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Publications

2017

  • 58. Lidbury I1, Mausz M1, Scanlan DJ, Chen Y. (2017) Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the marine methylated amine degradation pathway.(1equal contribution). The ISME Journal, 11: 1592-1601.
  • 57. M Taubert, C Grob, AM Howat, OJ Burns, J Pratscher, N Jehmlich, M von Bergen, HH Richnow, Y Chen, JC Murrell (2017) Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment Environmental Microbiology, 19(6): 2246–2257. see highlight by L Stein.
  • 56. CY Li, XL Chen, D Zhang, P Wang, Q Sheng, M Peng, BB Xie, QL Qin, PY Li, XY Zhang, HN Su, XY Song, M Shi, BC Zhou, LY Xun, Y Chen, YZ Zhang (2017) Structural mechanisms for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide. Molecular Microbiology 103:992–1003.
  • 55. Jameson E, Taubert M, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. (2017) DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol. 1539:57-74.

2016

  • 54. Zhu Y, Ksibe AZ, Schäfer H, Blindauer CA, Bugg TDH, Chen Y*. (2016) O2-independent demethylation of trimethylamine N-oxide by Tdm of Methylocella silvestris. The FEBS Journal. 283: 3979–3993.
  • 53. Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y*. (2016) Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Microbial Geonmics, 2(9): doi:10.1099/mgen.0.000080
  • 52. Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y*, Schäfer H* (2016) A mechanism for bacterial transformations of DMS to DMSO: a missing link in the marine organic sulfur cycle. Environmental Microbiology18(8), 2754–2766. See highlight by P Carini.
  • 51. Jameson E1, Fu T1, Brown IR,Paszkiewicz K, Purdy KJ, Frank S*, Chen Y*. (2016) Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis. (1equal contribution). Environmental Microbiology, 18(9) 2886-2898.
  • 50. Sibastian M, Smith AF, Gonzalez JM, Fredricks HF, Van Mooy B, Koblizek M, Brandsma J, Koster G, Mestre M, Mostajir B, Pitta P, Postle AD, Sanchez P, Gasol JM, Scanlan DJ, Chen Y. (2016) Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency. The ISME Journal, 10: 968-978.
  • 49. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Chen, Y. Neufeld JD, and Murrell, J.C. (2016) Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. Methods Mol Biol. 2016;1399:235-55.
  • 48. D. Kumaresan, A.M. Hillebrand-Voiculescu, D. Wisher, J. Stephenson, Y. Chen, J.C. Murrell (2016) Microbial life in unusual cave ecosystems sustained by chemosynthetic primary production. In Microbial Life of Cave Systems, Ed. AS Engel P 215-230.
  • 47. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Chen, Y. and Murrell, J.C. (2016) Chapter: Generating enriched metagenomes from active microorganisms with DNA stable isotope probing. Hydrocarbon and Lipid Microbiology Protocols 163-180.

2015

  • 46. Lidbury, I., Kimberley, G., Scanlan, D.J., Murrell, J.C. Chen, Y. (2015) Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade. Environmental Microbiology, 17(12):5048–5062. See highlight by L Bodrossy.
  • 45. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow H.H., Jehmlich N., von Bergen M., Chen, Y. and Murrell, J.C. (2015)Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environmental Microbiology, 17(10):4007-4018.
  • 44. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Dixon, J.L., Chen, Y. and Murrell, J.C. (2015) XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environmental Microbiology, 17(10):3937-3948.
  • 43. Eyice, O., Namura, M., Chen, Y., Mead, A., Samavedam, S., Schäfer, H. (2015) SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment. The ISME Journal, 9(11): 2336–2348.
  • 42. Zhang, D., Berry, J., Zhu, D., Wang, Y., Chen, Y., Jiang, Bo., Huang, S., Langford, H., Li, G., Davision, P.A., Xu, J., Aries, E., Huang, W.E. (2015) Magnetic nanoparticle mediated isolation of functional bacteria in a complex microbial community. The ISME Journal,9 (3):603-614.
  • 41. Lidbury, I. Murrell, J.C., Chen, Y.* (2015) 'Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling', The ISME Journal, 9 (3):610-619. (*corresponding author).
  • 40. Wischer, D., Kumaresan, D., Johnston, A., Khawand M. EI., Stephenson, J., Hillebrand-Voiculescu, A.M., Chen, Y., Murrell, J.C. (2015) Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave. The ISME Journal, 9(1):195–206.

