We are interested in synthetic biology, de novo protein design, and continuous directed evolution to artificially design functional parts in high throughput manner by utilizing automatic platforms, focusing on metabolism, energy, and regulatory network. Our research works were published on high impact journals including Science, Nature Biotechnology, Nature Microbiology, Nucleic Acids Research, and Metabolic Engineering.

1.Identified two key enzymes that complete the TCA cycle in cyanobacteria. This work has been featured as cover story in Chapter 3 of the classic microbiology textbook Brock Biology of Microorganisms (14 ^th Edition).

2.Discovered new photosystems that can absorb far-red light. This work was described as “text book changing stuff” by Professor Bill Rutherford from Imperial College London.

3.Enabled automated genetic circuit design in bacteria. Successfully built 7 segments display using E. coli. We also improved genetic circuit design using CRISPR system and realized genetic circuit design automation in the gut resident species Bacteroides thetaiotaomicron.

Chinese Government Award for Outstanding Self-Financed Students Abroad
Fred Wedler Outstanding Dissertation Award

1. Shuyi Zhang and Donald A. Bryant. (2011). The tricarboxylic acid cycle in cyanobacteria. Science, 334, 1551-1553, DOI: 10.1126/science.1210858 - This work was featured as cover story in Chapter 3 of the classic microbiology textbook Brock Biology of Microorganisms (14th Edition)

2. Kenchappa G. Kumaraswamy, Xiao Qian, Tiago Guerra, Shuyi Zhang, Donald A. Bryant and Charles G. Dismukes. (2013). Reprogramming the glycolytic pathway for increased hydrogen production in cyanobacteria: metabolic engineering of NAD+-dependent GAPDH. Energy & Environmental Science, 6(12):3722-3731, DOI: 10.1039/C3EE42206B
3. Shuyi Zhang, Gaozhong Shen, Zhongkui Li, John H. Golbeck and Donald A. Bryant. (2014). Vipp1 is essential for the biogenesis of Photosystem I but not thylakoid membranes in Synechococcus sp. PCC 7002. Journal of Biological Chemistry, 289(23), 15904-15914, DOI: 10.1074/jbc.M114.555631

4. Fei Gan, Shuyi Zhang, Nathan C. Rockwell, Shelley S. Martin, Clark J. Lagarias and Donald A. Bryant. (2014) Extensive remodeling of a cyanobacterial photosynthetic apparatus in Far-Red light. Science, 345, 1312-1317, DOI: 10.1126/science.1256963 - This work was described as “text book changing stuff” by Professor Bill Rutherford from Imperial College London.

5. Hans C. Bernstein, Allan Konopka, Matthew R. Melnicki, Eric A. Hill, Leo A. Kucek, Shuyi Zhang, Gaozhong Shen, Donald A. Bryant and Alexander S. Beliaev. (2014) Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002. Frontiers in Microbiology, 5, 488, DOI: 10.3389/fmicb.2014.00488

6. Shuyi Zhang and Donald A. Bryant. (2014) Learning new tricks from an old cycle: the TCA cycles of cyanobacteria, algae and plants. Perspectives in Phycology, 2, 73-86, Invited review article, DOI: 10.1127/pip/2014/0016

7. Shuyi Zhang and Donald A. Bryant. (2015) Biochemical validation of the the glyoxylate cycle in the cyanobacterium Chlorogloeopsis fritschii PCC 9212, Journal of Biological Chemistry 290 (22), 14019-14030, DOI: 10.1074/jbc.M115.648170

8. Shuyi Zhang, Yang Liu and Donald A. Bryant. (2015) Metabolic engineering of Synechococcus sp. PCC 7002 to produce poly-3-hydroxybutyrate and poly-3-hydroxybutyrate-co-4-hydroxybutyrate, Metabolic Enginneering, 32, 174-183, DOI: 10.1016/j.ymben.2015.10.001

9. Xiao Qian, Kenchappa G. Kumaraswamy, Shuyi Zhang, Colin Gates, Donald A. Bryant and Charles G. Dismukes. (2015) Inactivation of nitrate reductase alters metabolic branching of carbohydrate fermentation in the cyanobacterium Synechococcus sp. strain PCC 7002. Biotechnology & Bioengineering, 113(5):979-988, DOI: 10.1002/bit.25862

10. Anagha Krishnan, Shuyi Zhang, Yang Liu, Kinan A Tadmori, Donald A Bryant and G Charles Dismukes (2015) Consequences of ccmR deletion on respiration, fermentation and H2 metabolism in cyanobacterium Synechococcus sp. PCC 7002. Biotechnology & Bioengineering, 113(7):1448-1459, DOI: 10.1002/bit.25913

11. Shuyi Zhang, Xiao Qian, Shannon Chang, G Charles Dismukes and Donald A Bryant (2016) Natural and synthetic variants of the tricarboxylic acid cycle in cyanobacteria: introduction of the GABA shunt into Synechococcus sp. PCC 7002. Frontiers in Microbiology, 7, 1972, DOI: 10.3389/fmicb.2016.01972

12. Shuyi Zhang and Christopher A. Voigt. (2018) Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design. Nucleic Acids Research, gky884, DOI: 10.1093/nar/gky884

13. Kenchappa G Kumaraswamy, Anagha Krishnan, Gennady Ananyev, Shuyi Zhang, Donald A. Bryant and G Charles Dismukes. (2019) Crossing the Thauer limit: Rewiring Cyanobacterial Metabolism to Maximize Fermentative H ₂ Production. Energy & Environmental Science, 12, 1035-1045, DOI: 10.1039/C8EE03606C

14. Jonghyeon Shin, Shuyi Zhang, Bryan S. Der, Alec A.K. Nielsen, and Christopher A. Voigt. (2020) Programming Escherichia coli to function as a digital display. Molecular Systems Biology, 16: e9401, DOI: 10.15252/msb.20199401. Highlighted as Cover Article.

15. Mao Taketani, Jianbo Zhang, Shuyi Zhang, Alexander J. Triassi, Yu-Ja Huang, Linda G. Griffith & Christopher A. Voigt. (2020) Genetic circuit design automation for the gut resident species   Bacteroides thetaiotaomicron. Nature Biotechnology, DOI: 10.1038/s41587-020-0468-5

16. Ye Chen, Shuyi Zhang, Eric M. Young, and Christopher A. Voigt. (2020) Genetic circuit design automation for yeast. Nature Microbiology, In minor revision.