Zhili He

• Bioinformatics 2002 Certified Bioinformatics Specialist (CBS) and Master (CBM)
• BA 2001 Computing and Information Science, University of Guelph, ON, Canada
• PhD 1998 Research School of Biological Sciences, Australian National University, Australia
• MS 1989 Shanghai Institute of Plant Physiology, the Chinese Academy of Science, China
• BS 1986 Department of Biology, Hunan Normal University, China

Research Interests

My research interests are to understand the microbial ecology, functional genomics, metagenomics, physiology, and molecular mechanisms underlying important microbial processes in nature and controlled environments. This includes three directions:

• Microbial ecology to understand the diversity, composition, structure, interaction, dynamics and evolution of microbial communities related to the global climate change, long-term sustainability of bioenergy crops, and bioremediation using high throughput metagenomic technologies, such as microarrays (e.g., GeoChip, PhyloChip) and next generation sequencing.

• Systems microbiology and microbial functional genomics to understand gene functions, regulations, and networks of model organisms or near-model organisms, such as Desulfovibrio and Shewanella species for bioremediation, and Clostridium and Thermoanaerobacter species for biofuels production using a consolidated bioprocessing (CBP).

• Development of microarray-based biotechnologies and bioinformatics tools to achieve my research goals. Those directions unify my research into an interactive and cohesive research theme, which embeds basic research components, public interests, and an applied component.

Professional Experience

• Sep 2011 - present
  Adjunct Professor, Department of Botany and Microbiology, University of Oklahoma, Norman OK, USA
  Associate Director and Research Scientist, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
• Sep 2007 - Aug 2011
  Adjunct Associate Professor, Department of Botany and Microbiology, University of Oklahoma, Norman OK, USA
  Associate Director and Research Scientist, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
• Oct 2005 - Aug 2007
  Research Assistant Professor, Department of Botany and Microbiology, University of Oklahoma, Norman OK, USA
  Associate Director, Institute for Environmental Genomics University of Oklahoma, Norman OK, USA
• Sep 2005 - Sep 2005
  Research Assistant Professor & Bioinformatics Team Leader, University of Tennessee/ORNL, Oak Ridge, Tennessee, USA
• Feb 2003 - Aug 2005
  Postdoctoral Associate & Bioinformatics Team Leader, Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA
• Sep 2002 - Jan 2003
  Bioinformatics Instructor (part-time), Xintra Computer College, Scarborough/Toronto, Ontario, Canada
• Nov 2001 - Jan 2003
  Software Developer/Tester (part-time), Research in Motion, Waterloo, Ontario, Canada
• Oct 1998 - Dec 2002
  Postdoctoral Research Associate, University of Guelph, Guelph, Ontario, Canada (Confidential contracts and NO publications were allowed.)
• Dec 1997 - Sep 1998
  Researcher, Research Institute of Innovative Technology for the Earth, Kyoto, Japan
• Aug 1989 - Mar 1994
  Junior Researcher/Research Scientist, Shanghai Institute of Plant Physiology, the Chinese Academy of Sciences, Shanghai, China

Selected Publications

Manuscripts submitted

• Li X, Deng Y, Li Q, Lu C, Wang J, Zhang H, Zhu J, Zhou J, and He Z*. Responses of soil microbial communities to elevated ozone and wheat (Triticum aestivum L) cultivars revealed by GeoChip-based analysis (*Corresponding author, submitted to The ISME Journal).
• Frank Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL, Lu Z, He Z, Zhou J, and Wakelin SA. Influence of geogenic factors on microbial communities in metallogenic Australian soils (Submitted to The ISME Journal).
• Yang Y, Wu L, Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, Van Nostrand JD, Wang S, and Zhou J. Responses of the functional structure of soil microbial community to livestock grazing in Tibetan alpine grassland (Submitted to The ISME Journal).
• Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, and Stahl DA. Functional responses of methanogenic archaea to syntrophic growth (Submitted to The ISME Journal).
• Wang H, Lu Z, He Z, Zhou J, Xu X, Van Nostrand JD, and Zhang Z. Sediment Carbon and Phosphorus Biogeochemical Cycles and the Functional Gene Shifts of Wetlands Subjected to Experimental Warming (Submitted to Applied and Environmental Microbiology).
• Xu M, He Z, Deng Y, Wu L, Van Nostrand JD, Hobbie SE, Reich PB, and Zhou J. Elevated CO2 alters soil microbial functional structure and potential in carbon and nitrogen cycling (Submitted to Applied and Environmental Microbiology).
• Jiang H, He Z, He Q, Hemme CL, Wu L, and Zhou J. Performance of cellulose conversion to ethanol by fed-batch co-culture fermentation (Submitted to Applied and Environmental Microbiology).
• Zhou J, Liu W, Deng Y, Jiang YH, Xue K, He Z, Van Nostrand JD, Yang Y, and Wang A. Stochastic assembly leads to alternative communities with distinct functions (Submitted to PNAS).
• Lu Z, He Z, Parisi V, Kang S, Deng Y, Van Nostrand JD, Masoner J, Cozzarelli I, Suflita JM, and Zhou J. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer (Submitted to Environmental Science & Technology).
• Kang S, Van Nostrand JD, Gough HL, He Z, Hazen TC, Stahl DA, and Zhou J. Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments (Submitted to Environmental Microbiology).

