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• 2019

  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 journal › Article › peer-review

  Open Access

  • Robotics
  • platforms
  • Lycopene
  • Biosynthetic Pathways
  • Machine Learning
• 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., 2018, In: Chemical Communications. 54, 68, p. 9458-9461 4 p.

  Research output: Contribution to journal › Article › peer-review

  • fluorinase
  • Halogenation
  • Substrates
  • Enzymes

• 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 journal › Review article › peer-review

  • Metabolic Engineering
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Saccharomyces cerevisiae
  • Gene Knockout Techniques
  • Biotechnology

• 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 proceeding › Chapter

• 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 journal › Article › peer-review

  • Streptomyces
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Multigene Family
  • Genes
  • Chemical activation

• 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 journal › Review article › peer-review

  • Biocatalysis
  • Enzymes
  • Pharmaceutical Preparations
  • Oxidoreductases
  • Isomerases

• 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 journal › Article › peer-review

  • Alkenes
  • Catalysis
  • Regeneration
  • Stereoisomerism
  • Enzymes

• 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., Sep 28 2018, In: Nucleic acids research. 46, 17, e100.

  Research output: Contribution to journal › Article › peer-review

  • CRISPR-Associated Protein 9
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Nucleic Acid Repetitive Sequences
  • Genome
  • Transcription Activator-Like Effectors

• 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 journal › Article › peer-review

  • Forster resonance energy transfer
  • Fluorescence Resonance Energy Transfer
  • Biosensing Techniques
  • Biosensors
  • Matrix Metalloproteinase 14

• 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 journal › Article › peer-review

  • Polyploidy
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Yeast
  • Genes
  • Yeasts

• Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production

  Wang, Y., Ren, H. & Zhao, H., Mar 4 2018, In: Critical Reviews in Biochemistry and Molecular Biology. 53, 2, p. 115-129 15 p.

  Research output: Contribution to journal › Review article › peer-review

  • Biocatalysis
  • Enzymes
  • Metabolic engineering
  • Synthetic biology
  • Synthetic Biology

• 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 journal › Article › peer-review

  • Nucleotides
  • Yeast
  • Saccharomyces cerevisiae
  • Genes
  • Genome

• 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 journal › Article › peer-review

  • prokaryotes
  • Flavin Mononucleotide
  • Nucleotide Aptamers
  • metabolites
  • genome

• 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 journal › Article › peer-review

  • Skatole
  • indoleacetic acid
  • fermentation
  • Carboxy-Lyases
  • tryptophan

• 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 journal › Article › peer-review

  • Oxidoreductases
  • NAD phosphite oxidoreductase
  • Methanol
  • glutathione-independent formaldehyde dehydrogenase
  • Formaldehyde

• 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 journal › Article › peer-review

  • Biosensing Techniques
  • Biosensors
  • Metabolic engineering
  • Synthetic biology
  • Synthetic Biology

• 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 proceeding › Chapter

  • CRISPR-Cas Systems
  • Metabolic engineering
  • Metabolic Engineering
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Yeast

• 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 proceeding › Chapter

  • Biofuels
  • Microorganisms
  • Enzymes
  • Pharmaceutical Preparations

• 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 journal › Article › peer-review

  • queen honey bees
  • Bees
  • Honey
  • Nutrition
  • Pollen

• 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 journal › Article › peer-review

  • Bacteriocins
  • Escherichia coli
  • enterocin
  • Genes
  • Glycosylation

• 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 journal › Article › peer-review

  • Protein Sorting Signals
  • Escherichia coli
  • peptide
  • Screening
  • screening

• 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 journal › Review article › peer-review

  • Metabolic engineering
  • Metabolic Engineering
  • Yeast
  • Saccharomyces cerevisiae
  • Genes

• 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 journal › Review article › peer-review

  • Mixed Function Oxygenases
  • Enzymes
  • Biosynthesis
  • Biological Products
  • Cytochrome P-450 Enzyme System

• 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 journal › Article › peer-review

  • Xylose
  • Yeast
  • RNA Interference
  • Genes
  • Yeasts

• 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 journal › Article › peer-review

