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2017

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

genome
yeast
Yeast
Genes
Yeasts

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 journalArticle

Phosphonoacetic Acid
Multigene Family
Biological Products
Genes
Acids
2015

Improving and repurposing biocatalysts via directed evolution

Denard, C. A., Ren, H. & Zhao, H., Apr 1 2015, In : Current Opinion in Chemical Biology. 25, p. 55-64 10 p.

Research output: Contribution to journalReview article

Enzymes
Biocatalysis
Protein Engineering
Stereoselectivity
Chemical reactivity
2019

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

Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Cas Systems
Genes
Streptococcus thermophilus
Francisella tularensis
2015

Development of a One-Pot tandem reaction combining ruthenium-catalyzed alkene metathesis and enantioselective enzymatic oxidation to produce Aryl epoxides

Denard, C. A., Bartlett, M. J., Wang, Y., Lu, L., Hartwig, J. F. & Zhao, H., Jun 5 2015, In : ACS Catalysis. 5, 6, p. 3817-3822 6 p.

Research output: Contribution to journalArticle

Ruthenium
Epoxy Compounds
Alkenes
Olefins
Oxidation
2016

Standardization for natural product synthetic biology

Zhao, H. & Medema, M. H., Aug 2016, In : Natural Product Reports. 33, 8, p. 920-924 5 p.

Research output: Contribution to journalReview article

Synthetic Biology
Biological Products
Standardization
Multigene Family
Genes
2015

Metabolic engineering of Saccharomyces cerevisiae to improve 1-hexadecanol production

Feng, X., Lian, J. & Zhao, H., Jan 1 2015, In : Metabolic Engineering. 27, p. 10-19 10 p.

Research output: Contribution to journalArticle

Metabolic engineering
Metabolic Engineering
Yeast
Saccharomyces cerevisiae
Genes
2016

A brief overview of synthetic biology research programs and roadmap studies in the United States

Si, T. & Zhao, H., Dec 1 2016, In : Synthetic and Systems Biotechnology. 1, 4, p. 258-264 7 p.

Research output: Contribution to journalReview article

Synthetic Biology
Research
Government Agencies
Biological systems
2019

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

Enzymes
Biocatalysts
Catalysis
Biocatalysis
2018

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

Biofuels
Microorganisms
Enzymes
Pharmaceutical Preparations
2015

Orthogonal Fatty Acid Biosynthetic Pathway Improves Fatty Acid Ethyl Ester Production in Saccharomyces cerevisiae

Eriksen, D. T., HamediRad, M., Yuan, Y. & Zhao, H., Jul 17 2015, In : ACS synthetic biology. 4, 7, p. 808-814 7 p.

Research output: Contribution to journalArticle

Biosynthetic Pathways
Fatty acids
Yeast
Saccharomyces cerevisiae
Esters
2016

Tandem reactions combining biocatalysts and chemical catalysts for asymmetric synthesis

Wang, Y. & Zhao, H., Dec 1 2016, In : Catalysts. 6, 12, 194.

Research output: Contribution to journalReview article

Biocatalysts
catalysts
Catalysis
Catalysts
catalysis
2015

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 journalArticle

RNA-Binding Proteins
Transcriptome
Protein Engineering
RNA
Biological Phenomena
2016

Production of Adipic Acid from Sugar Beet Residue by Combined Biological and Chemical Catalysis

Zhang, H., Li, X., Su, X., Ang, E. L., Zhang, Y. & Zhao, H., Apr 20 2016, In : ChemCatChem. 8, 8, p. 1500-1506 7 p.

Research output: Contribution to journalArticle

sugar beets
Sugar beets
Catalysis
catalysis
acids

Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae

Shi, S., Si, T., Liu, Z., Zhang, H., Ang, E. L. & Zhao, H., May 10 2016, In : Scientific reports. 6, 25675.

Research output: Contribution to journalArticle

Metabolic Engineering
1-Butanol
Saccharomyces cerevisiae
Threonine
Yeasts

Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae

Quarterman, J., Skerker, J. M., Feng, X., Liu, I. Y., Zhao, H., Arkin, A. P. & Jin, Y. S., Jul 10 2016, In : Journal of Biotechnology. 229, p. 13-21 9 p.

Research output: Contribution to journalArticle

Galactose
Yeast
Fermentation
Saccharomyces cerevisiae
Ethanol

A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae

Shi, S., Liang, Y., Zhang, M. M., Ang, E. L. & Zhao, H., Jan 1 2016, In : Metabolic Engineering. 33, p. 19-27 9 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Yeast
Saccharomyces cerevisiae
Xylose
Genes
2015

RNAi-assisted genome evolution in saccharomyces cerevisiae for complex phenotype engineering

Si, T., Luo, Y., Bao, Z. & Zhao, H., Mar 20 2015, In : ACS synthetic biology. 4, 3, p. 283-291 9 p.

