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  • Huimin Zhao
2019

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

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., Dec 2019, In : Metabolic Engineering Communications. 9, e00101.

Research output: Contribution to journalArticle

Open Access

A continuing career in biocatalysis: Frances H. Arnold

Fasan, R., Jennifer Kan, S. B. & Zhao, H., Nov 1 2019, In : ACS Catalysis. 9, 11, p. 9775-9788 14 p.

Research output: Contribution to journalArticle

Activation of silent biosynthetic gene clusters using transcription factor decoys

Wang, B., Guo, F., Dong, S. H. & Zhao, H., Feb 1 2019, In : Nature chemical biology. 15, 2, p. 111-114 4 p.

Research output: Contribution to journalArticle

A gene cluster for taurine sulfur assimilation in an anaerobic human gut bacterium

Xing, M., Wei, Y., Hua, G., Li, M., Nanjaraj Urs, A. N., Wang, F., Hu, Y., Zhai, W., Liu, Y., Ang, E. L., Zhao, H. & Zhang, Y., Aug 15 2019, In : Biochemical Journal. 476, 15, p. 2271-2279 9 p.

Research output: Contribution to journalArticle

An efficient gene knock-in strategy using 5′-modified double-stranded DNA donors with short homology arms

Yu, Y., Guo, Y., Tian, Q., Lan, Y., Yeh, H., Zhang, M., Tasan, I., Jain, S. & Zhao, H., Dec 23 2019, (Accepted/In press) In : Nature chemical biology. 16, 4, p. 387-390 4 p.

Research output: Contribution to journalArticle

An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine

Yin, J., Wei, Y., Liu, D., Hu, Y., Lu, Q., Lui Ang, E., Zhao, H. & Zhang, Y., Oct 25 2019, In : Journal of Biological Chemistry. 294, 43, p. 15662-15671 10 p.

Research output: Contribution to journalArticle

A pathway for isethionate dissimilation in Bacillus krulwichiae

Tong, Y., Wei, Y., Hu, Y., Ang, E. L., Zhao, H. & Zhang, Y., 2019, In : Applied and environmental microbiology. 85, 15, e00793-19.

Research output: Contribution to journalArticle

Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca

Zhou, Y., Wei, Y., Lin, L., Xu, T., Ang, E. L., Zhao, H., Yuchi, Z. & Zhang, Y., Jan 1 2019, In : Biochemical Journal. 476, 4, p. 733-746 14 p.

Research output: Contribution to journalArticle

Biochemical and structural investigation of taurine:2-oxoglutarate aminotransferase from Bifidobacterium kashiwanohense

Li, M., Wei, Y., Yin, J., Lin, L., Zhou, Y., Hua, G., Cao, P., Ang, E. L., Zhao, H., Yuchi, Z. & Zhang, Y., Jan 1 2019, In : Biochemical Journal. 476, 11, p. 1605-1619 15 p.

Research output: Contribution to journalArticle

Building a global alliance of biofoundries

Hillson, N., Caddick, M., Cai, Y., Carrasco, J. A., Chang, M. W., Curach, N. C., Bell, D. J., Le Feuvre, R., Friedman, D. C., Fu, X., Gold, N. D., Herrgård, M. J., Holowko, M. B., Johnson, J. R., Johnson, R. A., Keasling, J. D., Kitney, R. I., Kondo, A., Liu, C., Martin, V. J. J. & 16 others, Menolascina, F., Ogino, C., Patron, N. J., Pavan, M., Poh, C. L., Pretorius, I. S., Rosser, S. J., Scrutton, N. S., Storch, M., Tekotte, H., Travnik, E., Vickers, C. E., Yew, W. S., Yuan, Y., Zhao, H. & Freemont, P. S., Dec 1 2019, In : Nature communications. 10, 1, 2040.

Research output: Contribution to journalComment/debate

Open Access

Characterization of Cas proteins for CRISPR-Cas editing in streptomycetes

Yeo, W. L., Heng, E., Tan, L. L., Lim, Y. W., Lim, Y. H., Hoon, S., Zhao, H., Zhang, M. M. & Wong, F. T., Jan 1 2019, In : Biotechnology and bioengineering. 116, 9, p. 2330-2338 9 p.

