S.L. Carroll, T. Yan, X. Liu, D.B. Watson, P.M. Jardine, C.S. Criddle, T.C. Hazen, and J.-Z. Zhou. 2006. Phylogenetic and functional biomakers as indicators of bacterial community responses to mixed-waste contamination. Environ. Sci. & Tech. 40: 2601-2607. [pdf].
9.Fields, M.W., J. Schryver, C. C. Brandt, T. Yan, J.-Z. Zhou, and A.V. Palumbo. 2006. Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples. Microbiol. Methods, 65: 144-152. [pdf].
10.Gao, H., Zamin Koo Yang, Liyou, Wu, Dorothea K. Thompson, and J.-Z. Zhou. 2006. Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. J. Bacteriol., 188:4560-4569. [pdf]. [suppl].
11.Gao, Haichun, Anna Obraztova, Nathan Stewart, Radu Popa, James K. Fredrickson, James M. Tiedje, Kenneth, H. Nealson, and Jizhong Zhou. 2006. Shewanella loihica sp nov., isolated from iron-rich microbial mats in the Pacific Ocean. Int J Syst Evol Microbiol ; 56: 1911-1916. [pdf]. [suppl].
12.Gao, W., Yongqing Liu, Carol S. Giometti, Liyou Wu, Xueduan Liu, Tinfeng Yan, Dawn Stanek, Dong Xu, Ying Xu, Matthew W. Fields, and J.-Z. Zhou. 2006. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1. BMC Genomics, 7:76. [pdf].
13.Gentile, M, T. Yan, S.M. Tiquia, M.W. Fields, J. Nyman, J.-Z. Zhou, and C. S. Criddle. 2006. Stability in a Denitrifying Fluidized Bed Reactor. Microbial Ecology, 52: 311-321. [pdf].
14.Gentry T.J., G.S. Wickham, C.W. Schadt, Z. He, and J. Zhou. 2006. Microarray applications in microbial ecology research. Microb. Ecol. 52:159-175.(Invited). [pdf].
15.Gentry, T., and J. Zhou. 2006. Microarray-Based Microbial Identification and Characterization. In Advanced Techniques in Diagnostic Microbiology, Edited by Yi-Wei Tang and Charles W. Stratton, pp 276-290. Springer, New York, NY (Invited). [pdf].
16.He, Qiang, K. Huang, Zhili He, E. Alm, M. W. Fields, Matthew W. Fields, Terry Hazen, Adams Arkin, Judy D. Wall, and J.-Z. Zhou. 2006. Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis. Appl. Environ. Microbiol. 72:4370-4381. [pdf]. [suppl].
17.Hwang, C., W.-M.Wu, T.J.Gentry, J. Carley, S.L.Carroll, C. Schadt, D. Watson, P.M. Jardine, J.-Z. Zhou, R.F. Hickey, C.S. Criddle, and M.W. Fields. 2006. Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor. Appl. Microbiol. Biotechnol. 71:748-760. [pdf].
18.Leaphart, A. B., D. K. Thompson, K. Huang, Eric Alm, X.-F. Wan A. Arkin, S. D. Brown, L. Wu, T. Yan, X. Liu, G. S. Wickham, and J.-Z. Zhou. 2006. Transcriptome Profiling of Shewanella oneidensis Gene Expression Following Exposure to Acidic and Alkaline pH. J. Bacteriol. 188:1633-42. [pdf]. [suppl].
19.Liebich, J., Song C. Chong, Chris Schadt, Z. He, and J.-Z. Zhou. 2006. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl. Environ. Microbiol. 72:1688-1691. [pdf]. [suppl].
20.Luo, F. Jianxin Zhong, Yunfeng Yang, Jizhong Zhou. 2006. Application of Random Matrix Theory to Microarray Data for Discovering Functional Gene Modules. Physics Review E. Physical Review E, 73 (031924), 1-5. [pdf].
21.Luo, F., J. Zhong, Y. Yang, R. H. Scheuermann, and J.-Z Zhou. 2006. Application of random matrix theory to biological networks. Physics Letters A: 357: 420-423. [pdf].
22.Mukhopadhyay A, He ZL, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen WQ, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, Oeller P, Redding A, Sun J, Wall J, Wei J, Yang ZM, Yen HC, J.Z. Zhou and Keasling JD. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics a pproach. J. Bacteriol. 188 : 4068-4078. [pdf].
23.Qiu, Xiaoyun, Michael J. Daly, Alexander Vasilenko, Marina V. Omelchenko, E. K. Gaidamakova, Liyou Wu, Jizhong Zhou, George W. Sundin and James M. Tiedje. 2006. Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. J. Bacteriol. 188:1199-1204. [pdf].
