IEG Members:Dr. Zhili He

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[edit] Zhili He, PhD

Department of Botany and Microbiology

Institute for Environmental Genomics

University of Oklahoma

Stephenson Research & Technology Center

101 David L. Boren Blvd.

Norman, OK 73019, USA

Phone: 405-325-3958, Fax: 405-325-7552, Email: zhili.he@ou.edu


A. Professional Profile

  • Extensive research experience in microbial physiology, functional genomics, anaerobic microbiology, microbial ecology, and molecular biology
  • Applications of microarray-based technologies to microbial genomic and community studies related to stress responses, bioremediation, and bioenergy
  • Bioinformatics experience in sequence analysis, probe/primer design, microarray construction and data analysis, and development of bioinformatics tools and algorithms
  • Computing programming, software development, database design and development
  • Supervisory experience with administrative staff, post-graduates, postdocs, and technicians
  • Secured and manage multi-million funding from DOE, USDA, NSF, OCAST, and Oklahoma State (Oklahoma Boenergy Center (OBC)
  • Various services (reviewer and member of editorial boards) for the scientific community
  • Teaching both undergraduates and graduates

B. Education and Certificates

Bioinformatics Certified Bioinformatics Specialist (CBS) and Master (CBM) 2002

BA Computing and Information Science, University of Guelph, ON, Canada 2001

PhD Research School of Biological Sciences, Australian National University, Australia 1998

MS Shanghai Institute of Plant Physiology, the Chinese Academy of Science, China 1989

BS Department of Biology, Human Normal University, China 1986

C. Interests

  • Microbial physiology, ecology, and molecular biology
  • Microbial functional genomics: gene functions, regulations and networks related to bioenergy, bioremediation, and stress responses
  • Bioinformatics, computer programming, database design and management
  • Biotechnology, and development of genomic applications

D. Professional Experience

Adjunct Associate Professor, Department of Botany and Microbiology; Associate Director, Institute for Environmental Genomics Jan 2007 – present University of Oklahoma, Norman OK, USA

Research Assistant Professor, Department of Botany and Microbiology; Associate Director, Institute for Environmental Genomics Nov 2005 – Dec 2007 University of Oklahoma, Norman OK, USA

Research Assistant Professor & Bioinformatics Team Leader Sep 2005 – Oct 2005 University of Tennessee/ORNL, Oak Ridge, Tennessee, USA

Postdoctoral Associate & Bioinformatics Team Leader Feb 2003 – Aug 2005 Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA

Bioinformatics Instructor (part-time) Sep 2002 – Jan 2003 Xintra Computer College, Scarborough/Toronto, Ontario, Canada

Software Developer/Tester (part-time) Nov 2001 – Jan 2003 Research in Motion, Waterloo, Ontario, Canada

Postdoctoral Research Associate Oct 1998 - Dec 2002 University of Guelph, Guelph, Ontario, Canada

Researcher Dec 1997 – Sep 1998 Research Institute of Innovative Technology for the Earth, Kyoto, Japan

PhD Student Apr 1994 - Nov 1997 Research School of Biological Sciences, Australian National University, Canberra, Australia

Junior Researcher/Research Scientist Aug 1989 - Mar 1994 Shanghai Institute of Plant Physiology, the Chinese Academy of Sciences, Shanghai, China

MS Student Aug 1986 - Jul 1989 Shanghai Institute of Plant Physiology, the Chinese Academy of Science, Shanghai, China

E. Manuscripts in Preparations

  1. He Z, He Q, Fields MW, Alm E, Wall JD, Hazen T, Arkin A, and Zhou J. Transcriptional analysis of Desulfovibrio vulgaris responses to salt adaptation.
  2. He Z, Li X, Schadt CW, Chong SC, Liebich J, Gentry TJ, and Zhou J. Development of CommOligo 2.0 to select optimal group-specific probes for complex microarrays.
  3. Liang Y, He Z, Wu L, Li G, and Zhou J. Development of a universal standard method for microarray data analysis.
  4. Deng Y, He Z, and Zhou J. Designing and modeling of mismatch probes with long oligonucleotides.
  5. 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. Impact of Elevated Nitrate on Sulfate-Reducing bacteria: implications of inhibitory mechanisms in addition to osmotic stress.

