PUBLICATIONS

-Theses

Xu P. (2013) Synthetic Pathway Design, Construction and Optimization: Towards Tailor-made Cell Factories for Flavonoids and Fatty Acids Production in E. coli. Rensselaer Polytechnic Institute, Troy, NY, USA. PhD dissertation.

Refereed papers in professional journals

-Published papers (*corresponding authors) 

Total citations: 5467, H-index: 39.ORCID: 0000-0002-0999-8546; Web of Science Research ID: C-6440-2011

1.     Azi F, Hong Y, Wu Z, Xu P*. (2023) Synthetic consortium of Ganoderma lucidum and Lactobacillus plantarum for enhanced natural products biosynthesis. Biochemical Engineering Journal. 108950.

2.     Zhu J, Gu Y, Yan Y, Ma J and Xu P*. (2023) Knocking out central metabolism genes to identify new targets and alternating substrates to improve lipid synthesis in Y. lipolytica. Frontiers in Bioengineering and Biotechnology. 11: 1098116.

3.     Marsafari M, Azi F, Dou S and Xu P*. (2022) Modular Co-Culture Engineering of Yarrowia Lipolytica for Amorphadiene Biosynthesis. Microbial Cell factories 21, 279.

4.     J. Ma, Y. Gu, Xu P*. (2022) Biosynthesis of cannabinoid precursor olivetolic acid in genetically engineered Yarrowia lipolytica. Communications Biology 5 (1), 1-7.

5.     Zeng Y, Hong Y, et al, and Xu P*. (2022) Advanced genome-editing technologies enable rapid and large-scale generation of genetic variants for strain engineering and synthetic biology. Current Opinion in Microbiology 69, 102175. 

6.     Liu H, Jin Y, Zhang R, Ning Y, Yu Y, Xu P*, Deng L. (2022) Recent advances and perspectives on production of value-added organic acids through metabolic engineering. Biotechnology Advances, 108076.

7.     Liu Y and Xu P*. (2022) Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia. Current opinion in Biotechnology. 76, 102754. 

8.     Xu P* and Zhou K. (2022) Editorial overview: Analytical biotechnology for healthcare, strain engineering, biosensing and synthetic biology. Current Opinion in Biotechnology 77, 102765-102765. 

9.     F Azi, Z Li, Xu P*, M Dong. (2022) Transcriptomic analysis reveals the antibacterial mechanism of phenolic compounds from kefir fermented soy whey against Escherichia coli 0157: H7 and Listeria monocytogenes. International Journal of Food Microbiology 383, 109953. 

10.  Qiu X, Gu Y, Du G, Zhang J, Xu P* and Li J. (2021) Conferring thermotolerant phenotype to wild type Yarrowia lipolytica improves cell growth and erythritol production. Biotechnology & Bioengineering. 118 (8), 3117-3127.

11.  Peng Z, Xu P, Song Y, Du G, Zhang J and Chen J. (2021) Cysteine-Mediated Cyclic Metabolism Drives the Microbial Degradation of Keratin. ACS Sustainable Chemistry & Engineering, 9 (29), 9861-9870

12.  Gu Y and Xu P*. (2021) Synthetic yeast brews neuroactive compounds. Nature Chemical Biology.17, 8-9. 

13.  Xu P*. (2021) Dynamics of microbial competition, commensalism and cooperation and its implications for coculture and microbiome engineering. Biotechnology and Bioengineering. 118 (1), 199-209. 

14.  Stephanopoulos G et al. Optimizing Oil Production in Oleaginous Yeast by Cell-Wide Measurements and Genome-Based Models. DOE-MIT-0008744. Report.

15.  Xu P*. (2021) In memory of Prof. Daniel I.C. Wang: Engineering Yarrowia lipolytica for the production of plant-based lipids: technical constraints and perspectives for a sustainable cellular agriculture economy. Synthetic Biology Journal 2 (4), 509-527

16.  Tong Y, Zhou J, Zhang L and Xu P*. (2021) A Golden-Gate based cloning toolkit to build violacein pathway libraries in Yarrowia lipolytica. ACS Synthetic Biology, 10(1), 115-124.

17.  Ma J, Gu Y and Xu P*. (2020) A roadmap to engineering antiviral natural products synthesis in microbes. Current opinion in Biotechnology. 66, 140-149.

18.  Edwards H and Xu P* (2020). Unstructured kinetic models to simulate an arabinose switch that decouples cell growth from metabolite production. Synthetic & Systems Biotechnology, 5(3): 222-229. 

