Publications

Dongming Xie Publications

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ORCID – Dongming Xie

 

Journal Publications (UMass Lowell, 2016~present)

  1. Abid U, Gibbons J, Qin J, Xie D (2025) Biorecycling of polyethylene (PE): an integrated effort in pretreatment, degradation, and upcycling. Frontiers in Bioengineering and Biotechnology Volume 13 – 2025 doi: https://doi.org/10.3389/fbioe.2025.1692651
  2. Kurt E, Qin J, Sa L, Anjo E, Xie D (2025) Enhancing Lipid Production in Yarrowia lipolytica Through Continuous Fermentation and Adaptive Laboratory Evolution in Bioreactors. Industrial Biotechnology 0(0):null doi: https://doi.org/10.1177/15509087251389709
  3. Qin J, Liu N, Abid U, Coleman SM, Wang Y, Fu Q, Yoon S, Alper HS, Xie D (2025) Metabolic Engineering of Yarrowia lipolytica for Conversion of Waste Cooking Oil into Omega-3 Eicosapentaenoic Acid. ACS Engineering Au 5: 128-139. doi: https://doi.org/10.1021/acsengineeringau.4c00053
  4. Ayafor C, Chang AC, Patel A, Abid U, Xie D, Sobkowicz MJ, Wong H-W (2025). In-Situ Product Removal for the Enzymatic Depolymerization of Poly(ethylene terephthalate) via a Membrane Reactor. ChemSusChem 18(3): e202400698 doi:https://doi.org/10.1002/cssc.202400698
  5. 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
  6. Coleman SM, Marx RJ, Martinez MK, Silvera AJ, Park J, Ramanan E, Kaown G, Yoon S, Xie D, Alper HS (2024) Considerations Regarding High Oil Density Bioreactor-Scale Fermentations of Yarrowia lipolytica Using CFD Modeling and Experimental Validation. Biotechnology Journal 19(12):e202400506 doi:https://doi.org/10.1002/biot.202400506
  7. Fu Q, Wang Y, Qin J, Xie D, McNally D, Yoon S (2024) Enhanced ER protein processing gene expression increases rAAV yield and full capsid ratio in HEK293 cells. Applied Microbiology and Biotechnology 108(1):459. http://doi.org/10.1007/s00253-024-13281-5
  8. Patel A, Chang AC, Abid U, Ayafor C, Wong H-W, Xie D, Sobkowicz MJ (2024) Enzymatic depolymerization of polyester: Foaming as a pretreatment to increase specific surface area. Journal of Applied Polymer Science 141(44):e56177 doi:https://doi.org/10.1002/app.56177
  9. 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 32: 3961–3972. doi: https://doi.org/10.1007/s10924-024-03223-7
  10. 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
  11. 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
  12. 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 Journal199:109074. doi: https://doi.org/10.1016/j.bej.2023.109074
  13. 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 Journal18: 2300119. doi: https://doi.org/10.1002/biot.202300119
  14. 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
  15. Soong YHV, 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. https://doi.org/10.1016/j.biotechadv.2023.108128
  16. 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
  17. 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
  18. 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
  19. 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.20210092
  20. 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
  21. 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
  22. 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.
  23. 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(4): 1658-1673. https://doi.org/10.1002/bit.27685.
  24. 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
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.

Journal Publications (Prior to UMass Lowell, 2000~2016)

