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Selected Publications

More information about our publications can be found via Google Scholar.

2025

Du, S.^{^†}; Lin, H.^{^†}; Luo, Q.; Man, C. L.; Lai, S. H.; Ho, K. F.; Leung, K. M. Y.; Lee, P. K. H.* House dust microbiome differentiation and phage-mediated antibiotic resistance and virulence dissemination in the presence of endocrine-disrupting chemicals and pharmaceuticals. Microbiome 2025, 13, 96. ^†Authors contributed equally.

Liu, Y.; Li, Y.; Chan, W. L.; Bao, Y.; Lee, P. K. H.; Nah, T.* Efficient production of reactive oxidants by atmospheric bacterial-derived organic matter in the aqueous phase. Environ. Sci. Technol. 2025, 59, 6757-6770.

2024

Du, S.; Tong, X.; Leung, M. H. Y.; Betts, R. J.; Woo, A. C.; Bastien, P.; Misra, N.; Aguilar, L.; Clavaud, C.; Lee, P. K. H.* Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions. ISME J. 2024, 18, wrae218.

Tong, X.; Luo, D.; Leung, M. H. Y.; Lee, J. Y. Y.; Shen, Z.; Jiang, W.; Mason, C. E.; Lee, P. K. H.* Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments. Microbiome 2024, 12, 198.

Nah, T.*; Lee, P. K. H.*; Lai, A. C.K.* Don't forget about the microbes on surfaces in indoor atmospheric chemistry. ACS ES&T Air 2024, 1, 743-746.

Yu, J.; Lee, J. Y. Y.; Tang, S. N.; Lee, P. K. H.* Niche differentiation in microbial communities with stable genomic traits over time in engineered systems. ISME J. 2024, 18, wrae042.

Bao, Y.; Ruan, Y.; Wu, J.; Wang, W.-X.; Leung, K. M. Y.; Lee, P. K. H.* Metagenomics-based microbial ecological community threshold and indicators of anthropogenic disturbances in estuarine sediments. Environ. Sci. Technol. 2024, 58, 780–794.

Liang, Z.; Zhou, L.; Chen, K.; Lin, Y. H.; Lai, A. C. K.; Lee, P. K. H.; Sit, P. H. L.; Yin, R.; Chan, C. K.* Formation of secondary aerosol by 222 nm Far-UVC irradiation on SO₂. Atmos. Environ. 2024, 330, 120559.

2023

Hao, C.; Lee, P. K. H.*; Lam, H.* metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering. Microbiome 2023, 11, 176.

Du, S.; Tong, X.; Lai, A. C. K.; Chan, C. K.; Mason, C. E.; Lee, P. K. H.* Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat. Commun. 2023, 14, 2676.

Leung, M. H. Y.; Tong, X.; Shen, Z.; Du, S.; Bastien, P.; Appenzeller, B. M. R.; Betts, R. J.; Mezzache, S.; Bourokba, N.; Cavusoglu, N.; Aguilar, L.; Misra, N.; Clavaud, C.; Lee, P. K. H.* Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons. Microbiome 2023, 11, 124.

Yu, J.; Tang, S. N.; Lee, P. K. H.* Universal dynamics of microbial communities in full-scale textile wastewater treatment plants and system prediction by machine learning. Environ. Sci. Technol. 2023, 57, 3345-3356.

Lee, J. Y. Y.; Miao, Y.; Chau, R. L. T.; Hernandez, M.; Lee, P. K. H.* Artificial intelligence-based prediction of indoor bioaerosol concentrations from indoor air quality sensor data. Environ. Int. 2023, 174, 107900.

Liu, Y.; Lee, P. K. H.; Nah, T.* Aqueous photooxidation of live bacteria with hydroxyl radicals under clouds-like conditions: Insights into the production and transformation of biological and organic matter originating from bioaerosols. Environ. Sci.: Process. Impacts 2023, 25, 1150-1168.

Liu, Y.; Lim, C. K.; Shen Z.; Lee, P. K. H.; Nah, T.* Effects of pH and light exposure on the survival of bacteria and their ability to biodegrade organic compounds in clouds: Implications for microbial activity in acidic cloud water. Atmospheric Chem. Phys. 2023, 23, 1731-1747.