  • Synthetic biology
  • Synthetic Biology
  • Biotechnology
  • Genetic engineering
  • Industry

• 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 journal › Article › peer-review

  • Forster resonance energy transfer
  • Biosensors
  • Energy Transfer
  • bioinstrumentation
  • cells
• 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 journal › Review article › peer-review

  • Ointments
  • Genes
  • Homologous Recombination
  • Genome
  • Synthetic Biology

• 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 journal › Article › peer-review

  • Escherichia coli
  • Yeast
  • Workflow
  • Biological Products
  • Saccharomyces cerevisiae

• 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 journal › Article › peer-review

  • Epitopes
  • Chromatin Immunoprecipitation
  • Genes
  • Chromatin
  • Throughput

• Automated multiplex genome-scale engineering in yeast

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

  Research output: Contribution to journal › Article › peer-review

  • genome
  • yeast
  • Yeast
  • Genes
  • Yeasts

• Breaking the silence: new strategies for discovering novel natural products

  Ren, H., Wang, B. & Zhao, H., Dec 1 2017, In: Current Opinion in Biotechnology. 48, p. 21-27 7 p.

  Research output: Contribution to journal › Review article › peer-review

  • Biological Products
  • Genes
  • Multigene Family
  • Throughput
  • Pharmaceutical Preparations

• Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

  Lian, J., Hamedirad, M., Hu, S. & Zhao, H., Dec 1 2017, In: Nature communications. 8, 1, 1688.

  Research output: Contribution to journal › Article › peer-review

  • Metabolic engineering
  • Metabolic Engineering
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • yeast
  • Yeast

• Combining Rh-Catalyzed Diazocoupling and Enzymatic Reduction to Efficiently Synthesize Enantioenriched 2-Substituted Succinate Derivatives

  Wang, Y., Bartlett, M. J., Denard, C. A., Hartwig, J. F. & Zhao, H., Apr 7 2017, In: ACS Catalysis. 7, 4, p. 2548-2552 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Succinic Acid
  • Alkenes
  • Oxidoreductases
  • Derivatives
  • Olefins

• CRISPR-Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters

  Zhang, M. M., Wong, F. T., Wang, Y., Luo, S., Lim, Y. H., Heng, E., Yeo, W. L., Cobb, R. E., Enghiad, B., Ang, E. L. & Zhao, H., Jun 1 2017, In: Nature chemical biology. 13, 6, p. 607-609 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Streptomyces
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Multigene Family
  • Polyketides
  • Complement Activation

• Discovery and engineering of a 1-butanol biosensor in Saccharomyces cerevisiae

  Shi, S., Choi, Y. W., Zhao, H., Tan, M. H. & Ang, E. L., Dec 2017, In: Bioresource Technology. 245, p. 1343-1351 9 p.

  Research output: Contribution to journal › Article › peer-review

  • 1-Butanol
  • Butenes
  • Biosensors
  • Yeast
  • metabolite

• Discovery of a Phosphonoacetic Acid Derived Natural Product by Pathway Refactoring

  Freestone, T. S., Ju, K. S., Wang, B. & Zhao, H., Feb 17 2017, In: ACS synthetic biology. 6, 2, p. 217-223 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Phosphonoacetic Acid
  • Multigene Family
  • Biological Products
  • Acids
  • Genes

• Engineering biological systems using automated biofoundries

  Chao, R., Mishra, S., Si, T. & Zhao, H., Jul 2017, In: Metabolic Engineering. 42, p. 98-108 11 p.

  Research output: Contribution to journal › Review article › peer-review

  • Microbial Genetics
  • Bioengineering
  • Biotechnology
  • Biological systems
  • Foundries

• Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry

  Chao, R., Liang, J., Tasan, I., Si, T., Ju, L. & Zhao, H., Apr 21 2017, In: ACS synthetic biology. 6, 4, p. 678-685 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Transcription Activator-Like Effector Nucleases
  • Transcription
  • Foundries
  • Genes
  • DNA

• Inducible Control of mRNA Transport Using Reprogrammable RNA-Binding Proteins

  Abil, Z., Gumy, L. F., Zhao, H. & Hoogenraad, C. C., Jun 16 2017, In: ACS synthetic biology. 6, 6, p. 950-956 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Carrier Proteins
  • Messenger RNA
  • RNA
  • RNA-Binding Proteins
  • Ligands

• Metabolic engineering of oleaginous yeasts for production of fuels and chemicals

  Shi, S. & Zhao, H., Nov 8 2017, In: Frontiers in Microbiology. 8, NOV, 2185.