F. Submitted Manuscripts

  1. Walker CB, He Z, Yang ZK, Stolyar SS, Jacobsen J, Ringbauer Jr JA, Wall JD, Zhou J, Arkin AP, and Stahl DA. Energy conservation by Desulfovibrio vulgaris in syntrophic growth with a hydrogenotrophic methanogen (submitted to Science).
  2. 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. Metagenomic Insights into Evolution of a Uranium-Contaminated Groundwater Microbial Community (Submitted to Nature).
  3. Rodrigues DF, Ivannova N, Zhou J, He Z, Webner M, and Tiedje JM. Architecture of thermal adaptation in Exiguobacterium sibiricum strain 255-15: a genome and transcriptome approach (Submitted to Genome Research).
  4. Andersen G, He Z, DeSantis T, Brodie E, and Zhou J. The Use of Microarrays in Microbial Ecology (An invited book chapter).
  5. Gentry TJ, He Z, and Zhou J. Detection and Characterization of Uncultivated Microorganisms using Microarrays (An invited book chapter).
  6. Fields MW, Clark ME, Zhou J, and He Z. Desulfovibrio vulgaris biofilms are not stationary (submitted to Applied and Environmental Microbiology).


G. Selected Publications

  1. He Z and Zhou J. Selection of oligonucleotide probes for microarrays. Molecular Microbial Ecology Manual 2nd (Invited review, in press).
  2. He Z and Zhou J (2008). Empirical evaluation of a new method for calculating signal to noise ratio (SNR) for microarray data analysis. Appl. Envir. Microbiol. (In press).
  3. 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. Journal of Bacteriology 189: 8944-8952.
  4. 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.
  5. Yergeau E, Kang S, He Z, Zhou J, and Kowalchuk GA. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 1: 163-179.
  6. 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.
  7. 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. Journal of Bacteriology 189: 6159-6167.
  8. 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. Applied and Environmental Microbiology 73: 5389-5400.
  9. 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. Applied Biochemistry and Biotechnology 137-140: 663-674.
  10. 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.
  11. Gentry TJ, Wickham JS, Schadt CW, He Z, and Zhou J (2006). Microarray Applications in Microbial Ecology Research. Microbial Ecology 52: 159-175 (Invited review).
  12. 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. Environmental Microbiology 8: 1950-1959.
  13. Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan X, Hazen TC, Arkin AP, Wall JD, Zhou J. and M.W. Fields (2006). Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase during electron donor depletion. Applied and Environmental Microbiology 72: 5578-5588.
  14. 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. Journal of Bacteriology 188: 4068-4078.
  15. 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. Applied and Environmental Microbiology 72: 4370-4381.
  16. 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. Journal of Bacteriology 188: 1817-1828.
  17. Liebich J, Schadt CW, Chong SC, He Z, Rhee SK and Zhou J (2006). Improvement of oligonucleotide design criteria for the development of functional gene microarrays for environmental applications. Applied and Environmental Microbiology 72: 1688-1691.
  18. 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 Research 33: 6114-6123.
  19. He Z, Wu L, Fields MW and Zhou J (2005). Comparison of microarray performance with different probe sizes for monitoring gene expression. Applied and Environmental Microbiology 71: 5154-5162.
  20. He Z, Wu L, Li X, Fields MW and Zhou J (2005). Empirical establishment of oligonucleotide probe design criteria. Applied and Environmental Microbiology 71: 3753-3760.
  21. Schadt CW, Liebich J, Chong SC, Gentry TJ, He Z, Pan H and J Zhou (2004). 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.
  22. 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 Physiology 115: 1569–1580.
  23. He Z, Tang ZC (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; Kexue TongBao (1993) 38: 2190-2193 (Chinese Version).
  24. He Z, Li JS, Tang ZC (1993). Stimulative Effect of osmotic stress on the K+ accumulation in sorghum roots. Acta Phytophysiol Sinica 19: 379–386.
  25. He Z, Wang HC (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.
  26. He Z, Wang HC (1991). Emergence of salt-induced proteins in alfalfa under NaCl stress. Acta Phytophysiol Sinica 17: 71–79.

