Find Research Outputs

Search results

• Directed evolution of the nonribosomal peptide synthetase AdmK generates new andrimid derivatives in vivo

  Evans, B. S., Chen, Y., Metcalf, W. W., Zhao, H. & Kelleher, N. L., May 27 2011, In: Chemistry and Biology. 18, 5, p. 601-607 7 p.

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

  • andrimid
  • non-ribosomal peptide synthase
  • Reengineering
  • Derivatives
  • Secondary Metabolism

• Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization

  Wang, M., Yu, C. & Zhao, H., Mar 1 2016, In: Biotechnology and bioengineering. 113, 3, p. 484-491 8 p.

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

  • xylose-glucose
  • Xylose
  • Glucose
  • Neurospora crassa
  • Biofuels

• 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

• Direct observation of TALE protein dynamics reveals a two-state search mechanism

  Cuculis, L., Abil, Z., Zhao, H. & Schroeder, C. M., Jun 1 2015, In: Nature communications. 6, 7277.

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

  • Transcription Activator-Like Effectors
  • effectors
  • proteins
  • Observation
  • deoxyribonucleic acid

• Discovery and Characterization of a Class IV Lanthipeptide with a Nonoverlapping Ring Pattern

  Ren, H., Shi, C., Bothwell, I. R., Van Der Donk, W. A., Van Der Donk, W. A., Van Der Donk, W. A., Zhao, H., Zhao, H., Zhao, H., Zhao, H. & Zhao, H., Jun 19 2020, In: ACS chemical biology. 15, 6, p. 1642-1649 8 p.

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

  • Aminopeptidases
  • Streptomyces
  • Cyclization
  • Endopeptidases
  • Bioactivity

• 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

• Divalent cations promote TALE DNA-binding specificity

  Cuculis, L., Zhao, C., Abil, Z., Zhao, H., Shukla, D. & Schroeder, C. M., Feb 20 2020, In: Nucleic acids research. 48, 3, p. 1406-1422 17 p.

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

  Open Access

  • Gene Editing
  • Divalent Cations
  • Transcription Activator-Like Effector Nucleases
  • DNA
  • Monovalent Cations

• DNA assembler: A synthetic biology tool for characterizing and engineering natural product gene clusters

  Shao, Z. & Zhao, H., 2012, Natural Product Biosynthesis by Microorganisms and Plants, Part C. Academic Press Inc., p. 203-224 22 p. (Methods in Enzymology; vol. 517).

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

  • Biosynthetic Pathways
  • Synthetic biology
  • Synthetic Biology
  • Multigene Family
  • Biological Products

• DNA assembler method for construction of zeaxanthin-producing strains of saccharomyces cerevisiae

  Shao, Z., Luo, Y. & Zhao, H., 2012, Microbial Carotenoids From Fungi: Methods and Protocols. Jose-Luis, B. (ed.). p. 251-262 12 p. (Methods in Molecular Biology; vol. 898).

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

  • Zeaxanthins
  • Saccharomyces cerevisiae
  • Synthetic Biology
  • Metabolic Engineering
  • Biosynthetic Pathways

• DNA assembly techniques for next-generation combinatorial biosynthesis of natural products

  Cobb, R. E., Ning, J. C. & Zhao, H., Feb 2014, In: Journal of Industrial Microbiology and Biotechnology. 41, 2, p. 469-477 9 p.

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

  • Biosynthesis
  • DNA
  • Biological Products
  • Biosynthetic Pathways
  • Synthetic biology

• DNA-Based Storage: Trends and Methods

  Yazdi, S. M. H. T., Kiah, H. M., Garcia-Ruiz, E., Ma, J., Zhao, H. & Milenkovic, O., Sep 2015, In: IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. 1, 3, p. 230-248 19 p., 7423733.

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

  • DNA
  • Trends
  • Storage System
  • Archives
  • Random Access

• DNA punch cards for storing data on native DNA sequences via enzymatic nicking

  Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J. P., Soloveichik, D., Zhao, H. & Milenkovic, O., Dec 1 2020, In: Nature communications. 11, 1, 1742.

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

  Open Access

  • punches
  • DNA sequences
  • cards
  • deoxyribonucleic acid
  • DNA

• Drug Discovery and Development by Combinatorial Biosynthesis

  Desieno, M. A., Denard, C. A. & Zhao, H., May 25 2011, Enzyme Technologies: Metagenomics, Evolution, Biocatalysis, and Biosynthesis. John Wiley and Sons, p. 251-283 33 p.

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

• Drug Discovery and Development via Synthetic Biology

  Cobb, R. E., Luo, Y., Freestone, T. & Zhao, H., Aug 27 2013, Synthetic Biology. Elsevier Inc., p. 183-206 24 p.