Published peer-review articles and book chapters

(87 publications in microbial functional genomics, microbial physiology and ecology, molecular biology, and bioinformatics, H index = 22 with more than 1600 citations up to December 31, 2011)

2012

• Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, and Fields MW. 2012. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics (in press).
• He Z, Van Nostrand JD, and Zhou J. 2012. Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol (Invited review, in press, DOI 10.1016/j.copbio.2011.12.021).
• He Z*, Deng Y, and Zhou J. 2012. Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 23: 49–55 (*corresponding author, invited review).
• He Z, Piceno Y, Deng Y, Xu M, Lu Z, DeSantis T, Andersen G, Hobbie SE, Reich PB, and Zhou J. 2012. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J 6: 259-272.
• Deng Y*, He Z*, Xu M, Qin Y, Van Nostrand JD, Wu L, Roe BA, Wiley G, Hobbie SE, Reich PB, and Zhou J. Pyrosequencing of 16S rRNA genes reveals a shift of soil microbial composition and structure under elevated carbon dioxide. Appl Environ Microbiol (in press).
• Liang Y, Van Nostrand JD, N’Guessan LA, Peacock AD, Deng Y, Long PE, Resch T, Wu L, He Z, Li G, Hazen, Lovley DR, and Zhou J. Microbial Functional Gene Diversity with a Shift of Subsurface Redox Condition. Appl Environ Microbiol (in press).
• Zhou J, Xue K, Xie J, Deng Y, Wu L, Cheng X, Fei S, Deng S, He Z, Van Nostrand JD, and Luo Y. Microbial mediation of carbon cycle feedbacks to climate warming. Nature Climate Change (in press, DOI: 10.1038/NCLIMATE1331).
• Trivedi P, He Z, Van Nostrand JD, Zhou J, Albrigo G, and Wang N. 2012. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J 6: 363-383.
• Lu Z , Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, and Zhou J. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J 6: 451-460.
• Zhou A, Chen Y, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumoh J, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, and Zhou J. 2012. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 78:1168-117.

