Publications

Selected Peer-reviewed Publications

• Tu W, Thompson IP, Huang WE. Engineering bionanoreactor in bacteria for efficient hydrogen production. Proc Natl Acad Sci U S A. 2024 Jul 16;121(29):e2404958121. doi: 10.1073/pnas.2404958121.
• Xu J, Li T, Huang WE, Zhou N-Y. Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene. Appl Environ Microbiol. 2024 May 6;:e0143623. doi: 10.1128/aem.01436-23.
• Tu W, Xu J, Thompson IP, Huang WE. Engineering artificial photosynthesis based on rhodopsin for CO(2) fixation. Nat Commun. 2023 Dec 4;14(1):8012. doi: 10.1038/s41467-023-43524-4. 
• Teng T, Huang WE, Li G, Wang X, Song Y, Tang X, Dawa D, Jiang B, Zhang D. Application of magnetic-nanoparticle functionalized whole-cell biosensor array for bioavailability and ecotoxicity estimation at urban contaminated sites. Sci Total Environ. 2023 Oct 20;896:165292. doi: 10.1016/j.scitotenv.2023.165292. 
• Tu W, Huang WE. Rhodopsin driven microbial CO(2) fixation using synthetic biology design. Environ Microbiol. 2023 Jan;25(1):126-130. doi: 10.1111/1462-2920.16243.
• Davison PA, Tu W, Xu J, Della Valle S, Thompson IP, Hunter CN, Huang WE. Engineering a Rhodopsin-Based Photo-Electrosynthetic System in Bacteria for CO(2) Fixation. ACS Synth Biol. 2022 Nov 18;11(11):3805-3816. doi: 10.1021/acssynbio.2c00397. 
• Lim B, Yin Y, Ye H, Cui Z, Papachristodoulou A, Huang WE. Reprogramming Synthetic Cells for Targeted Cancer Therapy. ACS Synth Biol. 2022 Mar 18;11(3):1349-1360. doi: 10.1021/acssynbio.1c00631.
• Chen JX, Lim B, Steel H, Song Y, Ji M, Huang WE. Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage. Microb Biotechnol. 2021 Nov;14(6):2481-2496. doi: 10.1111/1751-7915.13767. 
• Ng CK, Putra SL, Kennerley J, Habgood R, Roy RA, Raymond JL, Thompson IP, Huang WE. Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery. Microb Biotechnol. 2021 Jul;14(4):1580-1593. doi: 10.1111/1751-7915.13823.
• Lim B, Ratcliff J, Nawrot DA, Yu Y, Sanghani HR, Hsu CC, Peto L, Evans S, Hodgson SH, Skeva A, Adam M, Panopoulou M, Zois CE, Poncin K, Vasudevan SR, Dai S, Ren S, Chang H, Cui Z, Simmonds P, Huang WE, Andersson MI. Clinical validation of optimised RT-LAMP for the diagnosis of SARS-CoV-2 infection. Sci Rep. 2021 Aug 10;11(1):16193. doi: 10.1038/s41598-021-95607-1. 
• Zeng H, Rohani R, Huang WE, Yang A. Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis. BMC Bioinformatics. 2021 Sep 28;22(1):467. doi: 10.1186/s12859-021-04382-3.
• Chen XJ, Wang B, Thompson IP, Huang WE. Rational Design and Characterization of Nitric Oxide Biosensors in E. coli Nissle 1917 and Mini SimCells. ACS Synth Biol. 2021 Oct 15;10(10):2566-2578. doi: 10.1021/acssynbio.1c00223.
• Chen JX, Lim B, Steel H, Song Y, Ji M, Huang WE. Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage. Microb Biotechnol. 2021 Nov;14(6):2481-2496. doi: 10.1111/1751-7915.13767.
• Martin LK, Huang WE, Thompson IP. Bacterial wax synthesis. Biotechnol Adv. 2021 Jan-Feb;46:107680. doi: 10.1016/j.biotechadv.2020.107680. 
• Soldan R, Sanguankiattichai N, Bach-Pages M, Bervoets I, Huang WE, Preston GM. From macro to micro: a combined bioluminescence-fluorescence approach to monitor bacterial localization. Environ Microbiol. 2021 Apr;23(4):2070-2085. doi: 10.1111/1462-2920.15296. 