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

  • Synthetic biology
  • Synthetic Biology
  • Drug Discovery
  • Multigene Family
  • Biological Products

• Editorial: Synthetic biology and bioinformatics

  Medema, M. H. & Zhao, H., Aug 2016, In: Natural Product Reports. 33, 8, p. 913-914 2 p.

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

• Editorial overview: Opportunities and challenges in synthetic biology

  Chang, M. C. Y. & Zhao, H., Oct 1 2015, In: Current Opinion in Chemical Biology. 28, p. 5-6 2 p.

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

• Emerging molecular biology tools and strategies for engineering natural product biosynthesis

  Xu, W., Klumbys, E., Ang, E. L. & Zhao, H., Jun 2020, In: Metabolic Engineering Communications. 10, e00108.

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

  Open Access

  • Biosynthesis
  • Molecular biology
  • Biological Products
  • Molecular Biology
  • Enzymes

• Engineered biosynthesis of natural products in heterologous hosts

  Luo, Y., Li, B. Z., Liu, D., Zhang, L., Chen, Y., Jia, B., Zeng, B. X., Zhao, H. & Yuan, Y. J., Aug 7 2015, In: Chemical Society Reviews. 44, 15, p. 5265-5290 26 p.

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

  • Biosynthesis
  • Biological Products
  • Genes
  • Polyketides
  • Terpenes

• 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

• Engineered minicellulosomes for consolidated bioprocessing

  Liang, Y., Ang, E. L. & Zhao, H., Jul 11 2016, Handbook of Carbohydrate-Modifying Biocatalysts. Pan Stanford Publishing Pte. Ltd., Vol. 2. p. 965-992 28 p.

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

• Engineered pentafunctional minicellulosome for simultaneous saccharification and ethanol fermentation in Saccharomyces cerevisiae

  Liang, Y., Si, T., Ang, E. L. & Zhao, H., Jan 1 2014, In: Applied and environmental microbiology. 80, 21, p. 6677-6684 8 p.

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

  • ethanol fermentation
  • saccharification
  • Fermentation
  • yeast
  • ethanol

• 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

• Engineering chimeric RNA-binding proteins: Modular design, novel function

  Abil, Z., Denard, C. A., Hoogenraad, C. & Zhao, H., Jan 1 2014, Food, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting. AIChE, 1 p. (Food, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting; vol. 2).

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

• Engineering microbial factories for synthesis of value-added products

  Du, J., Shao, Z. & Zhao, H., Aug 2011, In: Journal of Industrial Microbiology and Biotechnology. 38, 8, p. 873-890 18 p.

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

  • Biofuels
  • Industrial plants
  • Alkaloids
  • Flavonoids
  • lignocellulose

• Engineering microbial hosts for production of bacterial natural products

  Zhang, M. M., Wang, Y., Ang, E. L. & Zhao, H., Aug 2016, In: Natural Product Reports. 33, 8, p. 963-987 25 p.

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

  • Biological Products
  • Actinobacteria
  • Genetic Engineering
  • Genetic engineering
  • Fermentation

• Engineering novel tandem catalytic reactions using organometallic catalysts and metalloenzymes

  Denard, C. A., Huang, H., Lu, L., Bartlett, M. J., Hartwig, J. F. & Zhao, H., Jan 1 2013, Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future. AIChE, 1 p. (Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future).

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

• Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome

  Abil, Z. & Zhao, H., Jul 6 2015, In: Molecular BioSystems. 11, 10, p. 2658-2665 8 p.

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

  • RNA-Binding Proteins
  • Transcriptome
  • Protein Engineering
  • RNA
  • RNA-Binding Motifs

• Engineering saccharomyces cerevisiae for biofuel production from lignocellulosic biomass

  Du, J. & Zhao, H., Dec 1 2011, 11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings. (11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings).

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

  • Pentoses
  • Biofuels
  • Yeast
  • Biomass
  • Xylose

• Evolutionary context-integrated deep sequence modeling for protein engineering

  Luo, Y., Vo, L., Ding, H., Su, Y., Liu, Y., Qian, W. W., Zhao, H. & Peng, J., 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 261-263 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12074 LNBI).

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

  • Protein
  • Proteins
  • Engineering
  • Fitness Landscape
  • Modeling

• 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

• Exploiting Issatchenkia orientalis SD108 for succinic acid production

  Xiao, H., Shao, Z., Jiang, Y., Dole, S. & Zhao, H., Aug 27 2014, In: Microbial cell factories. 13, 1, 121.

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

  • Organic acids
  • Succinic Acid
  • Acids
  • Yeast
  • Toxicity

• FairyTALE: A high-throughput TAL effector synthesis platform

  Liang, J., Chao, R., Abil, Z., Bao, Z. & Zhao, H., Feb 21 2014, In: ACS synthetic biology. 3, 2, p. 67-73 7 p.

