Dr. Patrick K. H. LEE

Ph.D. in Environmental Engineering, University of California, Berkeley
Staff title
Associate Dean (Undergraduate Studies)
Associate Professor

I am interested in solving biologically-related environmental problems. My academic background is in biochemical engineering, environmental engineering and environmental microbiology. I often work at the interface of fundamental and applied sciences. While I am interested in understanding microbiology at the molecular and cellular levels, it is also my goal to apply the fundamental findings in engineering applications to solve real-world problems. My previous research was centered on studying microbes that can transform the carcinogenic chlorinated-ethenes to harmless products. This research involved using a systems biology approach and various molecular and culturing techniques to study the genome, physiology and metabolism of laboratory model bacteria as well as complex microbial communities from the environment and bioreactor.

Other Information


  • Natural Sciences and Engineering Research Council Post-doctoral Fellowship, Canada, 2009
  • American Society for Microbiology Student Travel Award, 2005

Position(s) Available

Postdoctoral Fellow in the field of Bioenergy and Environmental Microbiology at the School of Energy and Environment


  • Duties
    The appointee will be involved in an interdisciplinary biofuels project that encompasses biocatalysis, microbiology, molecular biology, and genomic analysis.
  • Requirements
    A recent Ph.D. in biochemical engineering, bioengineering, microbiology, molecular biology, bioinformatics or a related discipline. Candidates should be familiar with advanced molecular techniques and have a strong background in computational analysis. Strong oral and written communication skills in English and the ability to work in a multi-disciplinary team are essential.
  • Application
    To apply, please submit your CV to Dr. Patrick Lee at patrick.kh.lee@cityu.edu.hk. Review of applications will begin immediately and applications will be accepted until the position is filled. Salary offered will be highly competitive, commensurate with qualifications and experience. Contract duration is for one year and can be renewed subject to performance. For more information, please email Dr. Patrick Lee. Only short-listed candidates will be contacted.


  • Men, Y., H. Feil, N. C. VerBerkmoes, M. B. Shah, D. R. Johnson, P. K. H. Lee, K. A. West, S. H. Zinder, G. L. Andersen, and L. Alvarez-Cohen. 2011. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME J. doi:10.1038/ismej.2011.111.
  • Lee, P. K. H., D. Cheng, P. Hu, K. A. West, G. J. Dick, E. L. Brodie, G. L. Andersen, S. H. Zinder, J. He, and L. Alvarez-Cohen. 2011. Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J. 5:1014-1024.
  • Lee, P. K. H., J. He, S. H. Zinder, and L. Alvarez-Cohen. 2009. Evidence for nitrogen fixation by Dehalococcoides ethenogenes strain 195. Appl. Environ. Microbiol. 75: 7551-7555.
  • Fan, C., P. K. H. Lee, W. J. Ng, L. Alvarez-Cohen, E. L. Brodie, G. L. Andersen, and J. He. 2009. Influence of trace erythromycin and erythromycin-H2O on carbon and nutrients removal and on resistance selection in sequencing batch reactors (SBRs). Appl. Microbiol. Biotechnol. 85: 185-195.
  • Lee, P. K. H., T. W. Macbeth, K. S. Sorenson, Jr., R. A. Deeb, and L. Alvarez-Cohen. 2008. Quantifying genes and transcripts to assess the in situ physiology of Dehalococcoides spp. in a trichloroethene-contaminated groundwater site. Appl. Environ. Microbiol. 74: 2728-2739.
  • West, K. A., D. R. Johnson, P. Hu, T. Z. DeSantis, E. L. Brodie, P. K. H. Lee, H. Feil, G. L. Andersen, S. H. Zinder, and L. Alvarez-Cohen. 2008. Comparative genomics of Dehalococcoides ethenogenes 195 and a Dehalococcoides-containing enrichment culture. Appl. Environ. Microbiol. 74:3533-3540.
  • Lee, P. K. H., M. E. Conrad, and L. Alvarez-Cohen. 2007. Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates. Environ. Sci. Technol. 41:4277-4285.
  • He, J., V. F. Holmes, P. K. H. Lee, and L. Alvarez-Cohen. 2007. Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl. Environ. Microbiol. 73:2847-2853.
  • Lee, P. K. H., D. R. Johnson, V. F. Holmes, J. He, and L. Alvarez-Cohen. 2006. Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl. Environ. Microbiol. 72:6161-6168.
  • Holmes, V. F., J. He, P. K. H. Lee, and L. Alvarez-Cohen. 2006. Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl. Environ. Microbiol. 72:5877-5883.
  • Johnson, D. R., P. K. H. Lee, V. F. Holmes, A. C. Fortin, and L. Alvarez-Cohen. 2005. Transcriptional expression of the tceA gene in a Dehalococcoides-containing microbial enrichment. Appl. Environ. Microbiol. 71:7145-7151.
  • Johnson, D. R., P. K. H. Lee, V. F. Holmes, and L. Alvarez-Cohen. 2005. An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Appl. Environ. Microbiol. 71:3866-3871.
Staff Image
Associate Dean, School of Energy and Environment (Undergraduate Studies) Associate Professor, School of Energy and Environment
Contact Information
Office: YEUNG-B5423
Phone: +(852)-3442-4625
Fax: +(852)-3442-0688
Email: patrick.kh.lee@cityu.edu.hk
Web: http://www.cityu.edu.hk/see_mer/personal/Patrick_Lee/index.html

Time slots for consultation

Research Interests
  • Biotechnology for energy and environment
  • Microbiology
  • Microbiome
  • Systems biology