• Huang WE, Lim B, Hsu CC, Xiong D, Wu W, Yu Y, Jia H, Wang Y, Zeng Y, Ji M, Chang H, Zhang X, Wang H, Cui Z. RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2. Microb Biotechnol. 2020 Jul;13(4):950-961. doi: 10.1111/1751-7915.13586. 
• Cui Z, Chang H, Wang H, Lim B, Hsu CC, Yu Y, Jia H, Wang Y, Zeng Y, Ji M, Liu W, Inverarity C, Huang WE. Development of a rapid test kit for SARS-CoV-2: an example of product design. Biodes Manuf. 2020 May 11;:1-4. doi: 10.1007/s42242-020-00075-7.
• Fan C, Davison PA, Habgood R, Zeng H, Decker CM, Gesell Salazar M, Lueangwattanapong K, Townley HE, Yang A, Thompson IP, Ye H, Cui Z, Schmidt F, Hunter CN, Huang WE. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proc Natl Acad Sci U S A. 2020 Mar 24;117(12):6752-6761. doi: 10.1073/pnas.1918859117.
• Song Y, Cartron ML, Jackson PJ, Davison PA, Dickman MJ, Zhu D, Huang WE, Hunter CN. Proteorhodopsin Overproduction Enhances the Long-Term Viability of Escherichia coli. Appl Environ Microbiol. 2019 Dec 13;86(1). doi: 10.1128/AEM.02087-19. 
• Fan C, Wu YH, Decker CM, Rohani R, Gesell Salazar M, Ye H, Cui Z, Schmidt F, Huang WE. Defensive Function of Transposable Elements in Bacteria. ACS Synth Biol. 2019 Sep 20;8(9):2141-2151. doi: 10.1021/acssynbio.9b00218.
• Ng CK, Putra SL, Kennerley J, Habgood R, Roy RA, Raymond JL, Thompson IP, Huang WE. Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery. Microb Biotechnol. 2021 Jul;14(4):1580-1593. doi: 10.1111/1751-7915.13823. 
• Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK, Handelsman J, de Lorenzo V, Pruzzo C, Timmis J, Martín JLR, Verstraete W, Jetten M, Danchin A, Huang W, Gilbert J, Lal R, Santos H, Lee SY, Sessitsch A, Bonfante P, Gram L, Lin RTP, Ron E, Karahan ZC, van der Meer JR, Artunkal S, Jahn D, Harper L. The urgent need for microbiology literacy in society. Environ Microbiol. 2019 May;21(5):1513-1528. doi: 10.1111/1462-2920.14611. 
• Huang WE, Nikel PI. The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back. Microb Biotechnol. 2019 Jan;12(1):5-7. doi: 10.1111/1751-7915.13337.
• Zhang Q, Song Y, Amor K, Huang WE, Porcelli D, Thompson I. Monitoring Cr toxicity and remediation processes - combining a whole-cell bioreporter and Cr isotope techniques. Water Res. 2019 Apr 15;153:295-303. doi: 10.1016/j.watres.2019.01.009. 
• Chen JX, Steel H, Wu YH, Wang Y, Xu J, Rampley CPN, Thompson IP, Papachristodoulou A, Huang WE. Development of Aspirin-Inducible Biosensors in Escherichia coli and SimCells. Appl Environ Microbiol. 2019 Mar 15;85(6). doi: 10.1128/AEM.02959-18.  
• Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP, Wu LJ, Huang WE. Development of SimCells as a novel chassis for functional biosensors. Sci Rep. 2017 Aug 3;7(1):7261. doi: 10.1038/s41598-017-07391-6.
• Hedbavna P, Rolfe SA, Huang WE, Thornton SF. Biodegradation of phenolic compounds and their metabolites in contaminated groundwater using microbial fuel cells. Bioresour Technol. 2016 Jan;200:426-34. doi: 10.1016/j.biortech.2015.09.092. 
• Zhang D, Ding A, Cui S, Hu C, Thornton SF, Dou J, Sun Y, Huang WE. Whole cell bioreporter application for rapid detection and evaluation of crude oil spill in seawater caused by Dalian oil tank explosion. Water Res. 2013 Mar 1;47(3):1191-200. doi: 10.1016/j.watres.2012.11.038. 
