Dr. Patrick K. H. LEE

Ph.D. in Environmental Engineering, University of California, Berkeley
Staff title
Associate Professor

Patrick Lee is an Associate Professor in the School of Energy and Environment. His academic background is in biochemical engineering, environmental engineering and environmental microbiology. He began his independent career in 2011 after completing his PhD and postdoctoral training at the University of California, Berkeley. He was the Associate Dean for Undergraduate Studies of the School from 2017 to 2021.

Together with members of his research group, Dr. Lee is interested in solving biologically-related energy and environmental problems and he often works at the interface of fundamental and applied sciences. While he is interested in understanding microbiology at the molecular and cellular levels, it is also his goal to apply the fundamental findings in engineering applications to solve real-world problems.

Dr. Lee’s research group is currently studying microbes in indoor and outdoor air, different environmental systems, and how to harness bacteria and their molecular parts to effectively produce renewable biobased chemicals. His group has expertise in wet-lab and computational techniques to manipulate and model bacteria. In addition to investigating single bacteria, his group is also interested in complex microbial communities. Through research and education, Dr. Lee strives to create a healthier, greener and more sustainable future for all.

For more information, please visit Dr. Lee’s Research Group website.

Other Information


  • Outstanding Supervisor Award, City University of Hong Kong, 2018
  • Special Recognition Award, World Cultural Council (WCC), 2018
  • Achievement Award, Bioenergy Society of Singapore, 2018
  • The President’s Awards, City University of Hong Kong, 2016 & 2020
  • Natural Sciences and Engineering Research Council Postdoctoral 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