Articles in Peer-reviewed Journals since Joining ISU

# corresponding author; * equal contribution.

49. A Method for Identifying Novel Strain Engineering Strategies by Mining Existing Data Concerning Genes of Unknown Function

A. Warner, Z. Shao#, and L. R. Jarboe# (in preparation, 2022)

48. Engineering Rhodosporidium toruloides for Producing Fatty Alcohols and Wax Esters

Y. Zhao and Z. Shao# (in preparation, 2022)

47. Engineering Issatchenkia orientalis for Citramalate Production

Z-Y. Wu*, W. Sun*, Y. Shen, P. Suthers, C. D. Maranas, J. D. Rabinowitz, Z. Shao#, and Y. Yoshikuni# (in preparation, 2022)

46. Discovery of Novel Xylose and Shikimate-specific Transporters Facilitates Microbial Consortium Design as a Chassis to Produce Benzylisoquinoline Alkaloids

M. Gao and Z. Shao# (in preparation, 2022)

45. The Untapped Potential of Non-obvious Regulatory Sequences Harbored in the Yeast Genome

C. Lopez and Z. Shao# (in preparation, 2022)

44. A Repackaged CRISPR Platform Increases Homology-directed Repair for Yeast Engineering

D. Ploessl, Y. Zhao, M. Cao, S. Ghosh, C. Lopez, M. Sayadi, S. Chudalayandi, A. Severin, L. Huang, M. Gustafson, and Z. Shao#
Nature Chemical Biology, 18, 38–46, DOI: 10.1038/s41589-021-00893-5 (2022)

43. Chapter 10: Recent Advances in Synthetic Biology Applications of Pichia Species

W. Sun*, Y. Zuo*, Z. Yao*, J. Gao*, Z. Shao#, and J. Lian#
Synthetic Biology of Yeasts: Tools and Applications, Springer, 1 (2022)

42. Microbial Synthesis of Wax Esters

Y-H. V. Soong, L. Zhao, N. Liu, P. Yu, C. Lopez, A. Olson, H-W. Wong, Z. Shao#, and D. Xie#
Metabolic Engineering, 67, 428-442, DOI: 10.1016/j.ymben.2021.08.002 (2021)

41. Renewable Fatty Acid Ester Production in Clostridium

J. Feng, J. Zhang, Y. Ma, Y. Feng, S. Wang, N. Guo, H. Wang, P. Wang, P. Jiménez-Bonilla, Y. Gu, J. Zhou, Z-T. Zhang, M. Cao, D. Jiang, S. Wang, X-W. Liu, Z. Shao, I. Borovok, H. Huang, and Yi Wang#
Nature Communications, 12, 4368, DOI: 10.1038/s41467-021-24038-3 (2021)

40. Revisiting the Unique Structure of Autonomously Replicating Sequences in Yarrowia lipolytica and Its Role in Pathway Engineering

C. Lopez, M. Cao#, Z. Yao, and Z. Shao#
Applied Microbiology and Biotechnology, 105, 5959-5972, DOI: 10.1007/s00253-021-11399-4 (2021)

39. A Genetic Toolbox for Metabolic Engineering of Issatchenkia orientalis

M. Cao, Z. Fatma, X. Song, P.-H. Hsieh, V. G. Tran, W. L. Lyon, M. Sayadi, Z. Shao, Y. Yoshikuni, and H. Zhao#             
Metabolic Engineering, 59, 87-97, DOI: 10.1016/j.ymben.2020.01.005 (2020)

38. Reverse Engineering of Fatty Acid-tolerant Escherichia coli Identifies Design Strategies for Robust Microbial Cell Factories

Y. Chen, E. Boggess, E. Ocasio, A. Warner, L. Kerns, V. Drapal, C. Gossling, W. Ross, Z. Shao, J. A. Dickerson, T. J. Mansell#, and L. R. Jarboe#                                                                                      
Metabolic Engineering, 61, 120-130, DOI: 10.1016/j.ymben.2020.05.001 (2020)

37. Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories

Y. Zhao, Z. Yao, D. Ploessl, G. Saptarshi, M. Monti, D. Schindler, M. Gao, Y. Cai, M. Qiao, C. Yang#, M. Cao#, and Z. Shao#
ACS Synthetic Biology, 9, 7, 1736-1752, DOI: 10.1021/acssynbio.0c00123 (2020)

36. Metabolic Engineering of an Acid-tolerant Yeast Strain Pichia kudriavzevii for Itaconic Acid Production

W. Sun, A. Vila-Santa, N. Liu, T. Prozorov, D. Xie, N. T. Faria, F. C. Ferreira, N. P. Mira#, and Z. Shao#
Metabolic Engineering Communications, 10, e00124, DOI: 10.1016/j.mec.2020.e00124 (2020)

35. Modulating Pathway Performance by Perturbing Local Genetic Context

C. Lopez, Y. Zhao, R. Masonbrink, and Z. Shao#
ACS Synthetic Biology, 9, 4, 706-717, DOI: 10.1021/acssynbio.9b00445 (2020)

34. Correlative Microbially-Assisted Imaging of Cellulose Deconstruction with Electron Microscopy

A. Londono-Calderon, W. Sun, Z. Shao, D.H. Alsem, T. Prozorov#
Microscopy and Microanalysis, 24 (S1), 382-383, DOI: 10.1017/S1431927618002404 (2018)

33. Building Microbial Factories for the Production of Aromatic Amino Acid Pathway Derivatives: From Commodity Chemicals to Plant-sourced Natural Products

M. Cao*, M. Gao*, M. Suastegui, Y. Mei, and Z. Shao#
Metabolic Engineering, 58, 94-132, DOI: 10.1016/j.ymben.2019.08.008 (2019)

32. Enhancing the Co-utilization of Biomass-Derived Mixed Sugars by Yeasts

M. Gao, D. Ploessl, and Z. Shao#
Frontier in Microbiology, 9: 3264, DOI: 10.3389/fmicb.2018.03264 (2018)

31. CRISPR–Mediated Genome Editing and Gene Repression in Scheffersomyces stipitis

M. Cao, M. Gao, D. Ploessl, C. Song, and Z. Shao#
Biotechnology Journal, 13, 1700598, DOI:10.1002/biot.201700598 (2018)

30. Expression of Tabersonine 16-Hydroxylase and 16-Hydroxytabersonine-O-Methyltransferase in Catharanthus roseus Hairy Roots

J. Sun*, L. Zhao*, Z. Shao, J. V. Shanks, and C. Peebles#
Biotechnology and Bioengineering, 115, 673-683, DOI: 10.1002/bit.26487 (2018)

29. Rapid Isolation of Centromeres from Scheffersomyces stipitis

M. Cao, A. Seetharam, A. Severin, and Z. Shao#
ACS Synthetic Biology, 6, 2028-2034, DOI: 10.1021/acssynbio.7b00166 (2017)

28. Multilevel Engineering of the Upstream Module of Aromatic Amino Acid Biosynthesis in Saccharomyces cerevisiae for High Production of Polymer and Drug Precursors

M. Suastegui, C. Y. Ng, A. Chowdhury, W. Sun, M. Cao, E. House, C. D. Maranas, and Z. Shao#
Metabolic Engineering, 42, 134-144, DOI: 10.1016/j.ymben.2017.06.008 (2017)

27. Centromeric DNA Facilitates Scheffersomyces stipitis Genetic Engineering

M. Cao, M. Gao, C. Lopez, Y. Wu, A. Seetharam, A. Severin, and Z. Shao#
ACS Synthetic Biology, 6,1545-1553, DOI: 10.1021/acssynbio.7b00046 (2017)

26. Yeast Factories for Production of Aromatic Compounds: from Building Blocks to Plant Secondary Metabolites

(featured as the front cover)
M. Suastegui, and Z. Shao#
Journal of Industrial Microbiology and Biotechnology, 43(11), 611-1624, DOI: 10.1007/s10295-016-1824-9 (2016)