19.  Ma J, Gu Y and Xu P*. (2020) Synthetic biology, systems biology and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform. Journal of Industrial Microbiology & Biotechnology. 47(9), 845-862. 

20.  Edwards H, Yang Z, and Xu P* (2020). Characterization of Met25 as a Color Associated Genetic Marker in Yarrowia lipolytica. Metabolic Engineering Communications.11: e00147.

21.  Liu H, Wang F, Deng L and Xu P*. (2020). Genetic and bioprocess engineering to improve squalene production in Yarrowia lipolytica. Bioresource Technology. 317:123991. 

22.  Gu Y, Ma J, Lv Y, Zhu Y, Ding X and Xu P*. (2020) Engineering Yarrowia lipolytica as a chassis for de novo synthesis of five aromatic-derived natural products and chemicals. ACS Synthetic Biology. 9 (8), 2096–2106. 

23.  Lv Y, Gu Y, Xu J, Zhou J and Xu P*. (2020) Coupling metabolic addiction with negative autoregulation to improve strain stability and pathway yield. Metabolic Engineering. 61, 79-88. 

24.  Xu P*, Masarfari M, Zha J and Koffas MA*. (2020) Microbial co-cultures for flavonoid synthesis. Trends in Biotechnology. 38 (7), 686-688. 

25.  Gu Y, Ma J, Zhu Y, Liu L and Xu P* (2020). Refactoring Ehrlich pathway for high-yield 2-phenylethanol production in Yarrowia lipolytica. ACS Synthetic Biology. 9(3), 623-633. IF = 5.6 (cited by 12 times)

26.  Qiu X, Xu P, Zhang J, and Li J (2020). Combining genetically-encoded biosensors with high throughput automatic strain screening to maximize erythritol production in Yarrowia lipolytica. Metabolic Engineering. 60, 66-76. IF = 7.3

27.  Xu P* (2020). Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch. Metabolic Engineering Communications. 10, e00127.

28.  Marsafari M and Xu P*. (2020). Debottlenecking mevalonate pathway for antimalarial drug precursor amorphadiene biosynthesis in Yarrowia lipolytica. Metabolic Engineering Communications. 10, e00112. 

29.  Tong Y, Zhou J, Zhang L and Xu P* (2020) Engineering oleaginous yeast Yarrowia lipolytica for violacein production: extraction, quantitative measurement and culture optimization. BioRxiv. 10.1101/687012.

30.  Marsafari M, Samizadeh H, Rabiei B, Mehrabi A, Koffas* M and Xu P*. (2020). Biotechnological production of flavonoids: an update on plant metabolic engineering, microbial host and genetically encoded biosensors. Biotechnology Journal. 15(8): 1900432. IF = 4.1

31.  Liu Y, Li J, Ledesma-Amaro R, Xu P, Du G and Liu L*. (2020) Towards next generation model microorganism chassis for biomanufacturing. Applied Microbiology and Biotechnology. 104, 9095–9108. IF = 3.9

32.  Marsafari M, Ma J, Koffas M and Xu P*. (2020) Genetically encoded biosensors for analyzing and controlling cellular process in yeast. Current Opinion in Biotechnology. 64, 175-182. IF = 8.3

33.  Yang Z, Edwards H and Xu P* (2020). CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing in Yarrowia lipolytica. Metabolic Engineering Communications. 10: e00112. (cited by 30 times)

34.  Xu P* (2020). Analytical solution for a hybrid Logistic-Monod cell growth model in batch and CSTR culture. Biotechnology and Bioengineering. 117(3): 873-878. IF = 4.0. “Highlights from Biotechnology and Bioengineering”, 2020, https://onlinelibrary.wiley.com/doi/toc/10.1002/(ISSN)1097-0290.

35.  Gao C, Xu P, Ye C, Chen X and Liu L. (2019) Genetic Circuit-Assisted Smart Microbial Engineering. Trends in Microbiology. 27(12): 1011-1024. IF = 13.6

36.  Gao C, Hou J, Xu P, Guo L, Chen X, Hu G, Ye C, Edwards H, Chen J, Chen W and Liu L. (2019). Programmable biomolecular switches for rewiring flux in Escherichia coli. Nature Communications, 10:3751. IF = 12.1 (cited by 20 times)

37.  Liu H, Marsafari M, Wang F, L Deng L and Xu P* (2019). Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica. Metabolic Engineering, 56: 60-68. IF = 7.3 (cited by 32 times)

38.  Lv Y, Marsafari M, Koffas M, Zhou J and Xu P* (2019). Optimizing oleaginous yeast cell factories for flavonoids and hydroxylated flavonoids biosynthesis. ACS Synthetic Biology, 8(11), 2514-2523. IF = 5.6 (cited by 40 times)