  1. Xie D, Jackson EN, Zhu Q (2015) Sustainable source of omega-3 eicosapentaenoic acid from metabolically engineered Yarrowia lipolytica: from fundamental research to commercial production. Applied Microbiology and Biotechnology 99(4):1599-1610. doi: https://doi.org/10.1007/s00253-014-6318-y
  2. Xue Z, Sharpe PL, Hong S-P, 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 Biotechnology 31(8):734-740. doi: https://doi.org/10.1038/nbt.2622
  3. Xie D, Shao Z, Achkar J, Zha W, Frost JW, Zhao H (2006) Microbial synthesis of triacetic acid lactone. Biotechnology and Bioengineering 93(4):727-736. doi: https://doi.org/10.1002/bit.20759
  4. Li W, Xie D, Frost JW (2005) Benzene-Free Synthesis of Catechol:  Interfacing Microbial and Chemical Catalysis. Journal of the American Chemical Society 127(9):2874-2882. doi: https://doi.org/10.1021/ja045148n
  5. Zhang J, Liu D, Yang Y, Xie D, Sun Y, Yang H, Zhong X (2004) Comparisons of fermentation processes of amphotericin and nystatin and glycerol fermentation with Candida krusei by adding amphotericin fermentation. Modern Chemical Industry 现代化工 24(5): 27-30.
  6. Liu Y, Liu D, Su Q, Liu J, Xie D (2003) Effects of phosphorus and nitrogen limitations on continuous production of glycerol in a multistage cascade bioreactor by Candida krusei. Biochemical Engineering Journal 15(2):101-106. doi: https://doi.org/10.1016/S1369-703X(02)00191-2
  7. Zhang J, Guo S, Wang Y, Xie D, Liu D, Wang Z (2003) Effect of electrolytic systems on electrochemical hydrogenation of mesophase coal tar pitch. Fuel Processing Technology 80(1):81-90. doi: https://doi.org/10.1016/S0378-3820(02)00239-4
  8. Liu Y, Liu D, Su Q, Liu J, Xie D (2002) Critical influence of osmotic pressure on continuous production of glycerol by an osmophilic strain of Candida krusei in a multistage cascade bioreactor. Process Biochemistry 38(3):427-432. doi: https://doi.org/10.1016/S0032-9592(02)00149-8
  9. Liu Y, Liu D, Xie D (2002) Improvement of glycerol production by Candida krusei in batch and continuous cultures using corn steep liquor. Biotechnology Letters 24(19):1539-1542 doi: https://doi.org/10.1023/A:1020319103262
  10. Xie D-M, Liu D-H, Zhu H-L, Liu Y-Q, Zhang J-A (2002) Model-based optimization of temperature and feed control strategies for glycerol production by fed-batch culture of osmophilic yeast Candida krusei. Biochemical Engineering Journal 11(2):111-121 doi: https://doi.org/10.1016/S1369-703X(02)00015-3
  11. Zhang J, Zhang X, Xie D, Liu D, Li Z (2002) Effect of Technological Factors on Electrochemical Hydrogenation of Lignin. The Canadian Journal of Chemical Engineering 80(4):1-5. doi: https://doi.org/10.1002/cjce.5450800402
  12. Liu Y, Liu D, Xie D (2002) Improvement of glycerol production by Candida krusei in batch and continuous cultures using corn steep liquor. Biotechnology Letters 24(19): 1539-1542. doi: https://doi.org/10.1023/A:1016170600048
  13. Zhang J, Liu D, Xie D, Wang Y, Sun Y (2002) Production of glycerol by fermentation using osmophilic yeast Candida krusei with different starchy substrates. Enzyme and Microbial Technology 30(6):758-762. doi: https://doi.org/10.1016/S0141-0229(02)00054-6
  14. Xie D, Liu D, Zhu H, Zhang J (2022) Optimization of glycerol fed-batch fermentation in different reactor states. Applied Biochemistry and Biotechnology 101(2):131-151. Doi: https://10.1385/ABAB:101:2:131
  15. Zhang J, Wei X, Xie D, Sun Y, Liu D (2002) Effects of oscillatory temperature and sparging nitrogen gas or carbon dioxide during later stage on glycerol fermentation. Journal of Chemical Industry and Engineering(China) 化工学报 53(9): 980-983.
  16. Xu Y-Y, Liu D-H, Xie D-M (2002) Study on the effects of forced oscillating period on mass transfer characteristic in airlift loop reactor. Journal of Chemical Engineering of Chinese Universities 高校化学工程学报 16(1): 13-16.
  17. Xie D-M, Liu D-H, Zhang J-A (2001) Temperature optimization for glycerol production by batch fermentation with Candida krusei. Journal of Chemical Technology & Biotechnology 76(10): 1057-1069. doi: https://doi.org/10.1002/jctb.484
  18. Xie D, Liu D, Zhu H, Liu T (2001) Multi-pulse feed strategy for glycerol fed-batch fermentation. Applied Biochemistry and Biotechnology 95(2): 103-112. doi: https://doi.org/10.1385/ABAB:95:2:103
  19. Xie D, Liu D, Liu T (2001) Modeling of glycerol production by fermentation in different reactor states. Process Biochemistry 36(12): 1225-1232. doi: https://doi.org/10.1016/S0032-9592(01)00164-9
  20. Xie D, Liu D (2001) Glycerol production by fermentation with periodic oscillating airlift operation in Airlift Reversible Loop Reactor (ARLR). Chinese Journal of Applied and Environmental Biology 应用与环境生物学报 7 (1): 72-75.
  21. Xie D, Liu D, Zhang Y, Zhu B, Liu Y, Liu T (2001) Glycerol production by fermentation with temperature variation. Journal of Microbiology 微生物学杂志 21: 13-14.
  22. Xie D, Liu D, Zhang Y, Zhu B, Su Z (2000) Enhancement of fermentative glycerol yield with heat shock treatment. Chinese Journal of Biotechnology 生物工程学报 16(3): 383-386.
  23. Xie D, Zhang Y, Liu T, Liu D (2000) CO2 stripping and vacuum operation in the latter stage of glycerol production by fermentation. Engineering & Chemical Metallurgy (China) 化工冶金 21: 417-419.
  24. Xie D, Liu D, Liu T (2000) Optimal feed strategy for fed-batch glycerol fermentation determined by maximum principle. Journal of Chemical Industry and Engineering(China) 化工学报 51 (S1), 236-239.
  25. Xie D, Liu D, Liu T (2000) Macroscopic Kinetic Models of Glycerol Batch Fermentation with Osmotolerant Yeast. Journal of Chemical Industry and Engineering(China) 化工学报 51 (S1), 248-251.
  26. Zhu B-T, Liu D-H, Ren H-Y, Xie D-M, Liu T-Z (2000) Experiments on optimal conditions for 1,3-propanediol fermentation. Engineering & Chemical Metallurgy (China) 化工冶金21(8): 420-422.

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 D, Miller E, Tyreus B, Jackson EN, Zhu Q (2017) Sustainable Production of Omega-3 Eicosapentaenoic Acid by Fermentation of Metabolically Engineered Yarrowia lipolytica. In: C.K. Lau, P. (eds) Quality Living Through Chemurgy and Green Chemistry. Green Chemistry and Sustainable Technology, pp.17-33. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-53704-6_2
    3. Xie D (2012) Using an advanced microfermentor system for strain screening and fermentation optimization. In: Microbial Metabolic Engineering: Methods and Protocols (Ed. Cheng, Q.), vol 834. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-483-4_14

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.