Publications

Dongming Xie Publications

Google Scholar – Dongming Xie

Research Gate – Dongming Xie

ORCID – Dongming Xie

 

Selected peer-reviewed journal papers:

  1. Marx R, Liu H, Yoon S, Xie D (2024) CFD evaluation of hydrophobic feedstock bench-scale fermenters for efficient high agitation volumetric mass transfer. Biotechnology Journal 19(2):2300384 doi: https://doi.org/10.1002/biot.202300384
  2. Patel A, Chang AC, Abid U, Ayafor C, Wong H-W, Xie D, Sobkowicz MJ (2024) Effects of Copolymer Structure on Enzyme-Catalyzed Polyester Recycling. Journal of Polymers and the Environment. doi: https://doi.org/10.1007/s10924-024-03223-7
  3. Kurt E, Qin J, Williams A, Zhao Y, Xie D (2023) Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals. Bioengineering 10(12):1357. DOI: https://doi.org/10.3390/bioengineering10121357
  4. Qin J, Kurt E, LBassi T, Sa L, Xie D (2023) Biotechnological production of omega-3 fatty acids: current status and future perspectives. Frontiers in Microbiology 14: 1280296. doi: https://doi.org/10.3389/fmicb.2023.1280296
  5. Abid U, Sun G, Soong Y-HV, Williams A, Chang AC, Ayafor C, Patel A, Wong H-W, Sobkowicz MJ, Xie D (2023) Evaluation of enzymatic depolymerization of PET, PTT, and PBT polyesters. Biochemical Engineering Journal 199:109074 doi:https://doi.org/10.1016/j.bej.2023.109074
  6. Soong Y-HV, Abid U, Chang AC, Ayafor C, Patel A, Qin J, Xu J, Lawton C, Wong H-W, Sobkowicz MJ, Xie D (2023) Enzyme selection, optimization, and production toward biodegradation of post-consumer poly(ethylene terephthalate) at scale. Biotechnology Journal 18: e2300119 doi:https://doi.org/10.1002/biot.202300119
  7. Soong Y-HV, Coleman SM, Liu N, Qin J, Lawton C, Alper HS, Xie D (2023) Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica. Biotechnology Advances 65:108128 doi:https://doi.org/10.1016/j.biotechadv.2023.108128
  8. Patel A, Chang AC, Mastromonaco A, Acosta Diaz M, Perry S, Ferki O, Ayafor C, Abid U, Wong H-W, Xie D, Sobkowicz MJ (2023) Aqueous buffer solution-induced crystallization competes with enzymatic depolymerization of pre-treated post-consumer poly (ethylene terephthalate) waste. Polymer 285:126370. doi: https://doi.org/10.1016/j.polymer.2023.126370
  9. Zheng H, Xie W, Ryzhov IO, Xie D (2023) Policy Optimization in Bayesian Network Hybrid Models of Biomanufacturing Processes. Informs Journal of Computing. 35:66-82.  https://doi.org/10.1287/ijoc.2022.1232.
  10. Xie D (2022) Continuous biomanufacturing with microbes-upstream progresses and challenges. Current Opinion in Biotechnology 78: 102793. https://doi.org/10.1016/j.copbio.2022.102793
  11. Patel A, Chang AC, Perry S, Soong YHS, Ayafor C, Wong HW, Xie D,  Sobkowicz MJ (2022) Melt Processing Pretreatment Effects on Enzymatic Depolymerization of Poly(ethylene terephthalate).  ACS Sustainable Chemistry & Engineering 10: 13619-13628. https://doi.org/10.1021/acssuschemeng.2c03142 
  12. Chang AC, Patel A, Perry S, Soong YV, Ayafor C, Wong HW, Xie D, Sobkowicz MJ (2022) Understanding Consequences and Tradeoffs of Melt Processing as a Pretreatment for Enzymatic Depolymerization of Poly(ethylene terephthalate). Macromol Rapid Commun. 43: e2100929. https://doi.org/10.1002/marc.202100929.
  13. Cao M, Tran VG, Qin J, Olson A, Mishra S, Schultz J, Huang C, Xie D, Zhao H (2022) Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone. Biotechnology and Bioengineering 119: 2529- 2540. https://doi.org/10.1002/bit.28159.
  14. Soong Y-HV, Sobkowicz MJ, Xie D (2022) Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes. Bioengineering 9: 98. https://doi.org/10.3390/bioengineering9030098.
  15. Soong Y, Zhao L, Liu N, Yu P, Lopez C, Olson A, Wong H, Shao Z, Xie D (2021) Microbial Synthesis of Wax Esters. Metabolic Engineering 67:428-442. https://doi.org/10.1016/j.ymben.2021.08.002.
  16. Liu, N., Soong, Y.‐H.V., Mirzaee, I., Olsen, A., Yu, P., Wong, H.‐W. and Xie, D. (2021), Biomanufacturing of Value‐Added Products from Oils or Fats: A Case Study on Cellular and Fermentation Engineering of Yarrowia lipolytica. Biotechnology and Bioengineering 118: 1658-1673. https://doi.org/10.1002/bit.27685.
  17. Xie W, Wang B, Li C, Xie D, Auclair J (2021) Interpretable Biomanufacturing Process Risk and Sensitivity Analyses for Quality-by-Design and Stability Control. Naval Research Logistics 69: 461-483. https://doi.org/10.1002/nav.22019.
  18. Sha S, Handelman G, Liu N, Xie D, Yoon S (2020) At-line N-linked glycan profiling for monoclonal antibodies with advanced sample preparation and high-performance liquid chromatography. Journal of Bioscience and Bioengineering, 130 (3): 327-333. https://doi.org/10.1016/j.jbiosc.2020.04.009.
  19. Sun W, Vila-Santa A, Liu N, Prozorov T, D Xie, Mira NP, Z Shao (2020) Metabolic engineering of an acid-tolerant yeast strain Pichia kudriavzevii for itaconic acid production. Metabolic Engineering Communications. 10: e00124. https://doi.org/10.1016/j.mec.2020.e00124.
  20. Liu Na, Liu B, Wang G, Soong YH, Tao Y, Liu W, Xie D (2020) Lycopene Production from Glucose, Fatty acid and Waste Cooking Oil by Metabolically Engineered Escherichia coli. Biochemical Engineering Journal. 155: 107488. https://doi.org/10.1016/j.bej.2020.107488.
  21. Soong Y, Liu N, Yoon S, Lawton C, Xie D (2019) Cellular and Metabolic Engineering of Oleaginous Yeast Yarrowia lipolytica for Bioconversion of Hydrophobic Substrates into High-Value Products. Engineering in Life Science. 19: 423-443. https://doi.org/10.1002/elsc.201800147.
  22. Xie D, Soong Y-H, Liu N, Qin J, Chen S, Keats J, Mirzaee I, Lawton C (2018) A new biomanufacturing platform for bioconversion of plant oils into high-value products., Advances in Biochemistry and Biotechnology, 2018: ABIO-149. DOI: 10.29011/2574-7258. 000049.
  23. Xie D (2017) Integrating cellular and bioprocess engineering in the nonconventional yeast Yarrowia lipolytica for biodiesel production: A review. Frontiers in Bioengineering and Biotechnology. 5: 65. https://doi.org/10.3389/fbioe.2017.00065.
  24. Xie D, Miller E, Sharpe P, Jackson E, Zhu Q (2017) Omega-3 production by fermentation of Yarrowia lipolytica: From fed-batch to continuous. Biotechnology and Bioengineering. 114(4), 798-812. https://doi.org/10.1002/bit.26216.
  25. Xie D, Jackson E, Zhu Q (2015) Sustainable Source of Omega-3 Eicosapentaenoic acid from Metabolically Engineered Yarrowia lipolytica: From Fundamental Research to Commercial Production. Appl.  Microbiol. Biotechnol. 99: 1599-1610.
  26. Xue Z, Sharpe PL, Hong SP, Yadav NS, Xie D, Short DR, Damude HG, Rupert RA, Seip JE, Wang J, Pollak DW, Bostick MW, Bosak MD, Macool DJ, Hollerbach DH, Zhang H, Arcilla DM, Bledsoe SA, Croker K, McCord EF, Tyreus BD, Jackson EN, Zhu Q (2013) Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nature Biotech. 31: 734-740.
  27. Xie D, Shao Z, Achkar J, Zha W, Frost JW, Zhao H (2005) Microbial synthesis of triacetic acid lactone. Biotechnol.  Bioeng. 93(4): 727-736.
  28. Li W, Xie D, Frost JW (2005) Benzene-Free Synthesis of Catechol: Interfacing Microbial and Chemical Catalysis. J. Am. Chem. Soc. 127(9): 2874-2882.

