Publications

2020: 

1. Suthers, P. F., Dinh, H. V., Fatma, Z., Shen, Y., Chan, S. H. J., Rabinowitz, J. D., Zhao, H., and Maranas, C. D. (October 2020) “Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production.” Metabolic Engineering Communications. 11, e00148. https://doi.org/10.1016/j.mec.2020.e00148

2. Ke, J., Wang, B., Yoshikuni, Y. (August 2020) “Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture.” Trends in Biotechnology. https://doi.org/10.1016/j.tibtech.2020.07.008

3. Volk, M. J., Lourentzou, I., Mishra, S., Vo, L. T., Zhai, C., and Zhao, H. (June 2020) “Biosystems Design via Machine Learning.” ACS Synthetic Biology. 9, 1514-1533. https://doi.org/10.1021/acssynbio.0c00129

4. Fatma, Z., Schultz, J. C., and Zhao, H. (April 2020) “Recent Advances in Domesticating Non-model Microorganisms.” Biotechnology Progress, 36, e3008. https://doi.org/10.1002/btpr.3008

5. Suthers, P. F., Maranas, C. D. (April 2020) “Challenges of Cultivated Meat Production and Applications of Genome‐Scale Metabolic Modeling.” AIChE Journal. 66, e16235. https://doi.org/10.1002/aic.16235

6. Huang, X., Cao, M., and Zhao, H. (March 2020) “Integrating Biocatalysis with Chemocatalysis for Selective Transformations.” Current Opinion in Chemical Biology, 55, 161-170. https://doi.org/10.1016/j.cbpa.2020.02.004

7. Gopalakrishnan, S., Dash, S., Maranas, C. D. (March 2020) “K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data.” Metabolic Engineering. 61, 197-205. https://doi.org/10.1016/j.ymben.2020.03.001

8. Wang, Y., Yu, X., and Zhao, H. (March 2020) “Biosystems Design by Directed Evolution.” AIChE Journal, 66, e16716. https://doi.org/10.1002/aic.16716

2019: 

9. Lian, J., Schultz, C., Cao, M., HamediRad, M., and Zhao, H. (2019) “Multi-functional Genome-wide CRISPR System for High Throughput Genotype-Phenotype Mapping.” Nature Communications, 10, 5794. https://doi.org/10.1038/s41467-019-13621-4

10. Fasan, R., Kan, S. B. J., and Zhao, H. (2019) “A Continuing Career in Biocatalysis: Frances H. Arnold.” ACS Catalysis, 9, 9775−9788. https://doi.org/10.1021/acscatal.9b02737

11. Dinh, H. V., Suthers, P. F., Chan, S. H. J., Shen, Y., Xiao, T., Deewan, A., Jagtap, S. S., Zhao, H., Rao, C. V., Rabinowitz, J. D., Maranas, C. D. (2019) “A Comprehensive Genome-scale Model for Rhodosporidium toruloides IFO0880 Accounting for Functional Genomics and Phenotypic data.” Metabolic Engineering Communications, 9, e00101. https://doi.org/10.1016/j.mec.2019.e00101

12. Tran, V. G., Cao, M., Fatma, Z., Song, X., and Zhao, H. (2019) “Development of a CRISPR/Cas9-based Tool for Gene Deletion in Issatchenkia orientalis.” mSphere, 4, e00345-19. https://doi.org/10.1128/mSphere.00345-19

13. Schultz, J. C., Cao, M., and Zhao, H. (2019) “Development of a CRISPR/Cas9 System for High Efficiency Gene Deletion in Rhodosporidium toruloides.” Biotechnology and Bioengineering, 116, 2103–2109. https://doi.org/10.1002/bit.27001

14. Pappireddi, N., Martin, L., and Wühr, M. (2019) “A Review on Quantitative Multiplexed Proteomics.” Chembiochem 20, 1210-1224. https://doi.org/10.1002/cbic.201800650

2018: 

15. Schultz, C., Lian, J., and Zhao, H. (2018) “Metabolic Engineering of Saccharomyces cerevisiae Using a Tri-functional CRISPR/Cas System for Simultaneous Gene Activation, Interference, and Deletion.” Methods in Enzymology, 608, 265-276. https://doi.org/10.1016/bs.mie.2018.04.010

16. Bao, Z., HamediRad, M., Xue, P., Xiao, H., Tasan, I., Chao, R., Liang, J., and Zhao, H. (2018) “Genome-scale Engineering of Saccharomyces cerevisiae with Single Nucleotide Precision.” Nature Biotechnology, 36, 505–508. https://doi.org/10.1038/nbt.4132

17. Lian, J., Mishra, S., and Zhao, H. (2018) “Recent Advances in Metabolic Engineering of Saccharomyces cerevisiae: New Tools and Their Applications.” Metabolic Engineering, 50, 85–108. https://doi.org/10.1016/j.ymben.2018.04.011

18. HamediRad, M., Lian, J., Li, H., and Zhao, H. (2018) “RNAi Assisted Genome Evolution Unveils Yeast Mutants with Improved Xylose Utilization.” Biotechnology and Bioengineering, 115, 1552-1560. https://doi.org/10.1002/bit.26570

19. Lian, J., HamediRad, M., and Zhao, H. (2018) “Advancing Metabolic Engineering of Saccharomyces cerevisiae using the CRISPR/Cas System.” Biotechnology Journal, 13, e1700601. https://doi.org/10.1002/biot.201700601

20. Wang, Y., Ren, H., and Zhao, H. (2018) “Expanding the Boundary of Biocatalysis: Design and Optimization of in vitro Tandem Catalytic Reactions for Biochemical Production.” Critical Reviews in Biochemistry and Molecular Biology, 53, 115-129. https://doi.org/10.1080/10409238.2018.1431201

21. Shi, S., Ang, E. L., and Zhao, H. (2018) “In vivo Biosensors: Mechanisms, Development, and Applications.” Journal of Industrial Microbiology & Biotechnology, 45, 491–516. https://doi.org/10.1007/s10295-018-2004-x

22. Stadlmeier, M., Bogena, J., Wallner, M., Wühr, M., and Carell, T. (2018) “A Sulfoxide-Based Isobaric Labelling Reagent for Accurate Quantitative Mass Spectrometry.” Angew Chem Int Ed Engl. 57, 2958-2962. https://doi.org/10.1002/anie.201708867

2017: 

23. Lian, J., HamediRad, M., Hu, S., and Zhao, H. (2017) “Combinatorial Metabolic Engineering using an Orthogonal Tri-functional CRISPR System.” Nature Communications, 8:1688. https://doi.org/10.1038/s41467-017-01695-x

24. Shi, S., and Zhao, H. (2017) “Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals.” Frontiers in Microbiology, 8:2185. https://doi.org/10.3389/fmicb.2017.02185