• Zhang D, Zhao Y, He Y, Wang Y, Zhao Y, Zheng Y, Wei X, Zhang L, Li Y, Jin T, Wu L, Wang H, Davison PA, Xu J, Huang WE. Characterization and modeling of transcriptional cross-regulation in Acinetobacter baylyi ADP1. ACS Synth Biol. 2012 Jul 20;1(7):274-83. doi: 10.1021/sb3000244. 
• Zhang D, He Y, Wang Y, Wang H, Wu L, Aries E, Huang WE. Whole-cell bacterial bioreporter for actively searching and sensing of alkanes and oil spills. Microb Biotechnol. 2012 Jan;5(1):87-97. doi: 10.1111/j.1751-7915.2011.00301.x.
• Wang Y, Chen Y, Zhou Q, Huang S, Ning K, Xu J, Kalin RM, Rolfe S, Huang WE. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS One. 2012;7(10):e47530. doi: 10.1371/journal.pone.0047530. 
• Zhang D, Fakhrullin RF, Özmen M, Wang H, Wang J, Paunov VN, Li G, Huang WE. Functionalization of whole-cell bacterial reporters with magnetic nanoparticle. Microb Biotechnol. 2011 Jan;4(1):89-97. doi: 10.1111/j.1751-7915.2010.00228.x.
• Rico A, Bennett MH, Forcat S, Huang WE, Preston GM. Agroinfiltration reduces ABA levels and suppresses Pseudomonas syringae-elicited salicylic acid production in Nicotiana tabacum. PLoS One. 2010 Jan 29;5(1):e8977. doi: 10.1371/journal.pone.0008977. 
• Song Y, Li G, Thornton SF, Thompson IP, Banwart SA, Lerner DN, Huang WE. Optimization of bacterial whole cell bioreporters for toxicity assay of environmental samples. Environ Sci Technol. 2009 Oct 15;43(20):7931-8. doi: 10.1021/es901349r. 
• Huang WE, Singer AC, Spiers AJ, Preston GM, Whiteley AS. Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1. Environ Microbiol. 2008 Jul;10(7):1668-80. doi: 10.1111/j.1462-2920.2008.01583.x. 
• Song Y, Hahn T, Thompson IP, Mason TJ, Preston GM, Li G, Paniwnyk L, Huang WE. Ultrasound-mediated DNA transfer for bacteria. Nucleic Acids Res. 2007;35(19):e129. doi: 10.1093/nar/gkm710.
• Huang WE, Huang L, Preston GM, Naylor M, Carr JP, Li Y, Singer AC, Whiteley AS, Wang H. Quantitative in situ assay of salicylic acid in tobacco leaves using a genetically modified biosensor strain of Acinetobacter sp. ADP1. Plant J. 2006 Jun;46(6):1073-83. doi: 10.1111/j.1365-313X.2006.02758.x.
• Huang WE, Wang H, Zheng H, Huang L, Singer AC, Thompson I, Whiteley AS. Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate. Environ Microbiol. 2005 Sep;7(9):1339-48. doi: 10.1111/j.1462-5822.2005.00821.x. 

Single Cell Biology

• Lee KS, Landry Z, Athar A, Alcolombri U, Pramoj Na Ayutthaya P, Berry D, de Bettignies P, Cheng JX, Csucs G, Cui L, Deckert V, Dieing T, Dionne J, Doskocil O, D'Souza G, García-Timermans C, Gierlinger N, Goda K, Hatzenpichler R, Henshaw RJ, Huang WE, Iermak I, Ivleva NP, Kneipp J, Kubryk P, Küsel K, Lee TK, Lee SS, Ma B, Martínez-Pérez C, Matousek P, Meckenstock RU, Min W, Mojzeš P, Müller O, Kumar N, Nielsen PH, Notingher I, Palatinszky M, Pereira FC, Pezzotti G, Pilat Z, Plesinger F, Popp J, Probst AJ, Riva A, Saleh AAE, Samek O, Sapers HM, Schubert OT, Stubbusch AKM, Tadesse LF, Taylor GT, Wagner M, Wang J, Yin H, Yue Y, Zenobi R, Zini J, Sarkans U, Stocker R. MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. Nat Microbiol. 2024 May;9(5):1152-1156. doi: 10.1038/s41564-024-01656-3.