H. Most Recent Poster Presentations (>50 since 2006)

  1. He Z, Deng Y, Van Nostrand JD, Wu L, Hemme CL, Gentry TJ, Arkin AP, Hazen TC, and Zhou J (2008). Further development and applications of Geochip 3.0 for microbial community analysis (February 2008, Genomics:GTL Annual Meeting, Washington DC).
  2. He Z, Li X, Deng Y and Zhou J (2008). Selection of group-specific oligonucleotide probes for microarrays (June 2008, the ASM general Meeting, Boston, MA).
  3. He Z, Baidoo E, Zhou A, He Q, Benke P, Phan R, Joachimiak M, Fields MW, Mukhopadhyay A, Alm EJ, Huang K, Wall JD, Hazen TC, Keasling JD, Arkin AP, and Zhou J (2008). Global transcriptional and metabolite analysis of Desulfovibrio vulgaris Hildenborough responses to long-term exposure to elevated NaCl (June 2008, the ASM general Meeting, Boston, MA).
  4. Jiang H, He Z, and Zhou J (2008). Effect of Thermophilic Anaerobic Bacterial Diversity on Ethanol Production from Cellulose Fermentation (June 2008, the ASM general Meeting, Boston, MA).
  5. Zhou A, He Z, Joachimiak MP, Dehal DS, Arkin AP, Hillesland K, Stahl D, Wall J, Hazen TC, and Zhou J (2008). The dynamics and genetic adaptation to salt stress in experimental evolution of Desulfovibrio vugaris Hildenborough (February 2008, Genomics:GTL Annual Meeting, Washington DC).
  6. Zhou A, He Z, Mukhopadhyay A, Hemme C, Keasling J, Arkin AP, Hazen TC, Wall JD, and Zhou J (2008). Genome-wide Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Hildenborough Response to Hydrogen Peroxide (June 2008, the ASM general Meeting, Boston, MA).
  7. Xu M, He Z, Kellogg LE, Kang S, Wu L, Reich PB, Hobbie S and Zhou J (2008). Influences of elevated atmospheric carbon dioxide levels on belowground microbial functional genes (June 2008, the ASM general Meeting, Boston, MA).
  8. Clark ME, He Z, Redding AM, Mukhopadhyay A, Zhou J, Keasling JD, Fields MW (2008). Transcriptomic and Proteomic Analysis of Desulfovibrio vulgaris ATCC 29579 Biofilms Under Conditions Conducive to Metal Reduction (June 2008, the ASM general Meeting, Boston, MA).
  9. Fang Z, He Z, He Q, Jiang H, Hemme C and Zhou J (2008). Enhanced Ethanol Production from Cellulose Fermentation by Thermophilic Co-cultures (June 2008, the ASM general Meeting, Boston, MA).
  10. Deng Y, He Z and Zhou J (2008). Evaluation of DNA gyrase subunit B (gyrB) microarrays (June 2008, the ASM general Meeting, Boston, MA).
  11. Deng Y, He Z, Li X and Zhou J (2008). Designing and modeling of mismatch probes with long oligonucleotides (June 2008, the ASM general Meeting, Boston, MA).
  12. Liang Y, He Z, Wu L, Li G, and Zhou J. Development of a universal standard method for microarray data analysis (June 2008, the ASM general Meeting, Boston, MA).
  13. Chen J, Gao H, Liang Y, He Z, and Zhou J (2008). Roles of OmcB and OmcE from Shewanella putrefaciens W3-18-1 in Iron (III) and Manganese (IV) Reduction (June 2008, the ASM general Meeting, Boston, MA).
  14. Tu Q, Deng Y, Hemme C, He Z, and Zhou J (2008). A Web-Based Pipeline for Comparative and Evolutionary Genomics Analyses (June 2008, the ASM general Meeting, Boston, MA).
  15. Liang Y, Gao H, He Z, Chen J, Liu X, Qiu Q and Zhou J (2008). Role of RtxB-EmrA-AggA type I secretion system in Shewanella oneidensis MR-1 pellicle formation (June 2008, the ASM general Meeting, Boston, MA).