Liang, Z.; Cheung, T. Y.; Chan, W. L.; Lim, C. K.; Lai, A. C. K.; Lee, P. K. H.; Chan, C. K.* Negligible increase in indoor endotoxin activity by 222 nm far-UVC illumination on bioaerosols. Environ. Sci.: Atmos. 2023, 3, 1212-1220.

Liang, Z.; Zhou, L.; Li, X.; Cuevas, R. A. I.; Tang, R.; Li, M.; Cheng, C.; Chu, Y.; Lee, P. K. H.; Lai, A. C. K.; Chan, C. K.* Secondary aerosol formation in incense burning particles by O₃ and OH oxidation via single particle mixing state analysis. Sci. Total Environ. 2023, 894, 164942.

Wang, M. H.; Zhang, H. H.; Chan, C. K.; Lee, P. K. H.; Lai, A. C. K.* Experimental study of the disinfection performance of a 222-nm Far-UVC upper-room system on airborne microorganisms in a full-scale chamber. Build. Environ. 2023, 236, 110260.

Archer, S. D. J.; Lee, K. C.; Caruso, T.; Alcami, A.; Araya, J. G.; Cary, S. C.; Cowan, D. A.; Etchebehere, C.; Gantsetseg, B.; Gomez-Silva, B.; Hartery, S.; Hogg, I. D.; Kansour, M. K.; Lawrence, T.; Lee, C. K.; Lee, P. K. H.; Leopold, M.; Leung, M. H. Y.; Maki, T.; McKay, C. P.; Al Mailem, D. M.; Ramond, J.-B.; Rastrojo, A.; Šantl-Temkiv, T.; Sun, H. J.; Tong, X.; Vandenbrink, B.; Warren-Rhodes, K. A.; Pointing, S. B.* Contribution of soil bacteria to the atmosphere across biomes. Sci. Total Environ. 2023, 871, 162137.

2022

Villada, J. C.; Duran, M. F.; Lim, C. K.; Stein, L. Y.; Lee, P. K. H.* Integrative genome-scale metabolic modeling reveals versatile metabolic strategies for methane utilization in Methylomicrobium album BG8. mSystems 2022, 7, e00073-22.

Wang, P.; Tong, X.; Zhang, N.; Miao, T.; Chan, J.; Huang, H.; Lee, P. K. H.*; Li, Y.* Fomite transmission follows invasion ecology principles. mSystems 2022, 7, e00211-22.

Liang, Z.^{^†}; Chan, W. L.^{^†}; Tian, X.; Lee, P. K. H.*; Chan, C. K.* Inactivation of Escherichia coli in droplets at different ambient relative humidities: Effects of phase transition, solute and cell concentrations. Atmos. Environ. 2022, 280, 119066. ^†Authors contributed equally.

Santl-Temkiv, T.; Amato, P.; Casamayor, E. O.; Lee, P. K. H.; Pointing, S. B.* Microbial ecology of the atmosphere. FEMS Microbiol. Rev. 2022, 46, fuac009.

Li, J.; Hu, D.; Lim, C. K.; Ren, J.; Yao, X.; Ma, C.; Chen, W.; Lee, P. K. H.*; Lam, R. H. W.* Selective single-bacteria extraction based on capture and release of microemulsion droplets. Sci. Rep. 2022, 12, 15461.

Liang, Z.; Zhou, L.; Cuevas, R. A. I.; Li, X.; Cheng, C.; Li, M.*; Tang, R.; Zhang, R.; Lee, P. K. H.; Lai, A. C. K.; Chan, C. K.* Sulfate formation in incense burning particles: A single-particle mass spectrometric study. Environ. Sci. Technol. Lett. 2022, 9, 718-725.

Lin, H. J.; Lao, J. Y.; Wang, Q.; Ruan, Y. F.*; He, Y. H.; Lee, P. K. H.; Leung, K. M. Y.; Lam, P. K. S.* Per- and polyfluoroalkyl substances in the atmosphere of waste management infrastructures: Uncovering secondary fluorotelomer alcohols, particle size distribution, and human inhalation exposure. Environ. Int. 2022, 167, 107434.