  Research output: Contribution to journal › Review article › peer-review

  • Metabolic Engineering
  • Yeasts
  • Genetic Engineering
  • Lipomyces
  • Yarrowia

• Orthogonal Genetic Regulation in Human Cells Using Chemically Induced CRISPR/Cas9 Activators

  Bao, Z., Jain, S., Jaroenpuntaruk, V. & Zhao, H., Apr 21 2017, In: ACS synthetic biology. 6, 4, p. 686-693 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Cells
  • Genes
  • Gene Regulatory Networks
  • Activator Appliances

• Probing the molecular determinants of fluorinase specificity

  Yeo, W. L., Chew, X., Smith, D. J., Chan, K. P., Sun, H., Zhao, H., Lim, Y. H. & Ang, E. L., 2017, In: Chemical Communications. 53, 17, p. 2559-2562 4 p.

  Research output: Contribution to journal › Article › peer-review

  • fluorinase
  • 5'-chloro-5'-deoxyadenosine
  • Substrates

• Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

  Si, T., Li, B., Comi, T. J., Wu, Y., Hu, P., Wu, Y., Min, Y., Mitchell, D. A., Zhao, H. & Sweedler, J. V., Sep 13 2017, In: Journal of the American Chemical Society. 139, 36, p. 12466-12473 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Ionization
  • Mass spectrometry
  • Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
  • Desorption
  • ionization

• Programmable DNA-Guided Artificial Restriction Enzymes

  Enghiad, B. & Zhao, H., May 19 2017, In: ACS synthetic biology. 6, 5, p. 752-757 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Enzymes
  • DNA
  • Pyrococcus furiosus
  • Genetic engineering
  • Cloning

• Strain development by whole-cell directed evolution

  Si, T., Lian, J. & Zhao, H., Jan 1 2017, Directed Enzyme Evolution: Advances and Applications. Springer International Publishing, p. 173-200 28 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • Multifactorial Inheritance
  • Phenotype
  • Workflow
  • Screening
  • Mutation

• SynV and SynX: A story more than DNA synthesis

  Ren, H. & Zhao, H., May 1 2017, In: Science China Life Sciences. 60, 5, p. 558-560 3 p.

  Research output: Contribution to journal › Article › peer-review

• Targeting Specificity of the CRISPR/Cas9 System

  Tasan, I. & Zhao, H., Sep 15 2017, In: ACS synthetic biology. 6, 9, p. 1609-1613 5 p.

  Research output: Contribution to journal › Review article › peer-review

  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Genes
  • Mutagenesis
  • DNA
  • Target tracking

• Twin-primer non-enzymatic DNA assembly: An efficient and accurate multi-part DNA assembly method

  Liang, J., Liu, Z., Low, X. Z., Ang, E. L. & Zhao, H., Jun 1 2017, In: Nucleic acids research. 45, 11, p. e94

  Research output: Contribution to journal › Article › peer-review

  • Plasmids
  • Automation
  • DNA
  • Synthetic Biology
  • Workflow

• Twin-primer non-enzymatic DNA assembly: An efficient and accurate multi-part DNA assembly method

  Liang, J., Liu, Z., Ang, E. L. & Zhao, H., 2017, Synthetic Biology Conference, SEED 2017: Engineering, Evolution, and Design. AIChE, p. 45-46 2 p. (Synthetic Biology Conference, SEED 2017: Engineering, Evolution, and Design).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Using natural products for drug discovery: the impact of the genomics era

  Zhang, M. M., Qiao, Y., Ang, E. L. & Zhao, H., May 4 2017, In: Expert Opinion on Drug Discovery. 12, 5, p. 475-487 13 p.

  Research output: Contribution to journal › Review article › peer-review

  • Drug Discovery
  • Genomics
  • Biological Products
  • Synthetic Biology
  • Metagenomics