  16. Van Nostrand JD, Deng Y, Wu L, Wu W, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle C, Jardine P, Hazen TC and Zhou J (2008). Microbial Functional Community Changes in a Groundwater Recirculation System during Periods of Resting, Reoxidation, and Recovery (June 2008, the ASM general Meeting, Boston, MA).
  17. Van Nostrand JD, Wu L, He Z, and Zhou J (2008). Use of Bst DNA polymerase for whole genome amplification (June 2008, the ASM general Meeting, Boston, MA).
  18. Wu L, Xie J, Kellogg L, He Z, Luo Q, and Zhou J (2008). The effect of climate warming on underground microbial communities and its interaction with aboveground plant populations revealed by microbial genomic analysis (June 2008, the ASM general Meeting, Boston, MA).
  19. Kang S, Kellogg LE, He Z, Hobbie SE, Reich PB and Zhou J (2008). Soil microbial community-level physiological profiles in grasslands under contrasting CO2 levels and plant diversity treatments (June 2008, the ASM general Meeting, Boston, MA).
  20. Waldron PJ, Wu L Van Nostrand JD, Watson DB, He Z, Schadt CW, Hazen TC and Zhou J (2008). Functional gene array-based analysis of microbial community structure in a gradient of nitrate and heavy metal-contaminated groundwaters (June 2008, the ASM general Meeting, Boston, MA).
  21. Kang S, Gough HL, Von Nostrand, JD, Stahl DA, He Z, Wu L, Hazen TC and Zhou J (2008). Microbial communities at the metal contaminated lake sediment (June 2008, the ASM general Meeting, Boston, MA).
  22. Liang Y, Van Nostrand JD, Peacock AD, Long PE, Wu L, He Z, G Li, and Zhou J (2008). Microarray-Based Functional Analysis of Microbial Communities for In-Situ Uranium Under Sulfate-Reducing vs. Fe-Reducing Conditions (June 2008, the ASM general Meeting, Boston, MA).
  23. He Z. GeoChip Development and Its Applications in Microbial Community Analysis (Keynote speaker, December 2007, the 10th Environmental Microbiology Conference, Guangzhou, China).
  24. Van Nostrand JD, Wu L, Wu W, Carroll S, He Z, Criddle C, Jardine P, Hazen TC, and Zhou J (2007). Changes in Microbial Community Function During a Period of Reoxidation in a Groundwater Recirculation System (September 2007, the 15th Annual International Conference on Microbial Genomics College Park, MD).
  25. He Z, Baidoo E, Zhou A, He Q, Benke P, Phan R, Fields MW, Mukhopadhyay A, Alm EJ, Huang K, Wall JD, Hazen TC, Keasling JD, Arkin AP, and Zhou J (2007). Exploration of salt adaptation mechanisms in Desulfovibrio vulgaris Hildenborough by global transcriptional and metabolite analyses (August 2007, VIMSS:ESPP Annual Strategic Planning Retreat, Berkeley, CA).
  26. Clark ME, He Z, Duley ML, Zane G, Edelmann RE, Elias DA, Zhou J, Wall JD, and Fields MW (2007). Structural role for flagella in biofilm formation and stability in Desulfovibrio vulgaris Hildenborough (August 2007, VIMSS:ESPP Annual Strategic Planning Retreat, Berkeley, CA).
  27. Zhou A, He Z, Mukhopadhyay A, Keasling J, Arkin AP, Hazen TC, and Zhou J (2007). The dynamics and genetic basis of adaptation to salt stress in Desulfovibrio vugaris Hildenborough (August 2007, VIMSS:ESPP Annual Strategic Planning Retreat, Berkeley, CA).