24.Rodriguez-Martinez, E.M., , Ernie X. Perez, Christopher W. Schadt2, Jizhong Zhou2, and Arturo A. Massol-Deya. 2006. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer in Vega Baja, Puerto Rico. International Journal of Environmental Research and Public Health: 3:292-300.(To request article, click here)
25.Roh, Y, Haichun Gao, Hojatollah Vali, David W. Kennedy, Zamin Yang, Weimin Gao, Alice C. Dohnalkova, Raymond D. Stapleton, Ji-Won Moon, Tommy J. Phelps, James K. Fredrickson, and, J. Zhou. 2006. Metal reduction and iron biomineralization by a psychrotolerant Fe(III)-reducing bacterium, Shewanella sp strain PV-4. Appl. Environ. Microbiol. 72:3236-3244. [pdf].
26.Schadt C.W. and J.-Z. Zhou. 2006. Advances in Microarray-Based Technologies for Soil Microbial Community Analyses. In Soil Biology Volume 8: Nucleic Acids and Proteins in Soil (Nannipieri, P. & Smalla K., ed). Springer-Verlag, Pp189-203. [pdf].
27.Walker, C. B. Walker, S. S. Stolyar, N. Pinel, H. C. Yen, Z. He, J.-Z. Zhou, J. D. Wall, D. A. Stahl. 2006. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain. Environ. Microbiol., 8:1950-1959. [pdf]. [suppl].
28.Wan, X.-F., J.-Z. Zhou, and D. Xu. 2006. CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. International Journal of General Systems. 35:109-125.
29.Wei X.-M., Tingfen Yan, Norman G. Hommes, Xiuduan Liu, Liyou Wu, Crystal McAlvin, Martin G. Klotz, Luis A. Sayavedra-Soto, Jizhong Zhou, and Daniel J. Arp. 2006. Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate. FEMS Microbiology Lett. 257:76-83. [pdf].
30.Windt, W.D, Haichun Gao, W. Kr?mer, Jan Dick, Nico Boon, J.-Z. Zhou, and Willy Verstraete. 2006. AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1. Microbiology, 152: 721-729. [pdf]. [suppl].
31.Wu, L*., X. Liu*, C. W. Schadt, and J.-Z. Zhou*. 2006. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl. Environ. Microbiol. 72:4931-4941. *equal contribution. (The 11th of the top 20 papers most requested in 2006 (October to December) by AEM). [pdf]. [suppl].
32.Wu, W.M., J. Carley, T. Gentry, M. A. Ginder-Vogel, M. Fienen, T. Mehlhorn, H. Yan, S. Caroll, J. Nyman, J. Luo, M. E. Gentile, M. W. Fields, R. F. Hickey, D. Watson, S. Fendorf, J.-Z. Zhou, P. Kitanidis, P. M. Jardine, and C. S. Criddle. 2006. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability. Environ. Sci. & Tech. 40: 3986-3995. [pdf]. [suppl].
33.Yan, T, J Zhou, and CL Zhang. 2006. Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. FEMS Microbiology Ecology: 57: 251-259. [pdf].
34.Zhou X, and J.Z Zhou. 2006. Oligosaccharide microarrays fabricated on aminooxyacetyl functionalized glass surface for characterization of carbohydrate-protein interaction. Biosensors & Bioelectronics, 21: 1451-1458. [pdf].
35.Zhou X, JZ Zhou. 2006. Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays. Proteomics, 6:1415-1426. [pdf].
36.Zhu M, Q Wu, Y Yang, JZ Zhou. 2006. A New Approach to Identify Functional Modules Using Random Matrix Theory. IEEE Sym-posium on Computational Intelligence in Bioinformatics and Computational Biology 1:117-123. [pdf].
1.Beliaev, Alexander S., Dawn M. Stanek, Joel A. Klappenbach, Liyou Wu, Daad A. Saffarini, Margie F. Romine, Kenneth H. Nealson, Jim K. Fredrickson, and Jizhong Zhou. 2005. Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J. Bacteriol., 187:7138-7145. [pdf]. [suppl].
2.Bencheikh-Latmani, R., Sarah Middleton Williams, Lisa Haucke, Craig S. Criddle, Liyou Wu, J.-Z. Zhou, Bradley M. Tebo. 2005. Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction. Appl. Environ. Microbiol., 71:7453-7460. [pdf]. [suppl].
3.Fields, M.W., Tingfen Yan, Sung-Keun Rhee, Susan L. Carroll, P. Jardine, C.S. Criddle and J.-Z. Zhou. 2005. Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste. FEMS Microbiol. Ecol. 53(3):417-428. [pdf].
4.Gao, W., Y. Liu, J. Zhou, and P. Hongjun. 2005. Effects of a Strong Static Magnetic Field on Bacterium Shewanella oneidensis: An Assessment by Using Whole Genome Microarray. Bioelectromagnetics, 26(7):558-563. [pdf].