 

Book Chapters:

  1. Liu, N., Soong, YH.V., Olson, A., Xie, D. (2022). Cellular Engineering of Yarrowia lipolytica for Biomanufacturing of High-Value Products from Oils and Fats. In: Darvishi Harzevili, F. (eds) Synthetic Biology of Yeasts. Springer, Cham. https://doi.org/10.1007/978-3-030-89680-5_3.
  2. Xie, Dongming; Miller, Edward; Tyreus, Bjorn; Jackson, Ethel N; Zhu, Quinn. Sustainable Production of Omega-3 Eicosapentaenoic Acid by Fermentation of Metabolically Engineered Yarrowia lipolytica. In book: Quality Living Through Chemurgy and Green Chemistry (Ed. Lau P.C.K.), pp.17-33. Springer, Berlin, 2017.
  3. Xie, Dongming. Using an advanced microfermentor system for strain screening and fermentation optimization. In: Methods in Molecular Biology (Ed. Cheng Q.), 834, pp217-231. (Microbial Metabolic Engineering), Humana Press, New York, 2012.

 

Patents

  1. Xie, D.; Soong Y.-H.; Liu, N.; Wong, H.-W. (2022) “MICROBIAL CONVERSION OF OILS AND FATS TO LIPID-DERIVED HIGH-VALUE PRODUCTS,” US Patent Application No. 17341767. 02/24/2022.
  2. EN Jackson, DR Short, D Xie, Z Xue, QQ Zhu (2012) Production of polyunsaturated fatty acids in oleaginous yeasts – US Patent 8,313,911.
  3.  QQ Zhu, X Fan, SP Hong, D Boughioukou, D Xie (2020) High level production of long-chain dicarboxylic acids with microbes. US Patent 10,626,424.
  4. QQ Zhu, SP Hong, D Xie, Z Xue, H Yoon, M Dauner (2015)  Down-regulation of a polynucleotide encoding a Sou2 sorbitol utilization protein to modify lipid production in microbial cells. US Patent 9,005,9403.