39.  Wan X, Marsafari M and Xu P*. (2019) Engineering metabolite-responsive transcriptional factors to sense small molecules in eukaryotes: current state and perspectives. Microbial Cell Factories. 18 (1), 61. IF = 4.2 (cited by 29 times)

40.  Lv Y, Edwards H, Zhou J and Xu P*. (2019) Combining 26s rDNA and the Cre-loxP system for iterative gene integration and efficient marker curation in Yarrowia lipolytica. ACS Synthetic Biology. 8(3):568-576. IF = 5.6 (cited by 34 times)

41.  Liu H, Marsafari M, Deng L and Xu P*. (2019) Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica. Applied Microbiology and Biotechnology. 103(7):3167–3179. IF = 3.9

42.  Lv Y, Qian S, Zhou J, Chen J and Xu P* (2019) Coupling feedback genetic circuits with growth phenotype for dynamic population control and intelligent bioproduction. Metabolic Engineering, 54:109-116. IF = 7.3 (cited by 49 times)

43.  Aris H, Borhani S, Cahn D, O’Donnell C, Tan E and Xu P*. (2019) Modeling transcriptional factor cross-talk to understand parabolic kinetics, bimodal gene expression and hysteresis behavior in biosensor design. Biochemical Engineering Journal, 144: 209-216. IF = 3.5

44.  Gao C, Wang S, Hu GP, Guo L, Chen X, Xu P and Liu L*. (2018) Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi-guided multiplexed metabolic tuning. Biotechnology and Bioengineering. 115 (3), 661-672. IF = 4.0 (cited by 40 times)

45.  Hu G, Zhou J, Chen X, Qian Y, Gao C, Guo L, Xu P, Chen W, Chen J, Li Y, Liu L. (2018) Engineering synergetic CO₂-fixing pathways for malate production. Metabolic engineering 47, 496-504. IF = 7.3

46.  Xu P*.  (2018) Production of chemicals using dynamic control of metabolic fluxes. Current Opinion in Biotechnology, 53, 12-19. IF = 8.3 (cited by 77 times)

47.  Jin EQ, Engel J and Xu P*. (2018) Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression. Synthetic and Systems Biotechnology. 2(4), 295-301.

48.  Johnson AO, Gonzalez-Villanueva M, Wong L, Steinbüchel A, Tee KL, Xu P*, Wong TS*. (2017) Design and application of genetically-encoded malonyl-CoA biosensors for metabolic engineering of microbial cell factories, Metabolic Engineering, 44:253-264. IF = 7.3 (cited by 56 times)

49.  Wong L. Engel J, Jin EQ, Holdridge B and Xu P*. (2017) YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica. Metabolic Engineering Communications, 5: 68-77. IF = 7.3. (Cited by 60 times)

50.  Xu P, Qiao K and Stephanopoulos G*. (2017). Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica. Biotechnology and Bioengineering, 114(7): 1521–1530. IF = 4.0 (Cited by 102 times). 

51.  Qiao K, Wasylenko T, Zhou K, Xu P and Stephanopoulos G*. (2017). Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism. Nature Biotechnology, 35, 173–177. IF = 36.6 (Cited by 220 times). “A step toward renewable diesel”, reported by MIT news. http://news.mit.edu/2017/yeast-convert-plant-sugars-oils-renewable-diesel-0116 

52.  Xu P, Rizzoni EA, Sul SY and Stephanopoulos G*. (2016) Improving metabolic pathway efficiency by statistical model based multivariate regulatory metabolic engineering. ACS Synthetic Biology, 6 (1), 148–158. IF = 5.6 (Cited by 75 times).

53.  Xu P, Qiao K, Ahn WK and Stephanopoulos G*. (2016) Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals. Proceedings of the National Academy of Sciences, U.S.A., 113(39): 10848–53. IF = 9.4 (Cited by 238 times). “Yeast makes diesel-like fuels”, featured by Nature Publishing Group, http://www.nature.com/nature/journal/v537/n7621/full/537452e.html. Oleaginous Yeasts Move One Step Closer to Becoming Industrial Biodiesel Producers” reported by U.S. Department of Energy Office of Biological and Environmental Research, https://public.ornl.gov/site/bernews/search_news_action.cfm?id=1689&webid 

54.  Silverman, A, Qiao K, Xu P and Stephanopoulos G*. (2015) Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica. Applied Microbiology and Biotechnology. 100(8):3781-98. IF = 3.9 (Cited by 53 times).