Wu, J.; Danko, D.; Afshinnekoo, E.; Bezdan, D.; Bhattacharyya, M.; Castro-Nallar, E.; Chmielarczyk, A.; Hazrin-Chong, N. H.; Deng, Y.; Dias-Neto, E.; Frolova, A.; Mason-Buck, G.; Iraola, G.; Jang, S.; Łabaj, P.; Lee, P. K. H.; Nieto-Caballero, M.; Osuolale, O. O.; Ouzounis, C. A.; Perlin, M. H.; Prithiviraj, B.; Rascovan, N.; Różańska, A.; Schriml, L. M.; Semmler, T.; Suzuki, H.; Ugalde, J. A.; Young, B.; Werner, J.; Zambrano, M. M.; Zhao, Y.; Mason, C.; Shi, T. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. Environ. Res. 2022, 207, 112183.

2021

Zhou, Y.^{^†}; Leung, M. H. Y.^{^†}; Tong, X.; Lee, J. Y. Y.; Lee, P. K. H.* City-scale meta-analysis of indoor airborne microbiota reveals that taxonomic and functional compositions vary with building types. Environ. Sci. Technol. 2021, 55, 15051-15062. ^†Authors contributed equally.

Tong, X.; Leung, M. H. Y.; Shen, Z.; Lee, J. Y. Y.; Mason, C. E.; Lee, P. K. H.* Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. Microbiome 2021, 9, 213.

Misra, N.; Clavaud, C.; Guinot, F.; Bourokba, N.; Nouveau, S.; Mezzache, S.; Palazzi, P.; Appenzeller, B. M. R.; Tenenhaus, A.; Leung, M. H. Y.; Lee, P. K. H.; Bastien, P.; Aguilar, L.; Cavusoglu, N. Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction. Sci. Rep. 2021, 11, 18302.

Wilkins, D.; Tong, X.; Leung, M. H. Y.; Mason, C. E.; Lee, P. K. H.* Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching. Microbiome 2021, 9, 129.

Leung, M. H. Y.^{^†}; Tong, X.^{^†}; Bøifot, K. O.^{^†}; Bezdan, D.; Butler, D. J.; Danko, D. C.; Gohli, J.; Green, D. C.; Hernandez, M. T.; Kelly, F. J.; Levy, S.; Mason-Buck, G.; Nieto-Caballero, M.; Syndercombe-Court, D.; Udekwu, K. I.; Young, B. G.; Mason, C. E.*; Dybwad, M.*; Lee, P. K. H.* Characterization of the public transit air microbiome and resistome reveals geographical specificity. Microbiome 2021, 9, 112. ^†Authors contributed equally.

The MetaSUB International Consortium^# A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021, 184, 3376-3393. ^#A member of the international consortium.

Yu, J.; Tang, S. N.; Lee, P. K. H.* Microbial communities in full-scale wastewater treatment systems exhibit deterministic assembly processes and functional dependency over time. Environ. Sci. Technol. 2021, 55, 5312-5323.

Zhou, Y.; Leung, M. H. Y.; Tong, X.; Lai, Y.; Tong, J. C. K.; Ridley, I. A.; Lee, P. K. H.* Profiling airborne microbiota in mechanically ventilated buildings across seasons in Hong Kong reveals higher metabolic activity in low-abundance bacteria. Environ. Sci. Technol. 2021, 55, 249-259.

Kim, Y.; Carrai, M.; Leung, M. H. Y. ; Chin, J.; Li, J.; Lee, P. K. H. ; Beatty, J.; Pfeiffer, D.; Barrs, V. Dysbiosis of the urinary bladder microbiome in cats with chronic kidney disease. mSystems 2021, 6, e00510-21.

Wang, P.; Zhang, N.; Miao, T.; Chan, J. P. T.; Huang, H.; Lee, P. K. H.; Li, Y. Surface touch network structure determines bacterial contamination spread on surfaces and occupant exposure. J. Hazard. Mater. 2021, 416, 126137.

Wang, P.; Zhang, N.; Lee, P. K. H.; Li, Y. Quantification of Lactobacillus delbrueckii subsp. Bulgaricus and its applicability as a tracer for studying contamination spread on environmental surfaces. Build. Environ. 2021, 197, 107869.

Wang, L.; Bian, Y.; Lim, C. K.; Niu, Z.; Lee, P. K. H.; Chen, C.; Zhang, L.; Daoud, W. A.; Zi, Y.* Tribo-charge enhanced hybrid air filter masks for efficient particulate matter capture with greatly extended service life. Nano Energy 2021, 85, 106015.