2011

• He Z, Van Nostrand JD, Deng Y, and Zhou J. 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 (Invited Feature Article).
• Xie J, He Z, Liu X, Liu X, Van Nostrand JD, Deng Y, Wu L, Zhou J, and Qiu G. 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.
• Hemme CL, Fields MW, He Q, Deng Y, Lin L, Tu Q, Mouttaki H, He Z, Barry K, Saunders E, Sun H, Land M, Hauser L, Lapidus A, Han CS, Xu J, Wiegel J, Phelps TJ, Rubin E, and Zhou J. 2011. Correlation of genomic and physiological traits of Thermoanaerobacter species with biofuel yields. Appl Environ Microbiol 77: 7998-8008.
• Lin L, Song H, Tu Q, Qin Y, Zhou A, Liu W, He Z, Zhou J, and Xu J. 2011. Thermoanaerobic glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria. PLoS Genet 7: e1002318 (doi:10.1371/journal.pgen.1002318).
• Liu A, Wu L, He Z, and Zhou J. 2011. Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection. Anal Bioanal Chem 401: 2003–2011.
• He Q, Hemme CL, Jiang H, He Z, and Zhou J. 2011. Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp. Bioresour Technol 102: 9586–9592.
• Wang J, Van Nostrand JD, Wu L, He Z, Li G, and Zhou J. Microarray-based evaluation of whole-community genome DNA amplification methods. Appl Environ Microbiol 77: 4241–4245.
• Van Nostrand JD, Wu L, Wu W, Huang Z, Gentry TJ, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, and Zhou J. Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer. Appl Environ Microbiol 77: 3860–3869.
• Zhou J, Deng Y, Luo F, He Z, and Yang Y. 2011. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. mBio 2: doi:10.1128/mBio.00122-11.
• Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K., Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, and Arkin AP. 2011. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol 9: 452-466.
• Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, Xie J, Van Nostrand JD, He Z, and Yang Y. 2011. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5: 1303–1313.
• Wang A, Gao L, Ren N, Xu J, Liu C, Gao G, Yu H, Liu W, Hemme CL, He Z, and Zhou J. 2011. Isolation and characterization of Shigella flexneri G3 for effective cellulosic saccharification under mesophilic conditions. Appl Environ Microbiol 77: 517-523.
• Liang Y, Van Nostrand JD, Deng Y, He Z, Wu L, Zhang X, Li G, and Zhou J. 2011. Functional gene diversity of soil microbial communities from oil-contaminated fields in China. ISME J 5: 403-413.
• Van Nostrand JD, Kang S, Deng Y, Liang Y, He Z, and Zhou J. 2011. Monitoring microbial activity with GeoChip. In JF Stolz and RS Oremland (eds), Microbial Metal and Metalloid Metabolism: Advances and Applications, pp261-282. ASM Press, Washington DC (Invited book chapter).
• Van Nostrand JD, He Z, and Zhou J. 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.
• Van Nostrand JD, He Z, and Zhou J. 2011. New developments and applications of microarrays for microbial community analysis in natural and impacted ecosystems. In: M. Moo-Young (ed) Comprehensive Biotechnology, 2e. Elsevier, Amsterdam, The Netherlands.
• Van Nostrand JD, He Z, Zhou J. 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, pp 509-520.
• 2010
  • He Z, Xu M, Deng Y, Kang S, Kellogg L, Wu L, Van Nostrand JD, Hobbie SE, Reich PB, and Zhou J. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett 13: 564-575.
  • He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Hazen TC, and Zhou J. 2010. GeoChip 3.0 as a high throughput tool for analyzing microbial community composition, structure, and functional activity. ISME J 4: 1167-1179.
  • He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall JD, Stahl D, Hazen TC, Keasling JD, Arkin, AP, and Zhou J. 2010. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl Environ Microbiol 76: 1574-1586.
  • Liang Y*, He Z*, Wu L, Deng Y, Li G, and Zhou J. 2010. Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol 76: 1088-1094 (*co-first authors).
  • Zhou J, He Z, Van Nostrand JD, Wu L, and Deng Y. 2010. Applying GeoChip analysis to disparate microbial communities. Microbe 5: 60-65 (Invited review).
  • Zhou A, He Z, Redding AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, He Q, Bender KS, Keasling JD, Stahl D, Fields MW, Hazen TC, Arkin, AP, Wall JD, and Zhou J. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 12: 2645-2657.
  • He Q, He Z, Joyner DC, Price MN, Yang ZK, Yen HB, Chakraborty R, Chen W, Keller M, Arkin AP, Hazen TC, Wall JD, and Zhou J. 2010. Impact of elevated nitrate on sulfate-reducing bacteria: implications of inhibitory mechanisms in addition to osmotic stress. ISME J 4: 1386-1397.
  • Zhou J, Deng Y, Luo F, He Z, Tu Q, and Zhi X. 2010. Functional molecular ecological networks. mBio 1: e00169-10 (doi:10.1128/mBio.00169-10).
  • Liang Y, Gao H, Chen J, Dong Y, Wu L, He Z, Liu X, Qiu G, and Zhou J. 2010. Pellicle formation in Shewanella oneidensis. BMC Microbiol 10: 291.
  • Liu W, Wang A, Cheng S, Logan B, Yu H, Deng Y, Van Nostrand JD, Wu L, He Z, and Zhou J. 2010. GeoChip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environ Sci Technol 44: 7729-7735.