55.  Lim CG, Wong L, Bhan N, Dvora H, Xu P, Koffas M*. (2015) Development of a recombinant Escherichia coli strain for overproduction of the plant pigment anthocyanin. Applied and Environmental Microbiology. 81(18):6276-84. IF = 3.9 (Cited by 57 times).

56.  Trantas EA, Koffas MA, Xu P and Ververidis F*. (2015) Biotechnology of flavonoids: Metabolic engineering with commercial applications when plants produce not enough or at all. Frontiers in Plant Science, 6:7. IF = 4.4 (Cited by 77 times).

57.  Bhan N, Li L, Cai C, Xu P, Linhardt R and Koffas M*. (2015) Enzymatic formation of a resorcylic acid by creating a structure-guided single-point mutation in stilbene synthase. Protein Science, 24: 167-173. IF = 3.9.

58.  Xu P, Li L, Zhang F, Stephanopoulos GN and Koffas MA*. (2014) Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proceedings of the National Academy of Sciences, U.S.A., 111(31):11299-304. IF = 9.4 (Cited by 370 times). “Rensselaer Polytechnic Institute Researchers Develop New Method of Fatty Acid Production Via Dynamic Regulation”, reported by RPI news. https://news.rpi.edu/content/2014/07/22/researchers-develop-new-method-fatty-acid-production 

59.  Xu P, Wang W, Li L, Bhan N, Zhang F and Koffas MA*. (2014) Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in E. coli. ACS Chemical Biology, 9(2): 451-458. IF = 4.4. (Cited by 110 times).

60.  Xu P, Bhan N and Koffas MA*. (2013) Engineering plant metabolism into microbes: from systems biology to synthetic biology. Current Opinion in Biotechnology. 24(2): 291-299. IF = 8.3 (Cited by 117 times).

61.  Bhan N, Xu P and Koffas MA*. (2013) Pathway and protein engineering approaches to produce novel and commodity small molecules. Current Opinion in Biotechnology, 24(6): 1137-1143. IF = 8.3 (Cited by 58 times).

62.  Wang W, Englaender J, Xu P, Linhardt RJ, Koffas MA*. (2013) Expression of low endotoxin 3-O-sulfotransferase in B. subtilis and B. megaterium. Applied Biochemistry and Biotechnology, 171(4): 954-962. IF = 1.6.

63.  Xu P, Gu Q; Wang W, Wong L, Bower A, Collins CH and Koffas MA*. (2013) Modular optimization of multi-gene pathway for fatty acids production in E. coli. Nature Communications, 4: 1409. IF = 12.4 (Cited by 386 times).

64.  Bhan N, Xu P, Khalidi O and Koffas MA*. (2013) Redirecting carbon flux into Malonyl-CoA to improve Resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework. Chemical Engineering Science, 103: 109-114. IF = 3.9 (Cited by 50 times).

65.  Xu P, Vansiri A, Bhan N and Koffas MA*. (2012) ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synthetic Biology, 1(7):256–266. IF = 5.6 (Cited by 215 times).

66.  Xu P, Ranganathan S, Fowler Z, Maranas CD and Koffas MA*. (2011) Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metabolic Engineering, 13(5): 578-587. IF = 7.3 (Cited by 275 times).

67.  Zhang L, Ding Z, Xu P et al. (2011) Methyl lucidenate F isolated from the ethanol-soluble-acidic components of G. lucidum is a novel tyrosinase inhibitor. Biotechnology and Bioprocess Engineering, 16(3): 457-461. IF = 2.2.

68.  Xu P and Koffas MA*. (2010) Metabolic engineering of E. coli for biofuel production, Biofuels, 1(3): 493-504. (Cited by 30 times).

69.  Zhang T, Xu P et al. (2009) Identification of biological wort turbidity caused by microbial contamination of Gairdner barley. Journal of the American Society of Brewing Chemists, 67(1): 33-37. IF = 1.2

70.  Xu P, Ding Z, Qian Z, Zhang K and Zhao C. (2008) Improved production of mycelial biomass and ganoderic acid by submerged culture of G. lucidum SB97 using complex media. Enzyme and Microbial Technology, 42(4): 325-331. IF = 2.9 (Cited by 95 times).

71.  Xu P, Qian Z, Zhao CX. (2008) Kinetic analysis of exo-polysaccharide and ganoderic acid production by submerged culture of Ganoderma lucidum. Chinese Journal of Applied & Environmental Biology, 14(4): 562-565.

72.  There are other more than 20 research articles published in Chinese journals from 2004 to 2009.

Accepted or in press papers

-Submitted papers 

73.  Ma J, Gu Y and Xu P*. (2022) Biosynthesis of cannabinoid precursor olivetolic acid by overcoming rate-limiting steps in genetically engineered Yarrowia lipolytica. Under review by Communications Biology.