  28. He Z, Liang Y, Gao H, Chen J, Hemme CL, Fredrickson JK, Nealson K, Tiedje JM, and Zhou J (2007). Computational and Experimental Study of Two Closely Related Shewanella putrefaciens Strains CN32 and W3-18-1 (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  29. He Z, Deng Y, Van Nostrand JD, Wu L, Hemme CL, Liebich J, Gentry TJ, Hazen TC, Arkin AP, and Zhou J (2007). GeoChip 3.0: Further Development and Applications of Functional Gene Arrays (FGAs) for Analysis of Microbial Communities (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  30. Deng Y, He Z, and Zhou J (2007). Development and Evaluation of DNA Gyrase Subunit B (gyrB) Database and Microarray for Archaea and Bacteria (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  31. He Q, He Z, Chen W, Yang Z, Alm EJ, Huang KH, Yen HC, Joyner DC, Keller M, Arkin AP, Hazen TC, Wall JD, and Zhou J (2007). Understanding the Suppression of Sulfate Reducing Bacteria by Nitrate: A Functional Genomics Approach (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  32. Zhou A, He Z, Hemme CL, Mukhopadhyay A, Keasling J, Arkin AP, Hazen TC, Wall JD, and Zhou J (2007). Genome-Wide Transcriptomic Analysis of Desulfovibrio vulgaris Hildenborough Response to Hydrogen Peroxide (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  33. Kellogg LK, Xu M, Wu L, He Z, and Zhou J (2007). Plant Species Diversity Negatively Affects Soil Microbial Functional Guilds (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  34. Walker CB, Yang ZK, He Z, Stolyar SS, Jaconbsen J, Ringbauer JA, Wall JD, Zhou J, and Arkin AP, and Stahl DA (2007). Energy Conservation Mechanisms for Syntrophic Growth of Desulfovibrio vulgaris and Methanococcus maripaludis (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  35. Liang Y, Chen J, Gao H, Yang ZK, He Z, Fredrickson JK, Tiedje JM, and Zhou J (2007). Mutational Analysis of arca, etra, crp in Shewanella putrefaciens CN32 and W3-18-1 (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  36. Chen J, Liang Y, Gao H, He Z, Fredrickson JK, Tiedje JM, and Zhou J (2007). Roles of omcB of Shewanella putrefaciens CN32 and W3-18-1 in Metal Reduction (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  37. Van Nostrand JD, Liang Y, Wu L, Wu W, Carroll S, He Z, Criddle C, Jardine P, Hazen TC, and Zhou J (2007). Changes in Microbial Community Function during a Period of Reoxidation in a Groundwater Recirculation System (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  38. Waldron PJ, Van Nostrand JD, Watson DB, Wu L, He Z, Hazen TC, and Zhou J (2007). Effects of Nitrate, pH and Uranium on the Subsurface Microbial Communities Revealed by Functional Gene Arrays (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  39. Wu L, Gentry TJ, Huang Z, Schadt CW, Wu W, Watson D, He Z, Criddle CS, Jiedje JM, Hazen TC, and Zhou J (2007). Microarray-Based Analysis of Microbial Community Composition and Dynamics in Uranium Bioremediation (May 2007, 107th ASM General Meeting, Toronto, ON, Canada).
  40. He Z, van Nostrand JD, Wu L, Gentry TJ, Deng Y, Schadt CW, Wu W, Liebich J, Chong SC, Gu B, Jardine P, Criddle C, Watson D, Hazen TC, and Zhou J (2007). Monitoring of Microbial Reduction and Reoxidation Activities in the FRC Sites Using GeoChip (February 2007, Bethesda, MD).