5.Gu, B., W.M Wu, M.A. Ginder-Vogel, H. Yan, M. W. Fields, J.Z. Zhou, S. Fendorf, C. S. Criddle, and P. M. Jardine. 2005. Bioreduction of Uranium in a Contaminated Soil Column. Environ Sci & Tech., 39, 4841-4847. [pdf].
6.He, Z., L. Wu, M. Fields, J.-Z. Zhou. 2005. Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression. Appl. Environ. Microbiol., 71: 5154-5162. [pdf]. [suppl].
7.He, Z., L. Wu, X. Li, M. Fields, J.-Z. Zhou. 2005. Empirical establishment of oligonucleotide probe design criteria. Appl. Environ. Microbiol, 71:3753-3760. (listed as one of the top 20 papers most requested in 2005 by AEM). [pdf]. [suppl].
8.Kataeva, I., J. Chang, H. Xu, C.H. Luan, J. Zhou, V.N. Uversky, D. Lin, P. Horanyi, Z.J. Liu, L.G. Ljungdahl, J. Rose, M. Luo, and B.C. Wang. 2005. Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli. J. Proteome Res. 2005 4:1942-1951. [pdf].
9.Kolker, E., Alex F. Picone, Michael Y. Galperin, Margaret F. Romine, Roger Higdon, Kira S. Makarova, Natali Kolker, Gordon A. Anderson, Kenneth J. Auberry, Gyorgy Babnigg, Alex S. Beliaev, Paul Edlefsen, Dwayne A. Elias, Yuri Gorby, Ted Holzman, Joel Klappenbach, Konstantinos T. Konstantinidis, Miriam L. Land, Mary S. Lipton, Lee-Ann McCue, Matthew Monroe, Ljiljana Pasa-Tolic, Grigoriy Pinchuk, Samuel Purvine, Xiaoyun Qiu, Margaret Serres, Sasha Tsapin, Brian A. Zakrajsek, Wenhong Zhu, Jizhong Zhou, Frank W. Larimer, Charles Lawrence, Monica Riley, Frank R. Collart, John R. Yates, III, Richard D. Smith, Carol Giometti, Kenneth Nealson, James K. Fredrickson, and James M. Tiedje. 2005. Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved Functional Annotations. Proc Nat. Acad. Sci.102: 2099-2104. [pdf]. [suppl].
10.Li, Xingyuan, Zhili He, and J.-Z. Zhou. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucl. Acids Res. 33:6114-6123. [pdf].
11.Liu, Y., W.-M. Gao, T. Yan, L. Wu, X. Liu, E. Alm, S. Wang, A. Arkin, M. W. Fields, D. K. Thompson, and J.-Z. Zhou. 2005. Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions. J. Bacteriol, 187: 2501-2507. [pdf].
12.Oda, Y., S. K. Samanta, L. Wu, X.-D. Liu, T.-F. Yan, J. Zhou, C. S. Harwood. 2005. Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris. J. Bacteriol., 187: 7784-7794. [pdf]. [suppl].
13.Qiu, X., G. W. Sundin, L. Wu, J.-Z. Zhou, and J. M. Tiedje. 2005. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation. J. Bacteriol, 187: 3556-3564. [pdf]. [suppl].
14.Stapleton, R., Zakee L. Sabree, Anthony V. Palumbo, Craig Moyer, Allan Devol, Yul Roh, and J.-Z. Zhou. 2005. Metal reduction at cold temperatures by Shewanella isolates from various marine environments. Aquat. Microb. Ecol. 38:71-79. [pdf].
15.Wu, W., B. Gu, M. W. Fields, M. Gentile,Y. Ku, H. Yan, S. Tiquia, T. Yan, J. Nyman, J.-Z. Zhou, P.M. Jardine, C. S. Criddle. 2005. Uranium (VI) reduction by denitrifying biomass. Bioremediation J., 9:49-61. [pdf].
1.Gao, H., Y. Wang, X. Liu, T. Yan, L. Wu, E. Alm, A. Arkin, D. K. Thompson, and J.-Z. Zhou. 2004. Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis. J. Bacteriol., 186: 7796-7803. [pdf]. [suppl].
2.Liu, Y., A. Venkateswaran, and J.-Z. Zhou. 2004. Functional genomic analysis of Deinococcus radiodurans resistance to ionizing radiation. European Symposium on Environmental Biotechnology on April 25-28, 2004.
3.Luo, F., L. Khan, F. Bastani, I-L. Yen and J.-Z. Zhou. 2004. A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles. BIOINFORMATICS, 20(16):2605-2617. [pdf].