2020

Zhou, Y.; Lai, Y.; Tong, X.; Leung, M. H. Y.; Tong, J. C. K.; Ridley, I. A.; Lee, P. K. H.* Airborne bacteria in outdoor air and air of mechanically ventilated buildings at city scale in Hong Kong across seasons. Environ. Sci. Technol. 2020, 54, 11732-11743.

Villada, J. C.; Duran, M. F.; Lee, P. K. H.* Interplay between position-dependent codon usage bias and hydrogen bonding at the 5′ end of ORFeomes. mSystems 2020, 5, e00613-20.

Leung, M. H. Y.; Tong, X.; Bastien, P.; Guinot, F.; Tenenhaus, A.; Appenzeller, B. M. R.; Betts, R. J.; Mezzache, S.; Li, J.; Bourokba, N.; Breton, L.; Clavaud, C.; Lee, P. K. H.* Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants. Microbiome 2020, 8, 100.

Nobu, M. K.; Narihiro, T.; Mei, R.; Kamagata, Y.; Lee, P. K. H.; Lee, P. H.; McInerney, M. J.; Liu, W. T. Liu. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 2020, 8, 111.

Kim, Y.*; Leung, M. H. Y.; Fournié, W. G.; Li, J.; Lee, P. K. H.; Pfeiffe, D. U. r. Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome. Animal Microbiome 2020, 2, 4.

2019

Villada, J. C.; Duran, M. F.; Lee, P. K. H.* Genomic evidence for simultaneous optimization of transcription and translation through codon variants in the pmoCAB operon of type Ia methanotrophs. mSystems 2019, 4, e00342-19.

Lim, C. K.; Villada, J. C.; Chalifour, A.; Duran, M. F.; Lu, H.; Lee, P. K. H.* Designing and engineeringMethylorubrum extorquens AM1 for itaconic acid production. Front. Microbiol. 2019, 10, 1027.

Tong, X.; Leung, M. H. Y.; Wilkins, D.; Cheung, H. H. L.; Lee, P. K. H.* Neutral processes drive seasonal assembly of the skin mycobiome. mSystems 2019, 4, e00004-19.

Jia, Y.; Leung, M. H. Y.; Tong, X.; Wilkins, D.; Lee, P. K. H.* Rare taxa exhibit disproportionate cell-level metabolic activity in enriched anaerobic digestion microbial communities. mSystems 2019, 4, e00208-18.

Lu, H.; Villada, J. C.; Lee, P. K. H.* Modular metabolic engineering for biobased chemical production. Trends Biotechnol. 2019, 37, 152-166.

2018

Jia, Y.; Ng, S. K.; Lu, H.; Cai, M.; Lee, P. K. H.* Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion. Biotechnol. Biofuels. 2018, 11, 117.

Gomez-Silvan, C.; Leung, M. H. Y.; Grue, K. A.; Kaur, R.; Tong, X.; Lee, P. K. H.* Andersen, G. L.* A comparison of methods used to unveil the genetic and metabolic pool in the built environment. Microbiome 2018, 6, 71.

Leung, M. H. Y.; Tong, X.; Wilkins, D.; Cheung, H. H. L.; Lee, P. K. H.* Individual and household attributes influence the dynamics of the personal skin microbiota and its association network. Microbiome 2018, 6, 26.

Leung, M. H. Y.; Tong, X.; Tong, J. C. K.; Lee, P. K. H.*Airborne bacterial assemblage in a zero carbon building: A case study. Indoor Air 2018, 28, 40-50.

Cai, M.; Ng, S. K.; Lim, C. K.; Lu, H.; Jia, Y.; Lee, P. K. H.* Physiological and metagenomic characterizations of the synergistic relationships between ammonia- and nitrite-oxidizing bacteria in freshwater nitrification. Front. Microbiol. 2018, 9, 280.

2017

Tong, X.; Leung, M. H. Y.; Wilkins, D.; Lee, P. K. H.* City-scale distribution and dispersal routes of mycobiome in residences. Microbiome 2017, 5, 131.

