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Associate Professor

Wei Huang BEng MSc DPhil

Associate Professor of Engineering Science

Fellow of St Edmund Hall

TEL: 01865 283786


Professor Wei Huang received a PhD at the University of Sheffield in 2002. He was lecturer and senior lecturer at University of Sheffield 2007-2014.

Wei moved to Oxford in October 2014 as associate professor. He was a EPSRC Fellow of Synthetic Biology. His research interests are synthetic biology, single cell biology and applications.

College Page

Research Interests

Wei's research is focused on synthetic biology, systems biology and single cell Raman biotechnology.

His team aims to establish a novel bioengineering platform for synthetic biology – SimCells (Simple Cells). A SimCell is a genetically reprogrammable “artificial cellular machine”, originally derived from a natural cell. Its ‘hardware’ is the optimised ‘shell’ of a cell, which enables specific cellular properties; its ‘software’ is engineered mini-genome which delivers defined functions. The optimised shell and minigenome in SimCells enables them to faithfully dedicate most of their energy and resources to a specific function without interference from unwanted pathways and networks, as in natural cells. A SimCell is a non-dividing, biochemically active, designable and simplified agent, which can be continuously produced by engineered parent cells. SimCells have the potential to open up a new frontier, enabling the development of new and smart materials for bioprocessing and manufacturing, bioenergy, healthcare, agriculture and environmental monitoring and protection.

He is one of the pioneers on single cell Raman biotechnology, developing Raman-stable isotope probing (Raman-SIP), Raman-fluorescent in-situ hybridisation (Raman-FISH) and Raman activated cell sorting (RACS) system, which can be used to characterise bacterial function and link phenotypes to genotypes of single cells. The single cell Raman technology has been licensed to industry for applications.

This research will transform current synthetic biology based on living cells or cell-free system by providing an artificial cellular machine between living and non-living systems, and leveraging advantages of both. SimCells have been used as novel biosensors for medical diagnosis and therapy, and as miniature factories for green energy. Safe deliverable probiotic SimCells have been developed to perform dose response activation of genes for therapeutic purpose. A bio-transformation system can be designed and constructed to produce biofuels from H2O and CO2, mediated by SimCells and powered by electrons and sunlight.

Research Groups

Current Grants

EPSRC, Fellowship for synthetic biology

PI, £1.0M, 2014-2019

Development of SimCells as building blocks for synthetic biology. EP/M002403/1.


Co-I, £430,764, 2018-2020

Effector gene persistence in bacterial plant pathogens. BB/R009236/1.


Co-I, sLoLa, £3.4M, 2015-2020.

Engineering new capacities for solar energy utilisation in bacteria. BB/M000265/1.


Co-I, £2.36M, 2016-2020.

Liquid Fuel and bioEnergy Supply from CO2 Reduction. EP/N009746/1.


Co-I, £100,449, 2018-2021.

Seedcorn. NE/S008721/1

Selected Publications

A full list of publications can be found 

  • Huang W.E.*, Lim B., Hsu C.C., Xiong D., Wu W., Yu Y., Jia H., Wang Y., Zeng Y., Ji M., Chang H., Zhang X., Wang H., Cui Z. (2020) RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2. Microbial Biotechnology 13:950-961. 

  • Fan C., Davison P.A., Habgood R., Zeng H., Decker C.M., Gesell Salazar M., Lueangwattanapong K., Townley H.E, Yang A., Thompson I.P., Ye H., Cui Z., Schmidt F., Hunter C.N., Huang W.E.* (2020) Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proceedings of the National Academy of Sciences of the United States of America 117:6752-6761.

  • Fan C., Wu Y.H., Decker C., Rohani R., Gesell Salazar M., Ye H., Cui Z., Schmidt F., Huang W.E.* (2019) Defensive Function of Transposable Elements in Bacteria. ACS Synthetic Biology 8:2141-2151.

  • Chen, J.X., Steel, H., Wu, Y-H, Wang, Y., Xu J., Rampley C.P.N., Thompson I.P., Papachristodoulou A, Huang W.E.* (2019) Development of aspirin inducible biosensors in Escherichia coli and SimCells. Applied & Environmental Microbiology 85:e02959-18. Highlighted by AEM Spotlight.

  • Hsu C.C., Xu J., Brinkhofa B., Wang H., Cui Z., Huang W.E.*, Ye H.* (2020) A Single-Cell Raman-based Platform to Identify Developmental Stages of Human Pluripotent Stem Cell-derived Neurons. Proceedings of the National Academy of Sciences of the United States of America 117: 18412-18423.

  • Jing, X., Gou, H., Gong, Y., Su, X., Xu, L. Ji, Y. Song, Y., Thompson, I.P., Xu, J. Huang, W.E.* (2018) Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean. Environmental Microbiology 20:2241-2255.

  • Song, Y., Kaster, A., Vollmers, J., Song, Y., Davison, P.A., Frentrup, M., Preston, G.M., Thompson, I.P., Murrell, J.C., Yin, H., Hunter, C.N., Huang, W.E.* (2017) Single cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea. Microbial Biotechnology 10:125-137.

  • Zhang, D., Berry, J.P., Zhu, D., Wang, Y., Chen, Y., Jiang, B., Huang, S., Langford, H., Li, G., Xu, J., Aries, E. and Huang, W.E.* (2015) Isolation and physiological characterisation of an uncultured degrader in a complex microbial community. ISME Journal 9:603-614. 

  • Li M, Canniffe D.P., Jackson P.J., Davison P.A., FitzGerald S., Dickman M.J., Burgess J.G., Hunter C.N., Huang W.E.* (2012) Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities. ISME Journal 6:875-885.

  • Huang W.E.*, Ferguson A., Singer A.C., Lawson K., Thompson I.P., Kalin R.M., Larkin M.J., Bailey M.J., Whiteley A.S. (2009) Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ hybridization. Applied and Environmental Microbiology 75:234-241.

  • Song Y., Li G., Thornton S.F., Thompson I.P., Banwart S.A., Lerner D.N., Huang W.E.* (2009) Optimization of bacterial whole cell bioreporters for toxicity assay of environmental samples. Environmental Science and Technology 43:7931-7938.

  • Huang W.E., Stoecker K., Griffiths R., Newbold L., Daims H., Whiteley A.S., Wagner M. (2007) Raman-FISH: Combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environmental Microbiology 9:1878-1889.

  • Song Y., Hahn T., Thompson I.P., Mason T.J., Preston G.M., Li G., Paniwnyk L., Huang W.E.* (2007) Ultrasound-mediated DNA transfer for bacteria. Nucleic Acids Research 35:e129.

  • Huang W.E., Wang H., Zheng H., Huang L., Singer A.C., Thompson I.P., Whiteley A.S. (2005) Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate. Environmental Microbiology 7:1339-1348.

  • Huang W.E.*, Griffiths R.I., Thompson I.P., Bailey M.J., Whiteley A.S. (2004) Raman microscopic analysis of single microbial cells. Analytical Chemistry 76:4452-4458.

*Corresponding author

DPhil Opportunities

I am currently open to supervising PhD students on synthetic biology and single cell biology