• Xu L, Liang Y, Huang WE, Shang LD, Chai LJ, Zhang XJ, Shi JS, Li B, Wang Y, Xu ZH, Lu ZM. Rapid detection of six Oceanobacillus species in Daqu starter using single-cell Raman spectroscopy combined with machine learning. Microb Biotechnol. 2024 Feb;17(2):e14416. doi: 10.1111/1751-7915.14416. 
• Xu J, Lodge T, Kingdon C, Strong JWL, Maclennan J, Lacerda E, Kujawski S, Zalewski P, Huang WE, Morten KJ. Developing a Blood Cell-Based Diagnostic Test for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Using Peripheral Blood Mononuclear Cells. Adv Sci (Weinh). 2023 Oct;10(30):e2302146. doi: 10.1002/advs.202302146. 
• Xu J, Luo Y, Wang J, Tu W, Yi X, Xu X, Song Y, Tang Y, Hua X, Yu Y, Yin H, Yang Q, Huang WE. Artificial intelligence-aided rapid and accurate identification of clinical fungal infections by single-cell Raman spectroscopy. Front Microbiol. 2023;14:1125676. doi: 10.3389/fmicb.2023.1125676.
• Yu T, Jadhav AC, Xu J, Harris AL, Nair V, Huang WE. Metabolic Reprogramming in Colon Cancer Cells Persistently Infected with Newcastle Disease Virus. Cancers (Basel). 2023 Jan 28;15(3). doi: 10.3390/cancers15030811. 
• Wang J, Meng S, Lin K, Yi X, Sun Y, Xu X, He N, Zhang Z, Hu H, Qie X, Zhang D, Tang Y, Huang WE, He J, Song Y. Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections. Anal Chim Acta. 2023 Jan 25;1239:340658. doi: 10.1016/j.aca.2022.340658. 
• Jing X, Gong Y, Xu T, Davison PA, MacGregor-Chatwin C, Hunter CN, Xu L, Meng Y, Ji Y, Ma B, Xu J, Huang WE. Revealing CO(2)-Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics. Biodes Res. 2022;2022:9782712. doi: 10.34133/2022/9782712. 
• Xu J, Yi X, Jin G, Peng D, Fan G, Xu X, Chen X, Yin H, Cooper JM, Huang WE. High-Speed Diagnosis of Bacterial Pathogens at the Single Cell Level by Raman Microspectroscopy with Machine Learning Filters and Denoising Autoencoders. ACS Chem Biol. 2022 Feb 18;17(2):376-385. doi: 10.1021/acschembio.1c00834.
• Liang P, Liu B, Wang Y, Liu K, Zhao Y, Huang WE, Li B. Isolation and Culture of Single Microbial Cells by Laser Ejection Sorting Technology. Appl Environ Microbiol. 2022 Feb 8;88(3):e0116521. doi: 10.1128/AEM.01165-21. 
• Zhang L, Li C, Peng D, Yi X, He S, Liu F, Zheng X, Huang WE, Zhao L, Huang X. Raman spectroscopy and machine learning for the classification of breast cancers. Spectrochim Acta A Mol Biomol Spectrosc. 2022 Jan 5;264:120300. doi: 10.1016/j.saa.2021.120300. 
• Wang J, Lin K, Hu H, Qie X, Huang WE, Cui Z, Gong Y, Song Y. In Vitro Anticancer Drug Sensitivity Sensing through Single-Cell Raman Spectroscopy. Biosensors (Basel). 2021 Aug 20;11(8). doi: 10.3390/bios11080286. 
• Xu J, Yu T, Zois CE, Cheng JX, Tang Y, Harris AL, Huang WE. Unveiling Cancer Metabolism through Spontaneous and Coherent Raman Spectroscopy and Stable Isotope Probing. Cancers (Basel). 2021 Apr 5;13(7). doi: 10.3390/cancers13071718. 
• Yi X, Song Y, Xu X, Peng D, Wang J, Qie X, Lin K, Yu M, Ge M, Wang Y, Zhang D, Yang Q, Wang M, Huang WE. Development of a Fast Raman-Assisted Antibiotic Susceptibility Test (FRAST) for the Antibiotic Resistance Analysis of Clinical Urine and Blood Samples. Anal Chem. 2021 Mar 30;93(12):5098-5106. doi: 10.1021/acs.analchem.0c04709. 