4.Palumbo, A.V., J. Schryver, M. Fields, C. Bagwell, and J.-Z. Zhou, T. Yan, X. Liu, and C. T. Brandt. 2004. Coupling of Functional Gene Diversity and Geochemical Data from Environmental Samples. Appl. Environ. Microbiol, 70:6525-6534. [pdf].
5.Post, V.M, R.C. Izaurralde, J.D. Jastrow, B.A. McCarl, J.E. Amonette, V.L. Bailey, P.M. Jardine, T.O. West, J. Zhou. 2004. Enhancement of carbon sequestration in US soils. BioScience, 54:895-908. [pdf].
6.Qiu, X.-Y., R. A. Hurt, L.-Y. Wu, C.-H. Chen, J. M. Tiedje, and J.-Z. Zhou. 2004. Detection and Quantification of Copper-Denitrifying Bacteria by Quantitative Competitive PCR. J. Microbiol Methods, 59:199-210. [pdf].
7.Rhee, S.K*, X. Liu, L. Wu, S. C. Chong, X. Wan and J.-Z. Zhou*. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-4317. *Equal contribution. [pdf].
8.Schadt, C. W., J. Liebich, S. C. Chong, T. J. Gentry, Z. He, H. Pan and J.-Z. Zhou. 2004. Design and Use of Functional Gene Microarrays (FGAs) for the Characterization of Microbial Communities. In: Savidge T, Pothulakis H (eds) Methods in Microbiology V34: Microbial Imaging, pp331-368, Academic Press, London (Invited). [pdf].
9.Tiquia, S.M., L. Wu, S. C. Chong, S. Passovets, D. Xu, Y. Xu, and J.-Z. Zhou. 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 36: 664-675.(To request article, click here)
10.Tiquia, S.M., M.W. Fields, and J.-Z. Zhou. 2004. Oligonucleotide-based functional gene arrays for analysis of microbial communities in the environment. Molecular Microbial Ecology Manual. Kowalchuk, G.G.; de bruijn, F.J.; Head I. M.; Akkermans, A.D.; van Elsas, J.D. (Eds.), Kluwer Academic Publishers, pp. 1743-1763. [pdf].
11.Wan, X.-F.*, N.C. VerBerkmoes*, L. A. McCue, D. Stanek, H. Connelly, L. Wu, X. Liu, T. Yan, A. Leaphart, R. L. Hettich, J.-Z. Zhou, and D. K. Thompson. 2004. Transcriptomic and proteomic characterization of the fur modulon in the metal-reducing bacterium Shewanella oneidensis. J. Bacteriol. 186: 8385-8400. *Equal contribution. [pdf].
12.Wan, X.-F., D. Xu, Andris Kleinhofs and J.-Z. Zhou. 2004. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evolutionary Biology 2004, 4:19. [pdf].
13.Wu, L., Dorothea K. Thompson, Xueduan Liu, Matthew W. Fields, Christopher E. Bagwell, James M. Tiedje, and J.-Z. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci & Tech., 38: 6775-6782. [pdf]. [suppl].
14.Ye, Q., Yul Roh, Susan L. Carroll, Benjamin Blair, J.-Z. Zhou,, C.-L. Zhang and Matthew W. Fields. 2004. Alkaline anaerobic respiration: Isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl. Environ. Microbiol, 70:5595-5602. [pdf].
15.Zhou X, and J.-Z. Zhou. 2004. Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal. Chem., 76:5302-5312. [pdf].
16.Zhou X, Liyou Wu, J.-Z. Zhou. 2004. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir, 20:8877-8885. [pdf].
17.Zhou, J.-Z and Thompson, D.K. 2004. Microarray technology and applications in environmental microbiology. Vol 82: pp 183-268. D.L. Sparks (Editor-in-Chief), Advances in Agronomy. Academic Press, New York (Invited). [pdf].
18.Zhou, J.-Z., B. Xia, H. Huang, A.V. Palumbo, and J. M. Tiedje. 2004. Microbial diversity and heterogeneity in sandy subsurface soils. Appl. Environ. Microbiol., 70: 1723-1734. [pdf].
19.Zhou, J.-Z., D.K. Thompson, Y. Xu, and James M. Tiedje. 2004. Microbial Functional Genomics. 624pp. John Wiley & Sons, Hoboken, New Jersey. (First comprehensive book in this field). [pdf].
1.Liu, X., S. M. Tiquia, G. Holguin, L. Wu, S. C. Nold, A. H. Devol, K. Luo, A. V. Palumbo, J. M. Tiedje, and J.-Z. Zhou. 2003. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Appl. Environ. Microbiol., 69:3549-3560. [pdf].
2.Liu, Xueduan*, Christopher Bagwell*, Liyou Wu, , Allan H. Devol, , and J.-Z. Zhou. 2003. Molecular Diversity of Sulfate-Reducing Bacteria from Two Different Continental Margin Habitats. Appl. Environ. Microbiol., 69:6073-6081. *Equal contribution. [pdf].