2014

2013

  • 36. Z Huang, F Ye, C Zhang, S Chen, Y Chen J Wu, M Togo, XH Xing (2013) Rational design of a tripartite fusion protein of heparinase I enables one-step affinity purification and real-time activity detection. J Biotech, 163:30¨C 37.
  • 35. S Chen, Z Huang, J Wu, Y Chen, F Ye, C Zhang, R Yatsunami, S Nakamura, X Xing (2013) Combination of site-directed mutagenesis and calcium ion addition for enhanced production of thermostable MBP-fused heparinase I in recombinant Escherichia coli. Appl. Microbiol. Biotechnol. 97(7):2907-16.

2012

  • 34. Y Wang, Y Chen, Q Zhou, S Huang, K Ning, J Xu, RM Kalin, S Rolfe, WE Huang (2012) A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS ONE, 7(10): e47530.

  • 33. Y. Chen* (2012) Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environmental Microbiology. 14(9)2308-2322. (*corresponding author).
  • 32. W-L Hung, W.G. Wade, Y. Chen, D.P. Kelly, A.P. Wood (2012) Design and evaluation of novel primers for the detection of genes encoding diverse enzymes of methylotrophy and autotrophy. Pol. J Microbiol. 61(1):11-22.

2011

  • 31. Chen, Y*. Patel, N.A., Crombie, A. Scrivens, J.H. & Murrell, J.C.* (2011) Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proceedings of the National Academy of Science, 108:17791-17796 (*corresponding author).
  • 30. Md.T Rahman, A Crombie, H Moussard, Y Chen and J C Murrell (2011) 'Acetate represses methane oxidation by Methylocella silvestris in a peat soil microcosm', Applied and Environmental Microbiology, 77:4234-4236.
  • 29. Y Chen*, D Kumaresan, JC Murrell (2011) Stable-isotope probing and its application in soil microbiology. Handbook of Soil Science (2nd Edition). Vol. I 28(3):30-38, Ed. PM Huang, Y Li and ME Sumner. Taylor & Francis Group. (*corresponding author).
  • 28. Md T Rahman, A Crombie, Y Chen, N Stralis-Pavese, L Bodrossy, N P McNamara, J C Murrell. (2011) The distribution and abundance of facultative methanotroph Methylocella. ISME J 5, 1061-1066.
  • 27. Y Chen, MG Dumont, JD Neufeld, JC Murrell (2011) 'Towards 'focused metagenomics': A case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics', in Handbook of Molecular Microbial Ecology, 491- 496, Editors: F J de Bruijn, John Wiley & Sons, Inc.
  • 26. A Cebron, B Louvel, P Faure, C France-Lanord, Y Chen, J C Murrell, C Leyval.(2011) Root exudates modify the diversity of active phenanthrene-degraders in an aged PAH-contaminated soil as revealed by stable isotope probing. Environmental Microbiology 13(3)722-736.
  • 25. Y Chen*, J C Murrell (2011) DNA-stable isotope probing. In Stable Isotope Probing and Related Technologies. 3-24. ((PDF Document)) Edited by JC Murrell & A Whiteley, ASM press (*corresponding author).

2010

  • 24. Y Chen*, JC Murrell. (2010) Methanotrophs in moss. Nature Geoscience ((PDF Document)) 3:(9)595-596. (*corresponding author).
  • 23. Y Chen, A Crombie, Md T Rahman, S N Dedysh, W Liesack, M B Stott, M Alam, A R Theisen, J C Murrell and P F Dunfield. (2010) Complete genome sequence of the aerobic methanotroph Methylocella silvestris BL2. Journal of Bacteriology, 192 (14)3840-3841.
  • 22. Y Chen, J Scanlan, L Song, A Crombie, Md T Rahman, H Schafer, J C Murrell (2010). Gamma-glutamylmethylamide is an essential intermediate for monomethylamine metabolism by Methylocella silvestris. Applied and Environmental Microbiology, 76:4530-4537.
  • 21. Y Chen, K L McAleer, J C Murrell. (2010) Monomethylamine as a nitrogen source for a non-methylotrophic bacterium Agrobacterium tumefaciens. Applied and Environmental Microbiology, 76:4012-4014.
  • 20. Y Chen, J C Murrell. (2010) When metagenomics meets stable isotope probing : recent progresses and future perspectives. Trends in Microbiology ((PDF Document)), 18 : 157-163.
  • 19. H Jiang, Y Chen, P Jiang, C Zhang, T J Smith, J C Murrell, X-H Xing. (2010) Methanotrophs: multifunctional bacteria with promising applications in environmental engineering. Biochemical Engineering Journal, 49: 277-288.
  • 18. Y Chen, J D Neufeld, M G. Dumont, M W. Friedrich, J. C Murrell (2010) Metagenomic analysis of isotopically enriched DNA. Methods Mol Biol. ((PDF Document)),668: 67-75.
  • 17. Y Chen, J. C Murrell (2010) Ecology of aerobic methanotrophs and their role in methane cycling. In Handbook of Hydrocarbon and Lipid Microbiology. 28: 3067-3076. Edited by KN Timmis. Springer.
  • 16. Y Chen, J Vohra and J. C Murrell (2010) Application of DNA Stable-isotope probing for bioremediation. Methods Mol Biol. 599:129-139.

