Qingyun Dan Lab | Johns Hopkins University

Publications/Patents

Independent work:

Coming soon!

Before joining JHU:

Selected publications: († co-first authorship; * corresponding authorship)

  1. Kevin Yin, Alexander Landera, Namil Lee, Anthony T Iavarone, Suzanne M Kosina, Thomas D Young, Kai Deng, Justin Baerwald, Yan Chen, Jennifer W Gin, Riley Benedict, Yan Chiu, Ezechinyere Ukabiala, Methun Kamruzzaman, Kunal Poorey, Trent R Northen, Christopher J Petzold, Anthe George, Pablo Cruz-Morales, Qingyun Dan*, & Jay D Keasling* (2026). Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules. Nature Communications (Accepted). [Link]
  2. Qingyun Dan, Yan Chiu, Namil Lee, Jose Henrique Pereira, Behzad Rad, Xixi Zhao, Kai Deng, Yiou Rong, Chunjun Zhan, Yan Chen, Seokjung Cheong, Chenyi Li, Jennifer W Gin, Andria Rodrigues, Trent R Northen, Tyler WH Backman, Edward EK Baidoo, Christopher J Petzold, Paul D Adams, Jay D Keasling* (2025). A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids. Nature Catalysis, 8(2), 147-161. Featured in UCB news. [Link]
  3. Qingyun Dan†, Sean A Newmister†, Kimberly R Klas, Amy E Fraley, Timothy J McAfoos, Amber D Somoza, James D Sunderhaus, Ying Ye, Vikram V Shende, Fengan Yu, Jacob N Sanders, W Clay Brown, Le Zhao, Robert S Paton, KN Houk, Janet L Smith, David H Sherman*, Robert M Williams* (2019). Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels–Alderase. Nature Chemistry, 11(11), 972-980. Cover article; Evaluated by F1000. [Link]

Other publications:

  1. Chunjun Zhan†, Guangxu Lan†, Qingyun Dan, Ning Qin, Allie Pearson, Peter Mellinger, Yuzhong Liu, Zilong Wang, Seokjung Cheong, Chang Dou, Chenyi Li, Robert W Haushalter*, Jay D Keasling* (2025). Hybrid biological-chemical strategy for converting polyethylene into a recyclable plastic monomer using engineered Corynebacterium glutamicum. Metabolic Engineering, 90, 106-116.
  2. Namil Lee, Woori Kim, Ji Hun Kim, Yongjae Lee, Soonkyu Hwang, Gahyeon Kim, Hyeseong Kim, Qingyun Dan, Matthias Schmidt, Yeo Joon Yoon, Suhyung Cho, Bernhard Palsson*, Jay D Keasling*, Byung-Kwan Cho* (2025). Regulatory orchestration of FK506 biosynthesis in Streptomyces tsukubaensis NRRL 18488 revealed through systematic analysis. iScience, 28(6), 112698.
  3. Elias Englund, Matthias Schmidt, Alberto A Nava, Sarah Klass, Leah Keiser, Qingyun Dan, Leonard Katz, Satoshi Yuzawa, Jay D Keasling* (2023). Biosensor guided polyketide synthases engineering for optimization of domain exchange boundaries. Nature Communications, 14(1), 4871.
  4. Chunjun Zhan, Namil Lee, Guangxu Lan, Qingyun Dan, Aidan Cowan, Zilong Wang, Edward EK Baidoo, Ramu Kakumanu, Bridget Luckie, Rita C Kuo, Joshua McCauley, Yuzhong Liu, Luis Valencia, Robert W Haushalter*, Jay D Keasling* (2023). Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition. Nature Metabolism, 5(7), 1127-1140.
  5. Jing Huang, Andrew Quest, Pablo Cruz-Morales, Kai Deng, Jose Henrique Pereira, Devon Van Cura, Ramu Kakumanu, Edward EK Baidoo, Qingyun Dan, Yan Chen, Christopher J Petzold, Trent R Northen, Paul D Adams, Douglas S Clark*, Emily P Balskus, John F Hartwig*, Aindrila Mukhopadhyay*, Jay D Keasling* (2023). Complete integration of carbene-transfer chemistry into biosynthesis. Nature, 617, 403–408.
  6. Samantha P Kelly†, Vikram V Shende†, Autumn R Flynn, Qingyun Dan, Ying Ye, Janet L Smith, Sachiko Tsukamoto, Matthew S Sigman*, David H Sherman* (2022). Data science-driven analysis of substrate-permissive diketopiperazine reverse prenyltransferase NotF: applications in protein engineering and cascade biocatalytic synthesis of (−)-eurotiumin A. Journal of the American Chemical Society, 144(42), 19326-19336.
  7. Yuzhong Liu†, Pablo Cruz-Morales†, Amin Zargar, Michael S Belcher, Bo Pang, Elias Englund, Qingyun Dan, Kevin Yin, Jay D Keasling* (2021). Biofuels for a sustainable future. Cell, 184(6), 1636-1647.
  8. Meredith A Skiba, Collin L Tran, Qingyun Dan, Andrew P Sikkema, Zachary Klaver, William H Gerwick, David H Sherman, Janet L Smith* (2020). Repurposing the GNAT fold in the initiation of polyketide biosynthesis. Structure, 28(1), 63-74.
  9. Meredith A Skiba†, Marissa M Bivins†, John R Schultz, Steffen M Bernard, William D Fiers, Qingyun Dan, Sarang Kulkarni, Peter Wipf, William H Gerwick, David H Sherman, Courtney C Aldrich, Janet L Smith* (2018). Structural basis of polyketide synthase O-methylation. ACS Chemical Biology, 13(12), 3221-3228.
  10. Amy E Fraley, Marc Garcia-Borràs, Ashootosh Tripathi, Dheeraj Khare, Eduardo V Mercado-Marin, Hong Tran, Qingyun Dan, Gabrielle P Webb, Katharine R Watts, Phillip Crews, Richmond Sarpong, Robert M Williams, Janet L Smith, KN Houk*, David H Sherman* (2017). Function and structure of MalA/MalA′, iterative halogenases for late-stage C–H functionalization of indole alkaloids. Journal of the American Chemical Society, 139(34), 12060-12068.

Book Chapters:

  1. Meredith A Skiba, Finn P Maloney, Qingyun Dan, Amy E Fraley, Courtney C Aldrich, Janet L Smith*, W Clay Brown* (2018). PKS–NRPS enzymology and structural biology: considerations in protein production. Methods in Enzymology, 604, 45-88.

Patents:

  1. Jay D Keasling, Qingyun Dan, Ziwang Wei, Cholapat Varongchayakul, Xina Wang, Yan Chiu, Yiou Rong (2026). Hybrid polyketide synthase biosynthesis of ketones and derivatives thereof. (US Patent Filed)
  2. Qingyun Dan, Namil Lee, Yan Chiu, Jay D Keasling (2025). Hybrid polyketide synthase biosynthesis of alcohols and derivatives thereof. (International PCT Patent Application No. PCT/US2025/028766)