Research output: Contribution to journalArticle

Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098

Nguyen, K., DeSieno, M. A., Bae, B., Johannes, T. W., Cobb, R. E., Zhao, H. & Nair, S. K., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 6, p. 1506-1518 13 p.

Research output: Contribution to journalArticle

Construction and Screening of an Antigen-Derived Peptide Library Displayed on Yeast Cell Surface for CD4+ T Cell Epitope Identification

Wen, F., Smith, M. R. & Zhao, H., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 213-234 22 p. (Methods in Molecular Biology; vol. 2024).

Research output: Chapter in Book/Report/Conference proceedingChapter

Delta integration CRISPR-Cas (Di-CRISPR) in saccharomyces cerevisiae

Shi, S., Liang, Y., Ang, E. L. & Zhao, H., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 73-91 19 p. (Methods in Molecular Biology; vol. 1927).

Research output: Chapter in Book/Report/Conference proceedingChapter

Development of a CRISPR/Cas9-based tool for gene deletion in Issatchenkia orientalis

Tran, V. G., Cao, M., Fatma, Z., Song, X. & Zhao, H., May 1 2019, In : mSphere. 4, 3, e00345-19.

Research output: Contribution to journalArticle

Open Access

Development of a CRISPR/Cas9 system for high efficiency multiplexed gene deletion in Rhodosporidium toruloides

Schultz, J. C., Cao, M. & Zhao, H., Aug 2019, In : Biotechnology and bioengineering. 116, 8, p. 2103-2109 7 p.

Research output: Contribution to journalArticle

Highly Efficient Single-Pot Scarless Golden Gate Assembly

Hamedirad, M., Weisberg, S., Chao, R., Lian, J. & Zhao, H., May 17 2019, In : ACS synthetic biology. 8, 5, p. 1047-1054 8 p.

Research output: Contribution to journalArticle

Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacterium Bifidobacterium kashiwanohense

Zhou, Y., Wei, Y., Nanjaraj Urs, A. N., Lin, L., Xu, T., Hu, Y., Ang, E. L., Zhao, H., Yuchi, Z. & Zhang, Y., Jan 1 2019, In : Bioscience Reports. 39, 6, Y.

Research output: Contribution to journalArticle

Open Access

Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping

Lian, J., Schultz, C., Cao, M., HamediRad, M. & Zhao, H., Dec 1 2019, In : Nature communications. 10, 1, 5794.

Research output: Contribution to journalArticle

Open Access

Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria

Xing, M., Wei, Y., Zhou, Y., Zhang, J., Lin, L., Hu, Y., Hua, G., N. Nanjaraj Urs, A., Liu, D., Wang, F., Guo, C., Tong, Y., Li, M., Liu, Y., Ang, E. L., Zhao, H., Yuchi, Z. & Zhang, Y., Dec 1 2019, In : Nature communications. 10, 1, 1609.

Research output: Contribution to journalArticle

Open Access

Towards a fully automated algorithm driven platform for biosystems design

HamediRad, M., Chao, R., Weisberg, S., Lian, J., Sinha, S. & Zhao, H., Nov 13 2019, In : Nature communications. 10, 1, 5150.

Research output: Contribution to journalArticle

Open Access
2018

A coupled chlorinase-fluorinase system with a high efficiency of trans -halogenation and a shared substrate tolerance

Sun, H., Zhao, H. & Ang, E. L., Jan 1 2018, In : Chemical Communications. 54, 68, p. 9458-9461 4 p.

Research output: Contribution to journalArticle

Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System

Lian, J., HamediRad, M. & Zhao, H., Sep 2018, In : Biotechnology Journal. 13, 9, 1700601.

Research output: Contribution to journalReview article

Applying advanced dna assembly methods to generate pathway libraries

Eriksen, D. T., Chao, R. & Zhao, H., Mar 15 2018, Synthetic Biology: Parts, Devices and Applications. Wiley-VCH Verlag, p. 331-347 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Auroramycin: A Potent Antibiotic from Streptomyces roseosporus by CRISPR-Cas9 Activation

Lim, Y. H., Wong, F. T., Yeo, W. L., Ching, K. C., Lim, Y. W., Heng, E., Chen, S., Tsai, D. J., Lauderdale, T. L., Shia, K. S., Ho, Y. S., Hoon, S., Ang, E. L., Zhang, M. M. & Zhao, H., Aug 16 2018, In : ChemBioChem. 19, 16, p. 1716-1719 4 p.