Mei, R.; Nobu, M. K.; Narihiro, T.; Kuroda, K.; Sierra, J. M.; Wu, Z.; Ye, L.; Lee, P. K. H.; Lee, P. H.; van Lier, J. B.; McInerney, M. J.; Kamagata, Y.; Liu, W. T. Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Res. 2017, 124, 77-84.

Wilkins, D.; Leung, M. H. Y.; Lee, P. K. H.* Microbiota fingerprints lose individually identifying features over time. Microbiome 2017, 5, 1.

Lu, H.; Ng, S. K.; Jia, Y.; Cai, M.; Lee, P. K. H.* Physiological and molecular characterizations of the interactions in two cellulose-to-methane cocultures. Biotechnol. Biofuels. 2017, 10, 37.

2016

Leung, Y. H.; Xu, X.; Ma, A. P. Y.; Liu, F.; Ng, A. M. C.; Shen, Z.; Gethings, L. A.; Guo, M.; Djurišić, A. B. *; Lee, P. K. H.*; Lee, H.; Chan, W. K.; Leung, F. C. C. Toxicity of ZnO and TiO2 to Escherichia coli cells. Sci. Rep. 2016, 6, 35243.

Leung, M. H. Y.; Chan, K. C. K.; Lee, P. K. H.* Skin fungal community and its correlation with bacterial community of urban Chinese individuals. Microbiome 2016, 4, 46.

Lu, H.; Chen, J.; Jia, Y.; Cai, M.; Lee, P. K. H.* Transcriptomic responses of the interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in a cellulose-grown coculture for enhanced hydrogen production. Appl. Environ. Microbiol. 2016, 82, 4546-4559.

Cai, M.; Wilkins, D.; Chen, J.; Ng, S. K.; Lu, H.; Jia, Y.; Lee, P. K. H.* Metagenomic reconstruction of key anaerobic digestion pathways in municipal sludge and industrial wastewater biogas-producing systems. Front. Microbiol. 2016, 7, 778.

Leung, M. H. Y.; Lee, P. K. H.* The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review. Microbiome 2016, 4, 21.

The MetaSUB International Consortium^#. The metagenomics and metadesign of the subways and urban biomes (MetaSUB) international consortium inaugural meeting report. Microbiome 2016, 4, 24. ^#A member of the international consortium.

Karthikeyan, R.; Krishnaraj, N.; Selvam, A.; Wong, J. W. C.; Lee, P. K. H.; Leung, M. K. H.; Berchmans, S. Effect of composites based nickel foam anode in microbial fuel cell using Acetobacter aceti and Gluconobacter roseus as a biocatalysts. Bioresour. Technol. 2016, 217, 113-120.

Jia, Y.; Wilkins, D.; Lu, H.; Cai, M.; Lee, P. K. H.* Long-term enrichment on cellulose or xylan causes functional and taxonomic convergence of microbial communities from anaerobic digesters. Appl. Environ. Microbiol. 2016, 82, 1519-1529.

Wilkins, D.; Leung, M. H. Y.; Lee, P. K. H.* Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes. Environ. Microbiol. 2016, 18, 1754-1763.

2015

Low, A.^{^†}; Shen, Z. Y.^{^†}; Cheng, D.; Rogers, M. J.; Lee, P. K. H.*; He, J.* A comparative genomics and reductive dehalogenase transcription study of two chloroethene-respiring bacteria, Dehalococcoides mccartyi strains MB and 11a. Sci. Rep. 2015, 5, 15204. ^†Authors contributed equally.

Wilkins, D.; Rao, S.; Lu, X.; Lee, P. K. H.* Effects of sludge inoculum and organic feedstock on active microbial communities and methane yield during anaerobic digestion. Front. Microbiol. 2015, 6, 1114.

Leung, M. H. Y.; Wilkins, D.; Lee, P. K. H.* Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups. Sci. Rep. 2015, 5, 11845.

Karthikeyan, O. P.; Chidambarampadmavathy, K.; Nadarajan, S.; Lee, P. K. H.; Heimann, K. Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium. Chemosphere. 2015, 141, 235-242.

Lu, H.; Lee, P. K. H.* Effects of cellulose concentrations on the syntrophic interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in coculture fermentation for biohydrogen production. Int. J. Hydrogen Energy. 2015, 40, 11800-11808.