3.Liu, Yongqing*, J.-Z. Zhou*, Marina Omelchenko, Alex Beliaev, Amudhan Venkateswaran, Julia Stair, Liyou Wu, Dorothea K. Thompson, Dong Xu, Igor B. Rogozin, Elena K. Gaidamakova, Min Zhai, Kira S. Makarova, Eugene V. Koonin, and Michael J. Daly. 2003. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. PNAS, 100: 4191-4196. *equal contribution. (Reviewed by Jeremy S.Edwards and John R. Battista. 2003. TRENDS in Biotechnology: 21: 381-382). [pdf]. [suppl].
4.Palumbo, A.V., Fisher, S., Tarver, J.R., Daniels, W.L., Yang, Z., Tiquia, S.M., Wu, L. and Zhou, J. and Amonette, J. 2003. Issues with the Use of Fly Ash for Carbon Sequestration. Proceedings of the Second National Conference on Carbon Sequestration. Hilton Mark Center, Alexandria, Virginia. May 5-8, 2003. [pdf].
5.Roh, Y., C.-L. Zhang, H. Vali, R.J. Lauf, J. Zhou, and T. J. Phelps. 2003. Biogeochemical and environmental factors in Fe biomineralization: magnetite and siderite formation. Clays and Clay Minerals. 51: 83-95. [pdf].
6.Treves, D. S., B. C. Xia, J.-Z. Zhou and J. M. Tiedje. 2003. A Two-Species Test of the Hypothesis That Spatial Isolation Influences Microbial Diversity in Soil. Microbial Ecol., 45:20-28. [pdf].
7.Wan, X., Xu, D., and J.-Z. Zhou. 2003. A new informatics method for measuring synonymous codon usage bias. In Intelligent engineering systems through artificial neural networks, vol 13, eds. Dagli et al., p1101-1018. New York, NY: ASME Press. [pdf].
8.Yan*, T.-F., M. W. Fields*, L.-Y. Wu, Y.-G. Zu, J. M. Tiedje and J.-Z. Zhou. 2003. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ. Microbiol., 5:13-24. *equal contribution. [pdf].
9.Yost, C, L. Hauser, F. Larimer, D.K. Thompson, A. Beliaev, J.-Z. Zhou, Y. Xu, and D. Xu. 2003. A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins. Omics: A Journal of Integrative Biology.7:177-191. [pdf].
10.Zhou, J.-Z. 2003. Microarrays for bacterial detection and microbial community analysis. Curr Opion. Microbiol, 6:288-294. (Invited). [pdf].
11.Zhou, J.-Z., Beicheng Xia, Heshu Huang, David S. Treves, Loren J. Hauser, Richard J. Mural, Anthony V. Palumbo, and James M. Tiedje. 2003. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biology and Biochemistry, 35:915-924. [pdf].
1.Beliaev, A. S, D. K. Thompson, M. Fields, L. Wu, D. P. Lies, K. H. Nealson, and J.-Z. Zhou. 2002. Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J. Bacteriol. 184: 4612-4616. [pdf].
2.Beliaev, A. S., D. K. Thompson, C. S. Giometti, G.-S. Li, J. Yates III, K. H. Nealson, J.M. Tiedje, J. F. Heidelberg, and J.-Z. Zhou. 2002. Gene and Protein Expression Profiles of Shewanella oneidensis During Anaerobic Growth with Different Electron Acceptors. Omics: A Journal of Integrative Biology 6: 39-60. [pdf].
3.Gu, B., D. B. Watson, L. Wu, D. H. Phillips, D. C. White, and J.-Z Zhou. 2002. Microbiological characteristics in a zero-valent iron reactive barrier. Environ. Monitoring Assessment: 77: 293-309. [pdf].
4.Palumbo A. V., J.-Z. Zhou, C. L. Zhang, R. D. Stapleton, B. L. Kinsall, and T. M. Phelps. 2002. Biotransformations and biodegradation in extreme environments. In: Biotransformations: Bioremediation Technology for Health and Environmental Protection (eds. Singh, V. P. and Stapleton, R. D.). Elsevier, London, P. 549-571.
5.Roh, Y., S. Liu, G. Li, H. Huang, T. J. Phelps, and J. Zhou. 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. Appl. Environ. Microbiol., 68:6013-6020. [pdf].
6.Taranenko N. I, R. Hurt, J.-Z Zhou, N. R. Isola, H. Huang, S.H. Lee, C. H. Chen. 2002. Laser desorption mass spectrometry for microbial DNA analysis. J. Microbiol. Methods 48: 101-106. [pdf].