Research output: Contribution to journalArticle

Biocatalysis for the synthesis of pharmaceuticals and pharmaceutical intermediates

Sun, H., Zhang, H., Ang, E. L. & Zhao, H., Apr 1 2018, In : Bioorganic and Medicinal Chemistry. 26, 7, p. 1275-1284 10 p.

Research output: Contribution to journalReview article

Cooperative asymmetric reactions combining photocatalysis and enzymatic catalysis

Litman, Z. C., Wang, Y., Zhao, H. & Hartwig, J. F., Aug 16 2018, In : Nature. 560, 7718, p. 355-359 5 p.

Research output: Contribution to journalArticle

CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci

Tasan, I., Sustackova, G., Zhang, L., Kim, J., Sivaguru, M., HamediRad, M., Wang, Y., Genova, J., Ma, J., Belmont, A. S. & Zhao, H., Jan 1 2018, In : Nucleic acids research. 46, 17, e100.

Research output: Contribution to journalArticle

Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface

Limsakul, P., Peng, Q., Wu, Y., Allen, M. E., Liang, J., Remacle, A. G., Lopez, T., Ge, X., Kay, B. K., Zhao, H., Strongin, A. Y., Yang, X. L., Lu, S. & Wang, Y., Apr 19 2018, In : Cell chemical biology. 25, 4, p. 370-379.e4

Research output: Contribution to journalArticle

Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains

Lian, J., Bao, Z., Hu, S. & Zhao, H., Jun 2018, In : Biotechnology and bioengineering. 115, 6, p. 1630-1635 6 p.

Research output: Contribution to journalArticle

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

Bao, Z., HamediRad, M., Xue, P., Xiao, H., Tasan, I., Chao, R., Liang, J. & Zhao, H., Jul 1 2018, In : Nature Biotechnology. 36, 6, p. 505-508 4 p.

Research output: Contribution to journalArticle

Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes

Tapsin, S., Sun, M., Shen, Y., Zhang, H., Lim, X. N., Susanto, T. T., Yang, S. L., Zeng, G. S., Lee, J., Lezhava, A., Ang, E. L., Zhang, L. H., Wang, Y., Zhao, H., Nagarajan, N. & Wan, Y., Dec 1 2018, In : Nature communications. 9, 1, 1289.

Research output: Contribution to journalArticle

Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole

Liu, D., Wei, Y., Liu, X., Zhou, Y., Jiang, L., Yin, J., Wang, F., Hu, Y., Nanjaraj Urs, A. N., Liu, Y., Ang, E. L., Zhao, S., Zhao, H. & Zhang, Y., Dec 1 2018, In : Nature communications. 9, 1, 4224.

Research output: Contribution to journalArticle

Insights into Cell-Free Conversion of CO2 to Chemicals by a Multienzyme Cascade Reaction

Singh, R. K., Singh, R., Sivakumar, D., Kondaveeti, S., Kim, T., Li, J., Sung, B. H., Cho, B. K., Kim, D. R., Kim, S. C., Kalia, V. C., Zhang, Y. H. P. J., Zhao, H., Kang, Y. C. & Lee, J. K., Dec 7 2018, In : ACS Catalysis. 8, 12, p. 11085-11093 9 p.

Research output: Contribution to journalArticle

In vivo biosensors: mechanisms, development, and applications

Shi, S., Ang, E. L. & Zhao, H., Jul 1 2018, In : Journal of Industrial Microbiology and Biotechnology. 45, 7, p. 491-516 26 p.

Research output: Contribution to journalArticle

Metabolic Engineering of Saccharomyces cerevisiae Using a Trifunctional CRISPR/Cas System for Simultaneous Gene Activation, Interference, and Deletion

Schultz, C., Lian, J. & Zhao, H., Jan 1 2018, Methods in Enzymology. Scrutton, N. (ed.). Academic Press Inc., p. 265-276 12 p. (Methods in Enzymology; vol. 608).