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

  • Transcription Activator-Like Effectors
  • Transcription
  • Throughput
  • DNA sequences
  • Transcription Activator-Like Effector Nucleases

• Fine-tuning the regulation of Cas9 expression levels for efficient CRISPR-Cas9 mediated recombination in Streptomyces

  Ye, S., Enghiad, B., Zhao, H. & Takano, E., May 1 2020, In: Journal of Industrial Microbiology and Biotechnology. 47, 4-5, p. 413-423 11 p.

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

  Open Access

  • Gene Editing
  • Streptomyces
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Genetic Recombination
  • Genes

• Flexible and Versatile Strategy for the Construction of Large Biochemical Pathways

  Yuan, Y., Andersen, E. & Zhao, H., Jan 15 2016, In: ACS synthetic biology. 5, 1, p. 46-52 7 p.

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

  • DNA
  • Plasmids
  • Yeast
  • Ligases
  • Networks (circuits)

• 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

• Functional Reconstitution of a Pyruvate Dehydrogenase in the Cytosol of Saccharomyces cerevisiae through Lipoylation Machinery Engineering

  Lian, J. & Zhao, H., Jul 15 2016, In: ACS synthetic biology. 5, 7, p. 689-697 9 p.

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

  • Oxidoreductases
  • Lipoylation
  • Yeast
  • Pyruvic Acid
  • Cytosol

• Further biochemical studies on aminopyrrolnitrin oxygenase (PrnD)

  Tiwari, M. K., Lee, J. K., Moon, H. J. & Zhao, H., May 15 2011, In: Bioorganic and Medicinal Chemistry Letters. 21, 10, p. 2873-2876 4 p.

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

  • Dimerization
  • Mutagenesis
  • Oxygenases
  • Escherichia coli
  • Catalyst activity

• Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae

  Ghosh, A., Zhao, H. & Price, N. D., Nov 4 2011, In: PloS one. 6, 11, e27316.

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

  • Pentoses
  • Xylose
  • Yeast
  • Arabinose
  • pentoses

• 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-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

  Suthers, P. F., Dinh, H. V., Fatma, Z., Shen, Y., Chan, S. H. J., Rabinowitz, J. D., Zhao, H. & Maranas, C. D., Dec 2020, In: Metabolic Engineering Communications. 11, p. e00148

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

  • Organic acids
  • Biomass
  • Yeast
  • Genes
  • Yeasts

• 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

• Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae

  Xiao, H. & Zhao, H., May 23 2014, In: Biotechnology for Biofuels. 7, 1, 78.

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

  • Furaldehyde
  • SUMO-1 Protein
  • Furfural
  • RNA
  • Yeast

• High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System

  Wang, Y., Cobb, R. E. & Zhao, H., 2016, Methods in Enzymology. O'Connor, S. E. (ed.). Academic Press Inc., p. 271-284 14 p. (Methods in Enzymology; vol. 575).

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

  • CRISPR-Cas Systems
  • Gene Editing
  • Streptomyces
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Genes

• High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

  Cobb, R. E., Wang, Y. & Zhao, H., Jun 19 2015, In: ACS synthetic biology. 4, 6, p. 723-728 6 p.

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

  • CRISPR-Cas Systems
  • Gene Editing
  • Streptomyces
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Genes

• Highlights of biocatalysis and biomimetic catalysis

  Zhao, H., Sep 2 2011, In: ACS Catalysis. 1, 9, p. 1119-1120 2 p.

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

• 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 journal › Article › peer-review

  • Software Design
  • Point Mutation
  • Cicatrix
  • DNA
  • Software design

• High throughput screening and selection methods for directed enzyme evolution

  Xiao, H., Bao, Z. & Zhao, H., Apr 29 2015, In: Industrial and Engineering Chemistry Research. 54, 16, p. 4011-4020 10 p.

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

  • Enzymes
  • Screening
  • Throughput
  • Costs

• High-throughput screening or selection methods for evolutionary enzyme engineering

  Shi, S., Zhang, H., Ang, E. L. & Zhao, H., May 17 2016, Understanding Enzymes: Function, Design, Engineering and Analysis. Pan Stanford Publishing Pte. Ltd., p. 707-744 38 p.

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

• Homology-integrated CRISPR-cas (HI-CRISPR) system for one-step multigene disruption in saccharomyces cerevisiae

  Bao, Z., Xiao, H., Liang, J., Zhang, L., Xiong, X., Sun, N., Si, T. & Zhao, H., Jan 1 2014, Food, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting. AIChE, p. 27-36 10 p. (Food, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting; vol. 1).

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

  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Yeast
  • gene targeting
  • Saccharomyces cerevisiae
  • Genes