7.Thompson, D.K, A. S. Beliaev, C. S. Giometti, S. L. Tollaksen, T. Khare, D. P. Lies, Kenneth H. Nealson, H. Lim, J. Yates III, C. C. Brandt, J. M. Tiedje, and J.-Z Zhou. 2002. Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl. Environ. Microbiol. 68:881-892. [pdf].
8.Xu, D., G. Li, L. Wu, J.-Z. Zhou, and Y. Xu. 2002. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics, 18:1432-1437, 2002. [pdf].
9.Zhou, J.-Z, and D. K. Thompson. 2002. Microarrays: Application in environmental microbiology. p. 1968-1979. Bitton, G. (Editor in Chief), The Encyclopedia in Environmental Microbiology, John Wiley & Sons, New York. (Invited).
10.Zhou, J.-Z. and D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opion. Biotech. 13:204-207. (Invited). [pdf].
11.Zhou, J.-Z., and J. M. Tiedje. 2002. New DOE program expands dramatically beyond microbial genomics. ASM News: 68:110-111. (Invited).
12.Zhou, J.-Z., and Jeffrey H. Miller. 2002. 2002. Microbial genomics - Challenges and opportunities: The 9th International Conference on Microbial Genomes. J. Bacteriol., 184: 4327-4333 (Invited). [pdf].
13.Zhou, J.-Z., B. Xia, D. S. Treves, T. L. Marsh, R. V. O'Neill, L. Wu, A. V. Palumbo and J. M. Tiedje. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68: 326-334. [pdf].
1.Gruntzig, V., S. C. Nold, J.-Z. Zhou, and J. M. Tiedje. 2001. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Appl. Environ. Microbiol. 67: 760-768. [pdf].
2.Hurt, R. A., X. Qiu, L. Wu, Y. Roh, A. V. Palumbo, J. M. Teidje, and J.-Z. Zhou. 2001. Simultaneous Recovery of RNA and DNA from Soils and Sediments. Appl. Environ. Microbiol. 67: 4495-4503. [pdf].
3.Murray, A. E., D. Lies, G. Li, K. Nealson, J-Z. Zhou, J. M. Tiedje. 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. PNAS, 98: 9853-9858. [pdf]. [suppl].
4.Qiu, X. Y., L.-Y. Wu, H. Huang, P. E. McDonel, A.V. Palumbo, J. M. Tiedje, and J.-Z. Zhou. 2001. Evaluation of PCR-generated chimeras: Mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67: 880-887. [pdf].
5.Schut, G. J., J.-Z. Zhou, and M. W. W. Adams. 2001. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex. J. Bacteriology 183: 7027-7036. [pdf].
6.Sepulveda-Torres, L. C., J.-Z. Zhou, C. Guasp, J. Lalucat, D. Knaebel, J. L. Plank and C. S. Criddle. 2001. Pseudomonas sp strain KC represents a new genomovar within Pseudomonas stutzeri. Int J Syst Evol Microbiol. 51: 2013–2019. [pdf].
7.Wu, L.Y., D. Thompson, G.-S. Li, R. Hurt, H. Huang, J. M. Tiedje, and J.-Z. Zhou. 2001. Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment. Appl. Environ. Microbiol. 67: 5780-5790 . [pdf].
8.Xia, B. C.; D. S. Treves, J.-Z. Zhou, J. M. Tiedje. 2001. Soil microbial community diversity and driving mechanisms. Prog. Nat. Sci. 11: 818-824.
9.Zhang C.-L., J. Horita, D. R. Cole, J.-Z. Zhou, D. R. Lovley, and T. J. Phelps. 2001. Temperature-dependent oxygen and carbon isotope fractionations of biogenic siderite. Geochimica et Cosmochimica Acta. 65: 2257-2271. [pdf].
10.Zhou, J.-Z., S. Liu, B.-C. Xia, C.-L. Zhang, A. V. Palumbo, and T. J. Phelps. 2001. Molecular characterization and diversity of thermophilic iron-reducing enrichment cultures from deep subsurface environments. Journal of Applied Microbiology 90: 96-105. [pdf].
2000 and before
1.Braker, G., J.-Z. Zhou, L.-Y. Wu, A. H. Devol, and J. M. Tiedje. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific northwest marine sediment communities. Appl. Environ. Microbiol. 66: 2096-2104. [pdf].
2.Braker, G., J.-Z. Zhou, L.-Y. Wu, A. H. Devol, and J. M. Tiedje. 2000. Unusual diversity in soil microbial communities. The 6th Chinese Society of Ecology. P. 29-40, (Invited).
3.Nold, S. C., J.-Z. Zhou, A. H. Devol, and J. M. Tiedje. 2000. Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria. Appl. Environ. Microbiol. 66: 4532-4535. [pdf].