Research output: Chapter in Book/Report/Conference proceedingChapter

Pathway design, engineering, and optimization

Garcia-Ruiz, E., HamediRad, M. & Zhao, H., Jan 1 2018, Advances in Biochemical Engineering/Biotechnology. Springer Science and Business Media Deutschland GmbH, (Advances in Biochemical Engineering/Biotechnology; vol. 162).

Research output: Chapter in Book/Report/Conference proceedingChapter

Quantifying the effects of pollen nutrition on honey bee queen egg laying with a new laboratory system

Fine, J. D., Shpigler, H. Y., Ray, A. M., Beach, N. J., Sankey, A. L., Cash-Ahmed, A., Huang, Z. Y., Astrauskaite, I., Chao, R., Zhao, H. & Robinson, G. E., Sep 2018, In : PloS one. 13, 9, e0203444.

Research output: Contribution to journalArticle

Rapid Discovery of Glycocins through Pathway Refactoring in Escherichia coli

Ren, H., Biswas, S., Ho, S., Van Der Donk, W. A. & Zhao, H., Oct 19 2018, In : ACS chemical biology. 13, 10, p. 2966-2972 7 p.

Research output: Contribution to journalArticle

Rapid Screening of Lanthipeptide Analogs via In-Colony Removal of Leader Peptides in Escherichia coli

Si, T., Tian, Q., Min, Y., Zhang, L., Sweedler, J. V., Van Der Donk, W. A. & Zhao, H., Sep 26 2018, In : Journal of the American Chemical Society. 140, 38, p. 11884-11888 5 p.

Research output: Contribution to journalArticle

Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications

Lian, J., Mishra, S. & Zhao, H., Nov 2018, In : Metabolic Engineering. 50, p. 85-108 24 p.

Research output: Contribution to journalReview article

Recent developments in the application of P450 based biocatalysts

Wei, Y., Ang, E. L. & Zhao, H., Apr 2018, In : Current Opinion in Chemical Biology. 43, p. 1-7 7 p.

Research output: Contribution to journalReview article

RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization

HamediRad, M., Lian, J., Li, H. & Zhao, H., Jun 2018, In : Biotechnology and bioengineering. 115, 6, p. 1552-1560 9 p.

Research output: Contribution to journalArticle

Synthetic biology advances and applications in the biotechnology industry: a perspective

Katz, L., Chen, Y. Y., Gonzalez, R., Peterson, T. C., Zhao, H. & Baltz, R. H., Jul 1 2018, In : Journal of Industrial Microbiology and Biotechnology. 45, 7, p. 449-461 13 p.

Research output: Contribution to journalArticle

Visualizing Spatiotemporal Dynamics of Intercellular Mechanotransmission upon Wounding

Wang, P., Liang, J., Shi, L. Z., Wang, Y., Zhang, P., Ouyang, M., Preece, D., Peng, Q., Shao, L., Fan, J., Sun, J., Li, S. S., Berns, M. W., Zhao, H. & Wang, Y., Sep 19 2018, In : ACS Photonics. 5, 9, p. 3565-3574 10 p.

Research output: Contribution to journalArticle

2017

A New Era of Genome Integration - Simply Cut and Paste!

Liu, Z., Liang, Y., Ang, E. L. & Zhao, H., Apr 21 2017, In : ACS synthetic biology. 6, 4, p. 601-609 9 p.

Research output: Contribution to journalReview article

A plug-and-play pathway refactoring workflow for natural product research in Escherichia coli and Saccharomyces cerevisiae

Ren, H., Hu, P. & Zhao, H., Aug 2017, In : Biotechnology and bioengineering. 114, 8, p. 1847-1854 8 p.

Research output: Contribution to journalArticle

A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis

Xiong, X., Zhang, Y., Yan, J., Jain, S., Chee, S., Ren, B. & Zhao, H., Jun 16 2017, In : ACS synthetic biology. 6, 6, p. 1034-1042 9 p.

Research output: Contribution to journalArticle

Automated multiplex genome-scale engineering in yeast

Si, T., Chao, R., Min, Y., Wu, Y., Ren, W. & Zhao, H., Jan 1 2017, In : Nature communications. 8, 15187.

Research output: Contribution to journalArticle