  • Hemme CL, Mouttaki H, Lee YJ, Goodwin L, Lucas S, Copeland A, Lapidus A, del Rio TG, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Krypides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, and Zhou J. 2010. Genome announcement: sequencing of multiple Clostridia genomes related to biomass conversion and biofuels production. J Bacteriol (in press, doi: doi:10.1128/JB.01064-10).
  • Liang Y, Gao H, Chen J, Dong Y, Wu L, He Z, Liu X, Qiu G, and Zhou J. 2010. Pellicle formation in Shewanella oneidensis. BMC Microbiol 10: 291.
  • Xiong J, Wu L, Tu S, Van Nostrand JD, He Z, Zhou J, and Wang G. 2010. Microbial communities and functional genes associated with soil arsenic contamination and rhizosphere of the arsenic hyper-accumulating plant Pteris vittata L. Appl Environ Microbiol 76: 7277-7284.
  • Parnell JJ, Rompato G, Latta LC IV, Pfrender ME, Van Nostrand JD, He Z, Zhou J, Andersen G, Champine P, Ganesan B, and Weimer1BC. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoS ONE 5: e12919.
  • Lin L, Song H, Ji Y, He Z, Pu Y, Zhou J, and Xu J. 2010. Ultrasound-mediated DNA transformation in thermophilic Gram-positive anaerobes. PLoS ONE 5: e12582.
  • Gao H, Barua S, Liang Y, Wu L, Dong Y, Reed S, Chen J, Culley D, Kennedy D, Yang Y, He Z, Nealson KH, Fredrickson JK, Tiedje JM, Romine M, and J Zhou. 2010. Impacts of Shewanella onedensis c-type cytochromes on aerobic and anaerobic respiration. Microb Biotechnol 3: 455-466.
  • Xu M, Wu W, Wu L, He Z, Van Nostrand JD, Deng Y, Luo J, Carley J, Ginder-Vogel M, Gentry TJ, Gu B, Watson D, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, Criddle CS, and Zhou J. 2010. Functional understanding of microbial community structures in contaminated sediments during in situ bioremediation/immobilization of uranium. ISME J 4: 1060-1070.
  • Hemme CL, Wu L, Deng Y, Gentry TJ, Fields MW, Fang Z, Barua S, Watson D, He Z, Richardson P, Hazen TC, Tiedje JM, Rubin E, and Zhou J. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4: 660-672.
  • Andersen G, He Z, DeSantis T, Brodie E, and Zhou J. 2010. The Use of Microarrays in Microbial Ecology in Environmental Molecular Microbiology, pp87-110 (Edited by Wen-Tso Liu and Janet K. Jansson), Caister Academic Press, Norfolk, UK.
  • Van Nostrand JD, Liang Y, He Z, Li G, and Zhou J. 2010. GeoChip: A high throughput genomic tool for linking community structure to functions. In Handbook of Hydrocarbon and Lipid Microbiology, pp.2677-2685. Springer Berlin Heidelberg, Germany.
  • Van Nostrand, JD, He Z, and Zhou J. 2010. Analysis of microbial communities by functional gene Arrays.In: L. Barton, M. Mandl and A. Loy (eds) in Geomicrobiology: Molecular and Environmental Perspective, pp109-126. Springer, New York (in press, invited book chapter).
• 2009
  • Liang Y, Li G, Van Nostrand JD, He Z, Wu L, Deng Y, Zhang X, and Zhou J. 2009. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microb Ecol 70: 324-333.
  • Van Nostrand JD, Wu W, Wu L, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, and Zhou J. 2009. GeoChip-based analysis of functional microbial communities in a bioreduced uranium-contaminated aquifer during reoxidation by oxygen. Environ Microbiol 11: 2611-2626.
  • Gentry TJ, He Z and Zhou J. 2009. Detection and characterization of uncultivated microorganisms using microarrays. In Uncultivated Microorganisms (Microbiology Monographs) Vol. 10: 35-58, Epstein, Slava S. (Ed.) Springer-Verlag Berlin Heidelberg.
  • Walker CB, He Z, Yang ZK, Stolyar SS, Jacobsen J, Ringbauer Jr JA, Wall JD, Zhou J, Arkin AP, and Stahl DA. 2009. The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol 191: 5793-5801.
  • Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HCB, Zhou J, Wall JD, Hazen TC, Arkin AP, and Stahl DA. 2009. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environ Microbiol 11: 2244-2252.
  • Feng X, Mouttaki H, Lin L, Huang R, Wu B, Hemme CL, He Z, Zhang B, Hicks LM, Xu J, Zhou J, and Tang YJ. 2009. Characterization of the central metabolic pathways in Thermoanaerobacter sp. strain X514 via isotopomer-assisted metabolite analysis. Appl Environ Microbiol 75: 5001-5008.
  • Liang Y, He Z, Gao H, Qiu G, Zhou J and Liu X. 2009. Characterization of cytochrome mutants for pellicle formation in Shewanella onedensis MR-1. Transactions of Nonferrous Metals Society of China 19: 700-706.
  • Waldron PJ, Wu L, Van Nostrand JD, Schadt CW, He Z, Watson DB, Jardine PM, Palumbo AV, Hazen TC, Zhou J. 2009. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environ Sci Technol 43: 3529-3534.
  • Wang F, Zhou H, Meng J, Peng X, Jiang L, Sun P, Zhang C, Van Nostrand JD, Deng Y, He Z, Wu L, Zhou J, and Xiao X. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci USA 106: 4840-4845.
  • Van Nostrand JD, Wu L, He Z, and Zhou J. 2009. 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).
• 2008
  • He Z and Zhou J. 2008. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl Environ Microbiol 74: 2957-2966.
  • He Z*, Van Nostrand JD, Wu L, and Zhou J. 2008. Development and application of functional gene arrays for microbial community analysis. Transactions of Nonferrous Metals Society of China 18: 1319-1327 (Invited review, *corresponding author).