4.Tiedje J. M., J.-C Cho, A. Murray, D. Treves, B.-C. Xia, and J.-Z. Zhou. 2000. Soil Teeming with Life: New Frontiers for Soil Science. p. 393-412. In Sustainable Management of Soil Organic Matter (eds, R. M. Rees, B. C. Ball, C. D. Campbell and C. A. Watson), CABI International. [pdf].
5.Xia, B.-C, J.-Z. Zhou, J. M. Tiedje. 2000. Structure of bacterial community in soil environment and its ecological characteristics. Acta Ecologica Sinica 20(4): 1201-1209.
6.Xu, D., Y. Xu, G.-S. Li, and J.-Z. Zhou. 2000. A computer program for generating gene-specific fragments for microarrays. P. 3-4, In Miyano, S., R. Shamir, and T. Takagi (eds), Currents in Computational Molecular Biology, Universal Academy Press, Inc, Tokyo, Japan. [pdf].
7.Zhou, J.-Z. and A. V. Palumbo. 2000. Sequence to function: The 7th Conference on Small Genomes. Genetica 108: vii-ix. [pdf].
8.Li, G.-S. and J.-Z Zhou. 1999. Genomics, microarray-based genomic technology and potential ecological applications. The 3rd Conference on Molecular Ecology, Beijing, P. 29-40, (Invited).
9.Palumbo, A. V., J-Z. Zhou, T. J. Phelps, B. Kinsall, C. Zhang, E. L. Majer, J. E. Peterson, T. Griffin S. M. Pfiffner. 1999. Ecology and bioremediation: a staged approach to site characterization. In: Uzochukwu and Reddy (eds), Proceedings of the 1998 National Conference on Environmental Remediation Science and Technology. Battelle Press, pp. 195-202.
10.Song, B.-G., M. M. Haggblom, J.-Z. Zhou, J. M. Tiedje, and N. J. Palleroni. 1999. Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp nov and Azoarcus toluclasticus sp nov. Int. Syst. J. Bact. 49: 1129-1140. [pdf].
11.Zhang C., R. Stapleton, J.-Z. Zhou, A. V. Palumbo, and T. J. Phelps. 1999. Iron reduction by psychotrophic enrichment cultures. FEMS Microbial Ecology 30: 367-371. [pdf].
12.Zhou JZ, AV Palumbo and JM Strong-Gunderson. 1999. Phylogenetic characterization of a mixed microbial community capable of degrading carbon tetrachloride. Appl. Biochem. Biotechnol. 80: 243-253. [pdf].
13.Deysh, S. N., N. S. Panikov, W. Liesack, R. Grobkopf, J.-Z. Zhou, and J. M. Tiedje. 1998. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science 282: 281-284. [pdf].
14.Xia, B.-C, J.-Z. Zhou, J. M. Tiedje. 1998. Effect of overlying vegetation on soil microbial community structure and their activity. Acta Scientiarum Naturalium Universitatis Sunyatseni 37(3): 94-98 (Chinese.(To request article, click here)
15.Xia, B.-C, J.-Z. Zhou, J. M. Tiedje. 1998. Application of molecular methods in microbial ecology. Acta Scientiarum Naturalium Universitatis Sunyatseni 37(2): 97-101 (Chinese).
16.Xia, B.-C, J.-Z. Zhou, J. M. Tiedje. 1998. Effect of vegetation on structure of soil microbial community. Chinese Journal of Applied Ecology 9(3): 296-300.
17.Zhou, J.-Z., S. V. Liu, C.-L. Zhang, A. V. Palumbo, and T. J. Phelps. 1998. Extremophilic iron-reducing bacteria: Their implications for possible life in extraterrestrial environments. The Third Symposium of Chinese Young Scientists, p. 47-52, Beijing, P. R. China.
18.Liu, S., J.-Z. Zhou, C.-L. Zhang, D. R. Cole and T. J. Phelps. 1997. Thermophilic Fe(III)-reducing bacteria from the deep subsurface: The evolutionary implications. Science 277: 1106-1109. [pdf].
19.Massol-Deya, A., R. Weller, L. Rio-Hernandez, J.-Z. Zhou, R. F. Hickey, and J. M. Tiedje. 1997. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl. Environ. Microbiol. 63: 270-276. [pdf].
20.Tiedje, J. M., J.-Z. Zhou, K. Nusslein, C. L. Moyer and R. R. Fulthorpe. 1997. Extent and patterns of soil microbial diversity. P. 35-41. In Martins, M. T. et al. (eds). Progress in Microbial Ecology, Brazilian Society for Microbiology, Sao Paulo.
21.Tiedje, J.M., K. Nüsslein, J.-Z. Zhou, B. Xia, C. Moyer, and F. Dazzo . 1997. The vast world of microbial diversity. In The 5th International Symposium on New Frontiers in Microbiology by the Japan Science and Technology Corporation. January 30-31, 1997, Tokyo, Japan.