Sales, C. M.*; Lee, P. K. H.* Resource recovery from wastewater: application of meta-omics to phosphorus and carbon management. Curr. Opin. Biotechnol. 2015, 33, 260-267.

Wubulihairen, M.; Lu, X.; Lee, P. K. H.; Ning, Z. Development and laboratory evaluation of a compact swirling aerosol sampler (SAS) for collection of atmospheric bioaerosols. Atmos. Pollut. Res. 2015, 6, 556-561.

Lee, P. K. H.; Men, Y.; Wang, S.; He, J.; Alvarez-Cohen, L. Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities. Environ. Sci. Technol. 2015, 49, 1585-1593.

Karthikeyan, R.; Wang, B.; Xuan, J.; Wong, J. W. C; Lee, P. K. H.; Leung, M. K. H. Interfacial electron transfer and bioelectrocatalysis of carbonized plant material as effective anode of microbial fuel cell. Electrochim. Acta. 2015, 157, 314-323.

Wilkins, D.; Lu, X. Y.; Shen, Z.; Chen, J.; Lee, P. K. H.* Pyrosequencing of mcrA and archaeal 16S rRNA genes reveals diversity and substrate preferences of methanogen communities in anaerobic digesters. Appl. Environ. Microbiol. 2015, 81, 604-613.

Djurišić, A. B.; Leung, Y. H.; Ng, A. M. C.; Xu, X. Y.; Lee, P. K. H.; Degger, N.; Wu, R. S. S. Toxicity of metal oxide nanoparticles: mechanisms, characterization, and avoiding experimental artefacts. Small 2015, 11, 26-44.

2014

Leung, M. H. Y.; Wilkins, D.; Li, E. K. T.; Kong, F. K. F.; Lee, P. K. H.* Indoor-air microbiome in an urban subway network: Diversity and dynamics. Appl. Environ. Microbiol. 2014, 80, 6760-6770.

Leung, Y. H.; Ng, A. M. C.; Xu, X.; Shen, Z.; Gethings, L. A.; Wong, M. T.; Chan, C. M. N.; Guo, M. Y.; Ng, Y. H.; Djurišić, A. B.*; Lee, P. K. H.*; Chan, W. K.; Yu, L. H.; Phillips, D. L.; Ma, A. P. Y.; Leung, F. C. C. Mechanisms of antibacterial activity of MgO: Non-ROS mediated toxicity of MgO nanoparticles towards Escherichia coli. Small 2014, 10, 1171-1183.

2013

Lu, X.; Rao, S.; Shen, Z.; Lee, P. K. H.* Substrate induced emergence of different active bacterial and archaeal assemblages during biomethane production. Bioresour. Technol. 2013, 148, 517-524.

Harding, K. C.; Lee, P. K. H.; Bill, M.; Buscheck, T. E.; Conrad, M. E.; Alvarez-Cohen, L. Effects of varying growth conditions on stable carbon isotope fractionation of trichloroethene (TCE) by tceA-containing Dehalococcoides mccartyi strains. Environ. Sci. Technol. 2013, 47, 12342-12350.

Lee, P. K. H.^{^†}; Cheng, D.^{^†}; West, K. A.; Alvarez-Cohen, L.; He, J. Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis. Environ. Microbiol. 2013, 15, 2293-2305. ^†Authors contributed equally.

Men, Y.; Lee, P. K. H.; Harding, K. C.; Alvarez-Cohen, L. Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions. Appl. Microbiol. Biotechnol. 2013, 97, 6439-6450.

West, K. A.; Lee, P. K. H.; Johnson, D. R.; Zinder, S. H.; Alvarez-Cohen, L. Global gene expression of Dehalococcoides within a robust dynamic TCE-dechlorinating community under conditions of periodic substrate supply. Biotechnol. Bioeng. 2013, 110, 1333-1341.

2012

Brisson, V. L.; West, K. A.; Lee, P. K. H.; Tringe, S. G.; Brodie, E. L.; Alvarez-Cohen, L. Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J. 2012, 6, 1702-1714.

Lee, P. K. H.; Dill, B. D.; Louie, T. S.; Shah, M.; VerBerkmoes, N. C.; Andersen, G. L.; Zinder, S. H.; Alvarez-Cohen, L. Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl. Environ. Microbiol. 2012, 78, 1424-1436.