2009

  • 15. B Han, Y Chen, G Abell, H Jiang, L Bodrossy, J Zhao, J. C Murrell, X-H Xing. (2009) Molecular ecology study of methanotroph community of an alkaline coal mine soil. FEMS Microbiology Ecology, 70: 196-207.
  • 14. Y Chen, L Wu, R Boden, A Hillebrand, D Kumaresan, H Moussard, M Baciu, Y Lu, J C Murrell (2009) Life without light: Microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. The ISME Journal, 3 (9): 1093-1104.
  • 13. F Ye, Y Kuang, S Chen, C Zhang, Y Chen, X-H Xing (2009) Characteristics of low molecular weight heparin production by an ultrafiltration membrane bioreactor using maltose binding protein fused heparinase I. Biochemical Engineering Journal, 46:193-198.
  • 12. B Han, T Su, H Wu, Z Gou, X-H Xing, H Jiang, Y Chen, X Li, J C Murrell. (2009) Paraffin oil as a methane vector for rapid and high cell density cultivation of Methylosinus trichosporium OB3b. Applied Microbiology Biotechnology, 83: 669-677.

2008

  • 11. Y Chen, M G. Dumont, J D. Neufeld, L Bodrossy, N Stralis-Pavese, N P. McNamara, N Ostle, M J.I. Briones, and J. C Murrell (2008) Revealing the uncultivated majority: Combining stable isotope probing, multiple displacement amplification and metagenomic analysis of uncultivated Methylocystis in acidic peatlands. Environmental Microbiology, 10 (10): 2609-2622.
  • 10. Y Chen, M G. Dumont, N P. McNamara, P M. Chamberlain, L Bodrossy, N Stralis-Pavese, J. C Murrell. (2008). Diversity of active methanotrophic community in acidic peatland as assessed by mRNA and SIP-PLFA analyses. Environmental Microbiology, 10 (2): 446- 459.
  • 9. Y Chen, N P. McNamara, M G. Dumont, L Bodrossy, N Stralis-Pavese, J. C Murrell. (2008) The impact of Calluna burning and removal on methanotrophs diversity and activity. Applied Soil Ecology, 40 (2): 291-298.
  • 8. J D. Neufeld, Y Chen, M G. Dumont, J. C Murrell. (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environmental Microbiology, 10 (6): 1526- 1535.
  • 7. I R. McDonald, L Bodrossy, Y Chen, J. C Murrell. (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Applied and Environmental Microbiology, 74 (5): 1305-1315.

Pre 2007

  • 6. Y Chen, M G. Dumont, A Cebron, J. C Murrell. (2007) Detection of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environmental Microbiology, 9 (11): 2855- 2869.
  • 5. Y Chen, X-H Xing, F Ye, Y Kuang, M Luo. (2007) Production of MBP-HepA fusion protein in recombinant Escherichia coli by optimization of culture medium. Biochemical Engineering Journal, 34: 114-121.
  • 4. A Cebron, L Bodrossy, Y Chen, A C. Singer, I P. Thompson, J I. Prosser, J. C Murrell. (2007) Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiology Ecology, 62: 12-23.
  • 3. Y Chen, X-H Xing, F Ye, Y Kuang. (2007) Soluble expression and rapid quantification of GFP-hepA fusion protein in recombinant Escherichia coli. Chinese Journal of Chemical Engineering. 15(1): 122-126.
  • 2. Y Kuang, X-H Xing, Y Chen, F Ye, Y Chen, Y Yan, Z Liu, R Bi. (2006) Production of heparin oligosaccharides by fusion protein of MBP-Heparinase I and the enzyme thermostability. Journal of Molecular Catalysis B: Enzymatic. 43: 90-95.
  • 1. Y Chen, X-H Xing, K Lou. (2005) Construction of recombinant E. coli for over-production of soluble heparinase I by fusion to maltose-binding protein. Biochemical Engineering Journal. 23: 155-159.