22.Zhou, J. Z., A. V. Palumbo, and J. M. Tiedje. 1997. Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes. Appl. Environ. Microbiol. 63: 2384-2390. [pdf].
23.Zhou, J.-Z., M. E. Davey, J. B. Figueras, E. Rivkina, D. Gilichinsky, and J. M. Tiedje. 1997. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913-3919. [pdf].
24.Chee-Sanford, J.C., J. W. Frost, M. R. Fries, J.-Z. Zhou, and J. M. Tiedje. 1996. Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Appl. Environ. Microbiol. 62: 964-973. [pdf].
25.Shih, C.-C., M. E. Davey, J. Z. Zhou, J. M. Tiedje, and C. S. Criddle. 1996. Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene. Appl. Environ. Microbiol. 62: 2953-2960. [pdf].
26.Tiedje, J. M., and J.-Z. Zhou. 1996. Analysis of non-culturable bacteria. pp. 53-65. In Methods for the examination of organismal diversity in soils and sediments, (G. S. Hall, ed). CAB International, New York.
27.Zhou, J.-Z., and A. Kleinhofs. 1996. Molecular evolution of nitrate reductase genes. J. Mol. Evol. 42: 432-442. [pdf].
28.Zhou, J.-Z., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322. [pdf].
29.Zhou, J.-Z., S.-J. Ma, and G. W. Hinman. 1996. Ecological exergy analysis: A new method for ecological energetics research. Ecological Modeling 84: 291-303. [pdf].
30.Zhou, J.-Z. and J. M. Tiedje. 1995. Variation of nitrate reductase genes in selected grass species. Genome 38: 919-927. [pdf].
31.Zhou, J.-Z. and J. M. Tiedje. 1995. Gene-transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol. Ecol. 4: 613-618. [pdf].
32.Zhou, J.-Z. and J. M. Tiedje. 1995. Development of phylogenetic probes specific to Burkholderia cepacia G4. pp. 65-75. In Hinchee, R. E., Douglas, G. S. and Ong, S. K. (eds), Monitoring and Verification of Bioremediation, Battle Press, Columbus.
34.Fries, MR, JZ Zhou, JC Chee-Sanford, and JM Tiedje. 1994. Isolation, characterization, and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60: 2802-2810. [pdf].
35.Zhou, J.-Z., A. Kilian, R. L. Warner, and A. Kleinhofs. 1994. An NADH nitrate reductase gene copy appears to have been deleted in barley. Theor. Appl. Genetics 88: 589-592. [pdf].
36.Zhou, J.-Z., S.-J. Ma, and C.-M. Chen. 1991. An index of ecosystem diversity. Ecol. Modeling 59: 151-163.
37.Zhou, J.-Z. and S.-J. Ma. 1990. Ecosystem stability. China Science and Technology Press. In Perspectives on Modern Ecology. pp. 54-71.
38.Zhou, J.-Z. 1987. On ecological engineering. The proceeding of Symposium of Ecological Society of China. Chengdu, China.
39.Zhou, J.-Z., and C.-M. Chen. 1987. Studies on predation and simulation models of Cyrtarrhinus lividipennis to Brown planthopper Nilaparvata lugens. Hunan Agri. Sci. 36: 35-46.
40.Zhou, J.-Z., and C.-M. Chen. 1987. Quantitative measurement of selectivity of predator for prey. Acta Ecologia Sinica 7: 50-56.
41.Zhou, J.-Z., and C.-M. Chen. 1987. Studies on predation and simulation models of wolf spider Lycosa pseudoannulata to brown planthopper Nilaparvata lugens 4. Simulation model and stability analysis about the model of mono predator/two prey species system. Acta Ecologia Sinica 7: 349-358.
42.Zhou, J.-Z., and C.-M. Chen. 1987. Predation of wolf spider Lycosa pseudoannulata to brown planthopper Nilaparvata lugens and simulation models there of: 3. Selective predation. Acta Ecologia Sinica 7: 228-237.
43.Zhou, J.-Z. 1986. A general model for insect population simulation. The proceeding of the Symposium of Youth Ecologists of China, Zhangjiajie, China.
44.Zhou, J.-Z., and C.-M. Chen. 1986. Studies on the predation and simulation models of wolf spider Lycosa pseudoannulata to brown planthopper Nilaparvata lugens 2. Simulation model and stability analysis of the monopredator-monoprey species system. Acta Ecologia Sinica 6: 238-247.
45.Zhou, J.-Z., and C.-M. Chen. 1986. Studies on predation and simulation models of Wolf spider Lycosa pseudoannulata to Brown planthopper Nilaparvata lugens I. Functional response. Chinese J. Biol. Control, 2(1): 2-9.