• Xu J, Li X, Guo Z, Huang WE, Cheng JX. Fingerprinting Bacterial Metabolic Response to Erythromycin by Raman-Integrated Mid-Infrared Photothermal Microscopy. Anal Chem. 2020 Nov 3;92(21):14459-14465. doi: 10.1021/acs.analchem.0c02489.
• Ng CK, Xu J, Cai Z, Yang L, Thompson IP, Huang WE, Cao B. Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes. Microb Biotechnol. 2020 Nov;13(6):1904-1916. doi: 10.1111/1751-7915.13636. 
• Hsu CC, Xu J, Brinkhof B, Wang H, Cui Z, Huang WE, Ye H. A single-cell Raman-based platform to identify developmental stages of human pluripotent stem cell-derived neurons. Proc Natl Acad Sci U S A. 2020 Aug 4;117(31):18412-18423. doi: 10.1073/pnas.2001906117. 
• Wang Y, Xu J, Kong L, Li B, Li H, Huang WE, Zheng C. Raman-activated sorting of antibiotic-resistant bacteria in human gut microbiota. Environ Microbiol. 2020 Jul;22(7):2613-2624. doi: 10.1111/1462-2920.14962. 
• Wang Y, Xu J, Kong L, Liu T, Yi L, Wang H, Huang WE, Zheng C. Raman-deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota. Microb Biotechnol. 2020 Mar;13(2):572-583. doi: 10.1111/1751-7915.13519. 
• Xu J, Preciado-Llanes L, Aulicino A, Decker CM, Depke M, Gesell Salazar M, Schmidt F, Simmons A, Huang WE. Single-Cell and Time-Resolved Profiling of Intracellular Salmonella Metabolism in Primary Human Cells. Anal Chem. 2019 Jun 18;91(12):7729-7737. doi: 10.1021/acs.analchem.9b01010. 
• Liang B, Gao Y, Xu J, Song Y, Xuan L, Shi T, Wang N, Hou Z, Zhao YL, Huang WE, Chen ZJ. Raman profiling of embryo culture medium to identify aneuploid and euploid embryos. Fertil Steril. 2019 Apr;111(4):753-762.e1. doi: 10.1016/j.fertnstert.2018.11.036. 
• Zhang S, Guo L, Yang K, Zhang Y, Ye C, Chen S, Yu X, Huang WE, Cui L. Induction of Escherichia coli Into a VBNC State by Continuous-Flow UVC and Subsequent Changes in Metabolic Activity at the Single-Cell Level. Front Microbiol. 2018;9:2243. doi: 10.3389/fmicb.2018.02243. 
• Xu J, Potter M, Tomas C, Elson JL, Morten KJ, Poulton J, Wang N, Jin H, Hou Z, Huang WE. A new approach to find biomarkers in chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) by single-cell Raman micro-spectroscopy. Analyst. 2019 Jan 28;144(3):913-920. doi: 10.1039/c8an01437j. 
• Jing X, Gou H, Gong Y, Su X, Xu, Ji Y, Song Y, Thompson IP, Xu J, Huang WE. Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean. Environ Microbiol. 2018 Jun;20(6):2241-2255. doi: 10.1111/1462-2920.14268. 
• Yuan X, Song Y, Song Y, Xu J, Wu Y, Glidle A, Cusack M, Ijaz UZ, Cooper JM, Huang WE, Yin H. Effect of Laser Irradiation on Cell Function and Its Implications in Raman Spectroscopy. Appl Environ Microbiol. 2018 Apr 15;84(8). doi: 10.1128/AEM.02508-17. 
• Xu J, Zhu D, Ibrahim AD, Allen CCR, Gibson CM, Fowler PW, Song Y, Huang WE. Raman Deuterium Isotope Probing Reveals Microbial Metabolism at the Single-Cell Level. Anal Chem. 2017 Dec 19;89(24):13305-13312. doi: 10.1021/acs.analchem.7b03461.
• Song Y, Cui L, López JÁS, Xu J, Zhu YG, Thompson IP, Huang WE. Raman-Deuterium Isotope Probing for in-situ identification of antimicrobial resistant bacteria in Thames River. Sci Rep. 2017 Nov 30;7(1):16648. doi: 10.1038/s41598-017-16898-x. 