74.  Marsafari M, Azi F and Xu P*. (2022) Modular Co-Culture Engineering of Yarrowia Lipolytica for Amorphadiene Biosynthesis. Under review by Microbial cell factory

75.  Xu P*. (2020) Applying chemical reaction transition theory to predict the latent transmission dynamics of coronavirus outbreak in China. MedRxiv, Under review. 

-Review papers

76.  Tang L, Xu P* and Zhang H. (2020) Editorial overview: tissue, cell and pathway engineering: programming biology for smart therapeutics, microbial cell factory and intelligent biomanufacturing. Current opinion in Biotechnology. 66, iii-vi. 

77.  Xu P* and Zhou K. (2022) Editorial overview: Analytical biotechnology for healthcare, strain engineering, biosensing and synthetic biology. Current opinion in Biotechnology. 76, Article 102765.

-Books 

78.  Analytical Biotechnology, Volume 76, Current Opinion in Biotechnology, Guest editor by Kang Zhou and Peng Xu. Published by Elsevier, 2022. IF = 10.3 Book link

79.  Tissue, Cell and Pathway Engineering, Volume 66, Current Opinion in Biotechnology, Guest editor by Li Tang, Peng Xu and Haoran Zhang. Published by Elsevier, 2020. IF = 10.3 Book link

-Chapters in books 

80.  Yang Z and Xu P*. (2021) Implementing CRISPR-Cas12a for Efficient Genome Editing in Yarrowia lipolytica. Methods in Molecular Biology, Ian Wheeldon and Mark Blenner (Eds): Yarrowia lipolytica. Chapter 7. IF = 

81.  Sun W, Yang Z and Xu P*. (2021) Engineering Yarrowia lipolytica for Production of Fatty Alcohols with YaliBrick Vectors. Methods in Molecular Biology. Ian Wheeldon and Mark Blenner (Eds): Yarrowia lipolytica. Chapter 11.

82.  Wong L, Holdridge B, Engel J and Xu P*. (2018) Genetic tools for streamlined and accelerated pathway engineering in Yarrowia lipolytica. Methods in Molecular Biology: Microbial Metabolic Engineering, 155-177.

83.  Xu P and Koffas MA. (2013) Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors. Methods in Molecular Biology: Synthetic Biology. 1073:107-29.

Refereed papers in conference proceedings

84.  Xu P, Ranganathan S, Maranas C and Koffas M. (2011) An integrated computational and experimental study to increase the intracellular malonyl-CoA: application to flavanone synthesis. IEEE. 2011 IEEE 37th Annual Northeast Bioengineering Conference (NEBEC).

Patents granted or submitted

1.     Xu J, Xu P and Lv Y. A molecular device to switch carbon flux and engineer naringenin addiction phenotype. China Patent grant No.: ZL 2019 1 1240 118.0

2.     Stephanopoulos G. Qiao K, and Xu P. Strain and bioprocess engineering for high-lipid production. U.S. Patent Application No.: 15/296,148; WO2017070065A1

Research reports and other publications 

-List of selected publications

1.     Lv Y, Gu Y, Xu J, Zhou J and Xu P*. (2020) Coupling metabolic addiction with negative autoregulation to improve strain stability and pathway yield. Metabolic Engineering. 61, 79-88. This article reports the engineering of feedback control system in yeast to improve strain stability. Dr. Xu is the leading PI.

2.     Gu Y, Ma J, Lv Y, Zhu Y, Ding X and Xu P*. (2020) Engineering Yarrowia lipolytica as a chassis for de novo synthesis of five aromatic-derived natural products and chemicals. ACS Synthetic Biology. 9 (8), 2096–2106. This article reported the engineering of Y. lipolytica to produce five high-value aromatic compounds. 

3.     Xu P* (2020). Analytical solution for a hybrid Logistic-Monod cell growth model in batch and CSTR culture. Biotechnology and Bioengineering. 117(3): 873-878. This article reported a new model and analytical solution to describe cell growth. 

4.     Liu H, Marsafari M, Wang F, L Deng L and Xu P* (2019). Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica. Metabolic Engineering, 56: 60-68. This paper reported the upgrading of low-cost acetic acids to high-value polyketides with genetically-engineered yeast. 

5.     Xu P, Qiao K, Ahn WK and Stephanopoulos G*. (2016) Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals. Proceedings of the National Academy of Sciences, U.S.A., 113(39): 10848–53. Dr. Xu is the first author and major contributor for this article.