  41. He Z, Gentry TJ, Wu L, Schadt CW, Van Nostrand JD, Wu W, Liebich J, Chong SC, Gu B, Jardine P, Criddle C, Watson D and Zhou J (2006). Monitoring of in situ Bioremediation Efficiency at the FRC Sites Is Revealed by a Comprehensive Functional Gene Array (October 2006, DOE ERSP PI Fall Meeting, Oak Ridge, TN, USA).
  42. Hemme CL, Gentry TJ, Deng Y, He Z, Wu L, Fields MW, Detter C, Barry K, Watson D, Richardson P, Hazen TC, Tiedje J, Rubin E and Zhou J (2006). Adaptation of a Microbial Community to Stress Conditions Prevalent at the FRC (October 2006, DOE ERSP PI Fall Meeting, Oak Ridge, TN, USA).
  43. He Z, He Q, Alm EJ, Wall JD, Fields MW, Hazen TC, Arkin AP, Zhou J (2006). Exploration of salt adaptation mechanisms in Desulfovibrio vulgaris Hildenborough (May 2006, 106th ASM General Meeting, Orlando, FL, USA).
  44. He Z, Deng Y, Schadt CW, Li X, Zhou J (2006). A software package for the design and analysis of microbial functional gene arrays (May 2006, 106th ASM general Meeting, Orlando, FL, USA).
  45. He Z, Schadt CW, Gentry T, Liebich J, Chong SC, Li X, Zhou J (2006). Design, Construction and Evaluation of a Comprehensive Functional Gene Array with 24K Oligonucleotides (May 2006, 106th ASM General Meeting, Orlando, FL, USA).
  46. 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 (May 2006, 106th ASM General Meeting, Orlando, FL, USA).
  47. He Q, Chen W, He Z, Yang Z, Alm EJ, Huang KH, Yen HC, Keller M, Hazen TC, Arkin AP, Wall JD, and Zhou J (2006). Nitrate stress response in Desulfovibrio vulgaris Hildenborough: whole-genome transcriptomics and proteomics analyses (May 2006, 106th ASM General Meeting, Orlando, FL, USA).
  48. Klonowska A, He Z, He Q, Yang Z, Hazen TC, Thieman S, Alm EJ, Arkin AP, Wall JD, Zhou J, and Fields MW (2006). Global transcriptomic analysis of chromium (VI) exposure of Desulfovibrio vulgaris Hildenborough under sulfate-reducing conditions (May 2006, 106th ASM General Meeting, Orlando, FL, USA).
  49. Clark ME, Wall JD, He Z, Zhou J, Keasling J, and Fields MW (2006). Possible roles of extracellular proteins and the megaplasmid in the formation of Desulfovibrio vulgaris biofilm (May 2006, 106th ASM General Meeting, Orlando, FL, USA).
  50. He Q, He Z, Chen Z, Yang Z, Alm EJ, Huang KH, Yen HC, Keller M, Hazen TC, Arkin AP, Wall JD, and Zhou J (2006). Nitrate stress response in Desulfovibrio vulgaris Hildenborough: whole-genome transcriptomics and proteomics analyses (February 2006, Bethesda, MD, USA).

I. Software

  1. Genomic DNA-based Microarray Data Analysis – GMADA Aug 2004–present
  2. Environmental Sequence and Genome Analysis Systems - ESGAS Apr 2004–present
  3. Oligonucleotide probe design program - CommOligo Jul 2003–Jun 2004
  4. Web Blackberry Client Systems Nov 2001–Dec 2002
  5. Laboratory Bioinformatics Software Systems Oct 1998–Dec 2002

J. Professional Memberships and Services

  1. A member of the Editorial Board of Applied and Environmental Microbiology (AEM)
  2. Reviewer for Applied and Environmental Microbiology (AEM), Applied Microbiology Biotechnology (AMB), ISME Journal, Journal of Bacteriology, Current Microbiology, Bioinformatics, BMC Bioinformatics, Gene, and Journal of Virological Methods
  3. Reviewer of DOE and NSF proposals
  4. The American Society for Microbiology (ASM)
  5. The American Association for the Advancement of Science (AAAS)
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