• Cui L, Yang K, Zhou G, Huang WE, Zhu YG. Surface-Enhanced Raman Spectroscopy Combined with Stable Isotope Probing to Monitor Nitrogen Assimilation at Both Bulk and Single-Cell Level. Anal Chem. 2017 Jun 6;89(11):5793-5800. doi: 10.1021/acs.analchem.6b04913. 
• Xu J, Webb I, Poole P, Huang WE. Label-Free Discrimination of Rhizobial Bacteroids and Mutants by Single-Cell Raman Microspectroscopy. Anal Chem. 2017 Jun 20;89(12):6336-6340. doi: 10.1021/acs.analchem.7b01160. 
• Tao Y, Wang Y, Huang S, Zhu P, Huang WE, Ling J, Xu J. Metabolic-Activity-Based Assessment of Antimicrobial Effects by D₂O-Labeled Single-Cell Raman Microspectroscopy. Anal Chem. 2017 Apr 4;89(7):4108-4115. doi: 10.1021/acs.analchem.6b05051. 
• Song Y, Kaster AK, Vollmers J, Song Y, Davison PA, Frentrup M, Preston GM, Thompson IP, Murrell JC, Yin H, Hunter CN, Huang WE. Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea. Microb Biotechnol. 2017 Jan;10(1):125-137. doi: 10.1111/1751-7915.12420. 
• Teng L, Wang X, Wang X, Gou H, Ren L, Wang T, Wang Y, Ji Y, Huang WE, Xu J. Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome. Sci Rep. 2016 Oct 19;6:34359. doi: 10.1038/srep34359. 
• Wang Y, Song Y, Tao Y, Muhamadali H, Goodacre R, Zhou NY, Preston GM, Xu J, Huang WE. Reverse and Multiple Stable Isotope Probing to Study Bacterial Metabolism and Interactions at the Single Cell Level. Anal Chem. 2016 Oct 4;88(19):9443-9450. doi: 10.1021/acs.analchem.6b01602. 
• Wang Y, Huang WE, Cui L, Wagner M. Single cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol. 2016 Oct;41:34-42. doi: 10.1016/j.copbio.2016.04.018.
• Song Y, Yin H, Huang WE. Raman activated cell sorting. Curr Opin Chem Biol. 2016 Aug;33:1-8. doi: 10.1016/j.cbpa.2016.04.002. 
• Cui L, Zhang YJ, Huang WE, Zhang BF, Martin FL, Li JY, Zhang KS, Zhu YG. Surface-Enhanced Raman Spectroscopy for Identification of Heavy Metal Arsenic(V)-Mediated Enhancing Effect on Antibiotic Resistance. Anal Chem. 2016 Mar 15;88(6):3164-70. doi: 10.1021/acs.analchem.5b04490.
• McIlvenna D, Huang WE, Davison P, Glidle A, Cooper J, Yin H. Continuous cell sorting in a flow based on single cell resonance Raman spectra. Lab Chip. 2016 Apr 21;16(8):1420-9. doi: 10.1039/c6lc00251j.
• Zhang P, Ren L, Zhang X, Shan Y, Wang Y, Ji Y, Yin H, Huang WE, Xu J, Ma B. Raman-activated cell sorting based on dielectrophoretic single-cell trap and release. Anal Chem. 2015 Feb 17;87(4):2282-9. doi: 10.1021/ac503974e.
• Zhang D, Berry JP, Zhu D, Wang Y, Chen Y, Jiang B, Huang S, Langford H, Li G, Davison PA, Xu J, Aries E, Huang WE. Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community. ISME J. 2015 Mar;9(3):603-14. doi: 10.1038/ismej.2014.161. 
• Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, Palatinszky M, Schintlmeister A, Schmid MC, Hanson BT, Shterzer N, Mizrahi I, Rauch I, Decker T, Bocklitz T, Popp J, Gibson CM, Fowler PW, Huang WE, Wagner M. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):E194-203. doi: 10.1073/pnas.1420406112.
• Huang WE, Song Y, Xu J. Single cell biotechnology to shed a light on biological 'dark matter' in nature. Microb Biotechnol. 2015 Jan;8(1):15-6. doi: 10.1111/1751-7915.12249. 