  • Deng Y, He Z*, Van Nostrand JD, Zhou J*. 2008. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics 9: 491 (*corresponding author).
  • Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, and Tiedje JM. 2008. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics 9: 547.
• 2007
  • He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, and Zhou J. 2007. GeoChip: A comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. ISME J 1: 67-77 (News Release by Nature Press Office: http://www.nature.com/ismej/press_releases/index.html).
  • Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, and Stahl DA. 2007. Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol 189: 8944-8952.
  • Yergeau E, Kang S, He Z, Zhou J, and Kowalchuk GA. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 1: 163-179.
  • Butler J, He Q, Nevin PK, He Z, Zhou J, and Lovley D. 2007. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics 8: 180.
  • Caffrey SM, Park HS, Voordouw JK, He Z, Zhou J, and Voordouw G. 2007. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol 189: 6159-6167.
  • Bender KS, Yen BCB, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, and Wall JD. 2007. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 73: 5389-5400.
  • Brown SD, Raman B, McKeown CK, Kale SP, He Z and Mielenz JR. 2007. Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray. Appl Biochem Biotechnol 137-140: 663-674.
  • Gentry TJ, Schadt CW, He Z, and Zhou J. 2007. Functional gene arrays for microbial community analysis. In Manual of Environmental Microbiology (Third edition), pp1052-1062 (Hurst CJ et al., eds), ASM Press, Washington DC, USA.
• 2006
  • Gentry TJ, Wickham JS, Schadt CW, He Z, and Zhou J. 2006. Microarray applications in microbial ecology research. Microb Ecol 52: 159-175 (Invited review).
  • Walker CB, Stolyar SS, Pinel N, Yen HC, He Z, Zhou J, Wall JD, Stahl DA. 2006. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain. Environ Microbiol 8: 1950-1959.
  • Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan X, Hazen TC, Arkin AP, Wall JD, Zhou J, and Fields MW. 2006. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Appl Environ Microbiol 72: 5578-5588.
  • Mukhopadhyay A, He Z, Yen HC, Alm EJ, He Q, Huang K, Baidoo EE, Chen W, Borglin SC, Redding A, Holman HY, Sun J, Joyner DC, Keller M, Zhou J, Arkin AP, Hazen TC, Wall JD, and Keasling JD. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol 188: 4068-4078.
  • He Q, Huang KH, He Z, Alm EJ, Fields MW, Hazen TC, Arkin AP, Wall JD, and Zhou J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl Environ Microbiol 72: 4370-4381.
  • Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou, J, Arkin AP and Singh AK. 2006. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol 188: 1817-1828.
  • Liebich J, Schadt CW, Chong SC, He Z, Rhee SK and Zhou J. 2006. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ Microbiol 72: 1688-1691.
• 2005
  • He Z, Wu L, Li X, Fields MW and Zhou J. 2005. Empirical establishment of oligonucleotide probe design criteria. Appl Environ Microbiol 71: 3753-3760 (One of the top 20 papers most requested in 2005 by AEM).
  • Li X*, He Z* and Zhou J. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation (*co-first author). Nucleic Acids Res 33: 6114-6123.
  • He Z, Wu L, Fields MW and Zhou J. 2005. Use of microarrays with different probe sizes for monitoring gene expression. Appl Environ Microbiol 71: 5154-5162.
  • Schadt CW, Liebich J, Chong SC, Gentry TJ, He Z, Pan H and Zhou J. 2005. Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities. In Methods in Microbiology Volume 34: 329-365. (Savidge T. and H. Pothulakis, eds) Academic Press, London, UK.
  • 2004 and before
  • He Z and Zhou J. 2004. Selection of oligonucleotide probes for microarrays. Molecular Microbial Ecology Manual, pp1880-1891. Springer Netherlands.
  • He Z, von Caemmerer S, Hudson GS, Price GD, Badger MR, Andrews TJ. 1997. Ribulose-1, 5-bisphosphate carboxylase/oxygenase activase deficiency delays senescence of ribulose-1, 5-bisphosphate carboxylase/oxygenase but progressively impairs its catalysis during tobacco leaf development. Plant Physiol 115: 1569-1580.
  • He Z, Tang Z. 1994. An Increased 66-kD Polypeptide associated with stimulation of K+ uptake in sorghum roots under PEG stress. Chinese Science Bulletin 39: 587-591 (English Version).
  • He Z, Tang Z. 1993. Relationship between increase in 66-kD polypeptide content and stimulation of K+ uptake in sorghum roots under drought stress. Kexue TongBao 38: 2190-2193 (Chinese Version).
  • He Z, Li J, and Tang Z. 1993. Stimulative Effect of osmotic stress on the K+ accumulation in sorghum roots. Acta Phytophysiol Sinica 19: 379-386.
  • He Z, and Wang H. 1992. Effect of NaCl Pretreatment on the accumulation and distribution of Na+, Cl- and proline in alfalfa under salt stress. Plant Physiology Communications 28: 330-334.
  • He Z, and Wang H. 1991. Emergence of salt-induced proteins in alfalfa under NaCl stress. Acta Phytophysiol Sinica 17: 71-79.