25. Electrochemical Conversion of Biologically-Produced Muconic Acid: Key Considerations for Scale-up and Corresponding Technoeconomic Analysis

J. Matthiesen, M. Suastegui, Y. Wu, M. Viswanathan, Y. Qu, M. Cao, N. Rodriguez-Quiroz, A. Okerlund, G. Kraus, R. Raman, Z. Shao, and J.-P.Tessonnier#
ACS Sustainable Chemistry & Engineering, 4 (12), 7098–7109, DOI: 10.1021/acssuschemeng.6b01981 (2016)

24. Innovating a Nonconventional Yeast Platform for Producing Shikimic Acid as the Building Block of High-value Aromatics

M. Gao, M. Cao, M. Suastegui, J. Walker, N. R. Quiroz, Y. Wu, D. Tribby, A. Okerlund, L. Stanley, J. V. Shanks, and Z. Shao#
ACS Synthetic Biology, 6:29-38, DOI: 10.1021/acssynbio.6b00132 (2016)

23. Investigating Strain Dependency in the Production of Aromatic Compounds in Saccharomyces cerevisiae

M. Suastegui, W. Guo, X. Feng#, and Z. Shao#
Biotechnology and Bioengineering, 113(12), 2676-2685, DOI: 10.1002/bit.26037 (2016)

22. A Photoacoustic Immunoassay for Biomarker Detection

Y. Zhao, M. Cao, J. F. McClelland, Z. Shao, and M. Lu#
Biosensors and Bioelectronics, 85, 261-266, DOI: 10.1016/j.bios.2016.05.028 (2016)

21. Combining Metabolic Engineering and Electrocatalysis: Application to the Production of Polyamides from Sugar

(featured as the front cover)
M. Suastegui*, J. E. Matthiesen*, J. M. Carraher, N. Hernandez, N. R. Quiroz, A. Okerlund, E. W. Cochran, Z. Shao#, and J.-P. Tessonnier#
Angewandte Chemie International Edition, 55, 2368-2373, DOI:10.1002/anie.201509653 (2016)

20. Anti-cancer Drugs

L. Zhao, Z. Shao, and J. V. Shanks#
Industrial Biotechnology: Products and Processes, Wiley-VCH, volume 4, 239-269, DOI: 10.1002/9783527807833.ch8 (2017)

19. Pathway Assembly and Optimization

M. Suastegui, M. Gao, and Z. Shao#
Biotechnologies for Biofuel Production and Optimization, 1st Edition, Elsevier, 139-164, DOI:10.1016/B978-0-444-63475-7.00006-6 (2016)

Patents since Joining ISU

(3). Methods and Compositions for Production of Aromatic and Other Compounds in Yeast

Z. Shao#, M. Cao, M. Suastegui, and M. Gao
Utility patent filed on 6/28/2018, P12286US01

(2). Building Yeast Factories for Production of Aromatic Compounds-from Building Blocks to Plant Secondary Metabolites

Z. Shao#, M. Cao, M. Suastegui, and M. Gao
Provisional Patent, ISURF#04508 (2017)

(1). Method To Produce Muconic Acid Using Yeast

Z. Shao# and M. Suastegui
Provisional patent, ISURF#04379 (2015)

Articles in Peer-reviewed Journals Before Joining ISU

18. Biochemical and Genetic Characterization of Issatchenkia orientalis as a Potential Platform Organism for Production of Organic Acids