• Wang T, Ji Y, Wang Y, Jia J, Li J, Huang S, Han D, Hu Q, Huang WE, Xu J. Quantitative dynamics of triacylglycerol accumulation in microalgae populations at single-cell resolution revealed by Raman microspectroscopy. Biotechnol Biofuels. 2014;7:58. doi: 10.1186/1754-6834-7-58. 
• Wang Y, Ji Y, Wharfe ES, Meadows RS, March P, Goodacre R, Xu J, Huang WE. Raman activated cell ejection for isolation of single cells. Anal Chem. 2013 Nov 19;85(22):10697-701. doi: 10.1021/ac403107p. 
• Li M, Huang WE, Gibson CM, Fowler PW, Jousset A. Stable isotope probing and Raman spectroscopy for monitoring carbon flow in a food chain and revealing metabolic pathway. Anal Chem. 2013 Feb 5;85(3):1642-9. doi: 10.1021/ac302910x.
• Li M, Xu J, Romero-Gonzalez M, Banwart SA, Huang WE. Single cell Raman spectroscopy for cell sorting and imaging. Curr Opin Biotechnol. 2012 Feb;23(1):56-63. doi: 10.1016/j.copbio.2011.11.019. 
• Li M, Canniffe DP, Jackson PJ, Davison PA, FitzGerald S, Dickman MJ, Burgess JG, Hunter CN, Huang WE. Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities. ISME J. 2012 Apr;6(4):875-85. doi: 10.1038/ismej.2011.150. 
• Li M, Ashok PC, Dholakia K, Huang WE. Raman-activated cell counting for profiling carbon dioxide fixing microorganisms. J Phys Chem A. 2012 Jun 28;116(25):6560-3. doi: 10.1021/jp212619n. 
• Huang WE, Li M, Jarvis RM, Goodacre R, Banwart SA. Shining light on the microbial world the application of Raman microspectroscopy. Adv Appl Microbiol. 2010;70:153-86. doi: 10.1016/S0065-2164(10)70005-8.
• Andrews JS, Rolfe SA, Huang WE, Scholes JD, Banwart SA. Biofilm formation in environmental bacteria is influenced by different macromolecules depending on genus and species. Environ Microbiol. 2010 Sep;12(9):2496-507. doi: 10.1111/j.1462-2920.2010.02223.x.
• Huang WE, Ward AD, Whiteley AS. Raman tweezers sorting of single microbial cells. Environ Microbiol Rep. 2009 Feb;1(1):44-9. doi: 10.1111/j.1758-2229.2008.00002.x. 
• Huang WE, Ferguson A, Singer AC, Lawson K, Thompson IP, Kalin RM, Larkin MJ, Bailey MJ, Whiteley AS. 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. Appl Environ Microbiol. 2009 Jan;75(1):234-41. doi: 10.1128/AEM.01861-08. 
• Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M. Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol. 2007 Aug;9(8):1878-89. doi: 10.1111/j.1462-2920.2007.01352.x.
• Huang WE, Griffiths RI, Thompson IP, Bailey MJ, Whiteley AS. Raman microscopic analysis of single microbial cells. Anal Chem. 2004 Aug 1;76(15):4452-8. doi: 10.1021/ac049753k. 

Others

• Timmis K, Huang WE, Timmis J. Strategies to minimize preventable morbidity and mortality resulting from pandemics like COVID-19. Environ Microbiol. 2020 Oct;22(10):4085-4092. doi: 10.1111/1462-2920.15217.
• Xu A., Wu Y., Chen Z., Wu G., Ling F., Huang W.E. Hu H.Y. (2020) Towards the new era of wastewater treatment of China: Development history, current status, and future directions. Water Cycle 1: 80-87.
• Blaud, A., Zaan, B., Menon, M., Lair, G.J. Zhang, D., Huber, P., Schiefer, J., Blum, W.E.H., Kitzler, B., Huang, W.E., van Gaans, P., Banwart, S. (2018) The abundance of nitrogen cycle genes and potential greenhouse gas fluxes depends on land use type and little on soil aggregate size. Applied Soil Ecology 125:1-11.
• Wu, Y., Shen, L., Hu, H., Hankins, N.P., Huang, W.E.* (2018) An efficient microalgal biomass harvesting method with a high concentration ratio using the polymer-surfactant aggregates process. Algal Research 30:86-93.