Software

• IEG Microbial Community Network Analysis Pipeline - IMCNAP May 2009-present
• Genomic DNA-based Microarray Data Analysis - GMADA Aug 2007-present
• Environmental Sequence and Genome Analysis Systems - ESGAS Apr 2004-Dec 2008
• Oligonucleotide probe design program - CommOligo Jul 2003-Jun 2004
• Web Blackberry Client Systems Nov 2001-Dec 2002

Professional Services and Memberships

• A member of the Editorial Board of Applied and Environmental Microbiology (AEM)
• A member of the Editorial Board of The Scientific World JOURNAL (Genomics)
• The American Society for Microbiology (ASM)
• The American Association for the Advancement of Science (AAAS)
• The International Society for Microbial Ecology (ISME)
• Reviewer for a variety of journals, including Applied and Environmental Microbiology (AEM), Applied Microbiology Biotechnology (AMB), the ISME Journal, Journal of Bacteriology, Microbiology, Canadian Journal of Microbiology, Current Microbiology, Bioinformatics, BMC Bioinformatics, Gene, Journal of Virological Methods, and Journal of Phytopathology
• Reviewer of DOE and NSF proposals

Awards

• 2009 R&D 100 Award by R&D Magazine for OU GeoChip developed by Jizhong Zhou, Zhili He, Liyou Wu, Joy D. Van Nostrand, and Ye Deng at the Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma. This is a prestigious award for providing a mark of excellence known to industry, government, and academia as proof that the product is one of the most innovative ideas of the year (2009).
• An Innovator of the Year 2010 Award by The Journal Record for the development of GeoChip and associated technologies in Oklahoma. This program recognizes businesses, organizations and individuals who embrace both the entrepreneurialism and innovation that make Oklahoma such a special place to live and work (2010).

Other links

[IEG Home page] [Detailed CV (pdf)]