Lee, P. K. H.; Warnecke, F.; Brodie, E. L.; Macbeth, T. W.; Conrad, M. E.; Andersen, G. L.; Alvarez-Cohen, L. Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site. Environ. Sci. Technol. 2012, 46, 1044-1054.

Men, Y.; Feil, H.; VerBerkmoes, N. C.; Shah, M. B.; Johnson, D. R.; Lee, P. K. H.; West, K. A.; Zinder, S. H.; Andersen, G. L.; Alvarez-Cohen, L. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME J. 2012, 6, 410-421.

2005 - 2011

Lee, P. K. H.; Cheng, D.; Hu, P.; West, K. A.; Dick, G. J.; Brodie, E. L.; Andersen, G. L.; Zinder, S. H.; He, J.; Alvarez-Cohen, L. Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J. 2011, 5, 1014-1024.

Lee, P. K. H.; He, J.; Zinder, S. H.; Alvarez-Cohen, L. Evidence for nitrogen fixation by Dehalococcoides ethenogenes strain195. Appl. Environ. Microbiol. 2009, 75, 7551-7555.

Fan, C.; Lee, P. K. H.; Ng, W. J.; Alvarez-Cohen, L.; Brodie, E. L.; Andersen, G.L.; He, J. Influence of trace erythromycin and erythromycin-H2O on carbon and nutrients removal and on resistance selection in sequencing batch reactors (SBRs). Appl. Microbiol. Biotechnol. 2009, 85, 185-195.

Lee, P. K. H.; Macbeth, T. W.; Sorenson, K. S.; Jr.; Deeb, R. A.; Alvarez-Cohen, L. Quantifying genes and transcripts to assess the in situ physiology of Dehalococcoides spp. in a trichloroethene-contaminated groundwater site. Appl. Environ. Microbiol. 2008, 74, 2728-2739.

West, K. A.; Johnson, D. R.; Hu, P.; DeSantis, T. Z.; Brodie, E. L.; Lee, P. K. H.; Feil, H.; Andersen, G. L.; Zinder, S. H.; Alvarez-Cohen, L. Comparative genomics of Dehalococcoides ethenogenes 195 and an enrichment culture containing unsequenced Dehalococcoides strains. Appl. Environ. Microbiol. 2008, 74, 3533-3540.

Lee, P. K. H.; Conrad, M. E.; Alvarez-Cohen, L. Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates. Environ. Sci. Technol. 2007, 41, 4277-4285.

He, J.; Holmes, V. F.; Lee, P. K. H.; Alvarez-Cohen, L. Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl. Environ. Microbiol. 2007, 73, 2847-2853.

Lee, P. K. H.; Johnson, D. R.; Holmes, V. F.; He, J.; Alvarez-Cohen, L. Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl. Environ. Microbiol. 2006, 72, 6161-6168.

Holmes, V. F.; He, J.; Lee, P. K. H.; Alvarez-Cohen, L. Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl. Environ. Microbiol. 2006, 72, 5877-5883.

Johnson, D. R.; Lee, P. K. H.; Holmes, V. F.; Fortin, A. C.; Alvarez-Cohen, L. Transcriptional expression of the tceA gene in a Dehalococcoides-containing microbial enrichment. Appl. Environ. Microbiol. 2005, 71, 7145-7151.

Johnson, D. R.; Lee, P. K. H.; Holmes, V. F.; Alvarez-Cohen, L. An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Appl. Environ. Microbiol. 2005, 71, 3866-3871.

Book Chapters

Leung, M. H. Y.; Tong, X.; Lee, P. K. H.* Indoor microbiome and airborne pathogens. In Comprehensive Biotechnology 3rd Edition (Vol. 6). M. Moo-Young, A. Moreira, B. Grodzinski, C. Ye, C. Webb, M. Butler, S. N. Agathos and Z. Cui (Eds). Elsevier, 2019. ISBN: 978-0-444-64047-5.

Ma, A. Y. W.; Cheung, B. K. W.; Kwok, K. C. M.; Cai, M.; Lee, P. K. H.*. Anaerobic digestion for energy recovery. In Recycling of Solid Waste for Biofuels and Bio-chemicals. O. P. Karthikeyan, K. Heimann and S. S. Muthu (Eds). Springer Publishing, 2016. ISBN 978-981-10-0150-5.

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