• Chao HJ, Chen YF, Fang T, Xu Y, Huang WE, Zhou NY. HipH Catalyzes the Hydroxylation of 4-Hydroxyisophthalate to Protocatechuate in 2,4-Xylenol Catabolism by Pseudomonas putida NCIMB 9866. Appl Environ Microbiol. 2016 Jan 15;82(2):724-31. doi: 10.1128/AEM.03105-15. 
• Meckenstock RU, Elsner M, Griebler C, Lueders T, Stumpp C, Aamand J, Agathos SN, Albrechtsen HJ, Bastiaens L, Bjerg PL, Boon N, Dejonghe W, Huang WE, Schmidt SI, Smolders E, Sørensen SR, Springael D, van Breukelen BM. Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers. Environ Sci Technol. 2015 Jun 16;49(12):7073-81. doi: 10.1021/acs.est.5b00715.
• Perron GG, Lee AE, Wang Y, Huang WE, Barraclough TG. Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations. Proc Biol Sci. 2012 Apr 22;279(1733):1477-84. doi: 10.1098/rspb.2011.1933. 
• Huang WE, Oswald SE, Lerner DN, Smith CC, Zheng C. Dissolved oxygen imaging in a porous medium to investigate biodegradation in a plume with limited electron acceptor supply. Environ Sci Technol. 2003 May 1;37(9):1905-11. doi: 10.1021/es020128b.
• Huang WE, Smith CC, Lerner DN, Thornton SF, Oram A. Physical modelling of solute transport in porous media: evaluation of an imaging technique using UV excited fluorescent dye. Water Res. 2002 Apr;36(7):1843-53. doi: 10.1016/s0043-1354(01)00393-1. 
• Li G, Huang W*, Lerner DN, & Zhang X (2000) Enrichment of degrading microbes and bioremediation of petrochemical contaminants in polluted soil. Water Research 34(15):3845-3853.

Book chapters (Selected)

• Wang, Y., Zhang, D., Davison, P.A. and Huang, W.E.* (2014) Bacterial whole cell biosensors for the detection of contaminants in water and soils. Methods in Molecular Biology – Environmental Microbiology 155-168.
• Li, M., Boardman, D.G., Ward, A. and Huang, W.E.* (2014) Single-cell Raman sorting. Methods in Molecular Biology – Environmental Microbiology 147-153.
• Wang, Y., Song, Y., Zhu, D., Ji, Y., Wang, Y., McIlvenna, D., Yin, H., Xu, J. and Huang W.E.* (2013) Probing and sorting single cells -the application of a Raman-activated cell sorter. Spectroscopy Europe 25: 16-20.
• Song, Y., Zhang, D., Polizzi, K., Zhang, G.E., Li G. and Huang, W.E.* (2012) Bacterial whole cell bioreporters in environmental health. Biosensors and Environmental Health, chapter 8:127-148.
• Read, D.S., Huang, W.E., Whiteley, A.S. (2010) Raman-FISH. Handbook of Hydrocarbon and Lipid Microbiology. 4:4027-4038, Timmis, KN. ed. Springer.

 Patents

• Developer of novel biosensors and gene trapping using Acinetobacter sp. ADP1 as a host, Patent No. WO2008/056144.
• Nucleic Acid Transfer Techniques, Patent number: GB2452543A.
• Biosensor and used thereof, Patent number: (2011) PCT/GB2011/052228, WO2012/066321A1.
• Construction and application for magnetic nanoparticles (MNPs) coating biosensor. (2010) ZL201010513790.5.
• Construction of Raman Flow Cytometry and application on cell/particles separation. (2010) WO2012/055304.
• Alkane production - Biodiesel Synthesis by Bacteria, WO2013/128184.
• Cell sorting WO 2017/144886.
• Biofilm transformation filed by Oxford University on 10/09/2019.
• Modified cell GB1915526.6, filed by Oxford University on 25/10/2019.
• Primers for detecting novel coronavirus SARCoV-2 and test kits, methods and applications Thereof, Chinese Patent Application No. CN202010232072.4, filed on 27th March 2020 (Oxford University Innovation project 17730).
• Switch design for stabilisation of LAMP reaction, Patent Application No. GB No. 2012480.6 (filing date 11 Aug 2020).