H. Xiao*, Z. Shao*, Y. Jiang*, and H. Zhao
Microbial Cell Factories, 13:121 (2014)

17. Manipulating Natural Product Biosynthetic Pathways via DNA Assembler

Z. Shao, and H. Zhao
Current Protocols in Chemical Biology, 6(2):65-100 (2014)

16. Activation and Characterization of a Cryptic Polycyclic Tetramate Macrolactam Biosynthetic Gene Cluster

Y. Luo, H. Huang, J. Liang, M. Wang, L. Lu, Z. Shao, R. E. Cobb, and H. Zhao
Nature Communications, 4, 2894 (2013)

15. Construction and Engineering of Large Biochemical Pathways via DNA Assembler

Z. Shao and H. Zhao
Methods in Molecular Biology, 1073, 85-106 (2013)

14. Refactoring the Silent Spectinabilin Biosynthetic Pathway Using a Plug-and-Play Scaffold

Z. Shao, G. Rao, C. Li, Z. Abil, Y. Luo, and H. Zhao
ACS Synthetic Biology, 2(11):662-9 (2013)

13. DNA Assembler Method for Construction of Zeaxanthin Producing Strains of Saccharomyces cerevisiae

Z. Shao, Y. Luo, and H. Zhao
Methods in Molecular Biology, 898, 251-62 (2012)

12. Systematic Characterization of a Panel of Constitutive Promoters for Applications in Pathway Engieering in Saccharomyces cerevisiae

J. Sun, Z. Shao, H. Zhao, N. Nair, F. Wen, J. Xu, and H. Zhao
Biotechnology and Bioengineering, 09(8): 2082-92 (2012)

11. DNA Assembler: a Synthetic Biology Tool for Characterizing and Engineering Natural Product Gene Clusters

Z. Shao and H. Zhao
Methods in Enzymology, 517, 203-24 (2012)

10. Engineering Microbial Factories for Synthesis of Value-added Products

J. Du*, Z. Shao*, and H. Zhao
Journal of Industrial Microbiology and Biotechnology, 38, 873-90 (2011)

9. Rapid Characterization and Engineering of Natural Product Biosynthetic Pathways via DNA Assembler

Z. Shao, Y. Luo, and H. Zhao
Molecular Biosystems, 7, 1056-9 (2011)

8. Cloning and Heterologous Expression of the Spectinabilin Biosynthetic Gene Cluster from Streptomyces spectabilis

Y. S. Choi, T. W. Johannes, M. Simurdiak, Z. Shao, H. Lu, and H. Zhao
Molecular Biosystems, 6(2): 336-8 (2010)

7. Improving Cellular Malonyl-CoA Level in Escherichia coli via Metabolic Engineering

W. Zha, S. B. Rubin-Pitel, Z. Shao, and H. Zhao
Metabolic Engineering, 11, 192-8 (2009)

6. DNA Assembler, an in vivo Genetic Method for Rapid Construction of Large Recombinant DNA

Z. Shao*, H. Zhao*, and H. Zhao
Nucleic Acids Research, 37(2), e16 (2009)

5. Biosynthesis of 2-Hydroxyethylphosphonate, an Unexpected Intermediate Common to Multiple Phosphonate Biosynthetic Pathways

Z. Shao, J. Blodgett, B. Circello, A. Eliot, R. Woodyer, G. Li, A. van der Donk, W. M. Metcalf, and H. Zhao
Journal of Biological Chemistry, 283, 23161-8 (2008)

4. Heterologous Production of Fosfomycin and Identification of the Minimal Fosfomycin Biosynthetic Cluster

R. Woodyer, Z. Shao, W. M. Metcalf, W. A. van der Donk, and H. Zhao
Chemical & Biology, 13, 1171-82 (2006)

3. Biomolecular Engineering

Z. Shao, E. Ang, and H. Zhao
Encyclopedia of Chemical Processing Marcel Dekker, Inc., 171-182 (2006)

2. Microbial Synthesis of Triacetic Acid Lactone

D. Xie, Z. Shao, J. Achkar, W. Zha, J. W. Frost, and H. Zhao
Biotechnology and Bioengineering, 93, 727-36 (2006)

1. Rational Pathway Engineering of Type I Fatty Acid Synthase Allows Biosynthesis of Triacetic Acid Lactone from D-Glucose in vivo

W. Zha, Z. Shao, J. W. Frost, and H. Zhao
Journal of the American Chemical Society, 126, 4534-5 (2004)