Research output: Contribution to journalArticle

RNA Interference
RNA
Yeast
Saccharomyces cerevisiae
Genes
2016

Combinatorial pathway engineering for optimized production of the anti-malarial FR900098

Freestone, T. S. & Zhao, H., Feb 1 2016, In : Biotechnology and bioengineering. 113, 2, p. 384-392 9 p.

Research output: Contribution to journalArticle

Antimalarials
Libraries
Screening
Organophosphonates
Throughput

Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate

Sun, H., Yeo, W. L., Lim, Y. H., Chew, X., Smith, D. J., Xue, B., Chan, K. P., Robinson, R. C., Robins, E. G., Zhao, H. & Ang, E. L., Jan 1 2016, In : Angewandte Chemie - International Edition. 55, 46, p. 14277-14280 4 p.

Research output: Contribution to journalArticle

Fluorination
Methionine
Kinetics
Substrates
5'-fluoro-5'-deoxyadenosine
2015

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 journalEditorial

Synthetic Biology
Genetic Engineering
Biosensing Techniques
2016

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 proceedingChapter

High-throughput Screening
Enzymes
Engineering

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 journalArticle

DNA
Plasmids
Ligases
Yeast
Networks (circuits)
2019

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

Peptide Library
T-Lymphocyte Epitopes
Major Histocompatibility Complex
Yeasts
Peptides
2018
Biocatalysis
Enzymes
Synthetic Biology
Metabolic engineering
Metabolic Engineering

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

Metabolic engineering
Metabolic Engineering
Yeast
Saccharomyces cerevisiae
Clustered Regularly Interspaced Short Palindromic Repeats
2015

Industrial biotechnology: Tools and applications

Zhao, H. & Tan, T., Nov 15 2015, In : Biotechnology Advances. 33, 7, p. 1393-1394 2 p.

Research output: Contribution to journalEditorial

Biotechnology
Industry
2019

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

Software Design
Point Mutation
Cicatrix
DNA
Software design
2015

Rapid prototyping of microbial cell factories via genome-scale engineering

Si, T., Xiao, H. & Zhao, H., Nov 15 2015, In : Biotechnology Advances. 33, 7, p. 1420-1432 13 p.

Research output: Contribution to journalReview article

Rapid prototyping
Industrial plants
Genes
Genome
Biological systems
2019

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

Clustered Regularly Interspaced Short Palindromic Repeats
Gene Knockout Techniques
Gene Deletion
Guide RNA
Genes

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
Genomics
Genes
Yeasts
Genome
Basidiomycota
2015

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 journalArticle

Biosynthesis
Biological Products
Genes
Polyketides
Terpenes
2017
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Ionization
Mass spectrometry
Desorption
Mass Spectrometry
2015

Structure-guided design and biosynthesis of a novel FR-900098 analogue as a potent Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr) inhibitor

Cobb, R. E., Bae, B., Li, Z., Desieno, M. A., Nair, S. K. & Zhao, H., Feb 14 2015, In : Chemical Communications. 51, 13, p. 2526-2528 3 p.

Research output: Contribution to journalArticle

Biosynthesis
Phosphates
Antimalarials
Derivatives
xylulose-5-phosphate
2016

CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973

Wendt, K. E., Ungerer, J., Cobb, R. E., Zhao, H. & Pakrasi, H. B., Jun 23 2016, In : Microbial cell factories. 15, 1, 115.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Synechococcus
Mutagenesis
Cyanobacteria
Genes

Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose

Guo, W., Sheng, J., Zhao, H. & Feng, X., Feb 1 2016, In : Microbial cell factories. 15, 1, 24.

Research output: Contribution to journalArticle

Metabolic engineering
Metabolic Engineering
Xylose
Fatty Alcohols
Yeast
2019

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

Bifidobacterium
Taurine
Pyridoxal
Transaminases
Pyridoxal Phosphate

A pathway for isethionate dissimilation in Bacillus krulwichiae

Tong, Y., Wei, Y., Hu, Y., Ang, E. L., Zhao, H. & Zhang, Y., Jan 1 2019, In : Applied and environmental microbiology. 85, 15, e00793-19.

Research output: Contribution to journalArticle

Bacillus (bacteria)
Bacillus
Bacteria
bacterium
bacteria
2017

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 journalArticle

Plasmids
Automation
DNA
Synthetic Biology
Workflow
2015

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., May 15 2015, In : ACS synthetic biology. 4, 5, p. 585-594 10 p.

Research output: Contribution to journalArticle

CRISPR-Associated Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
Yeast
Saccharomyces cerevisiae
Genes
2016

TALE proteins search DNA using a rotationally decoupled mechanism

Cuculis, L., Abil, Z., Zhao, H. & Schroeder, C. M., Oct 1 2016, In : Nature chemical biology. 12, 10, p. 831-837 7 p.

Research output: Contribution to journalArticle

DNA
DNA-Binding Proteins
Proteins
Nucleic Acid Conformation
Transcription Activator-Like Effectors
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

Ointments
Genes
Homologous Recombination
Genome
Synthetic Biology
2016
Antibiotics
Yeast
Saccharomyces cerevisiae
Plasmids
Genes
2019

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
biotechnology
Biotechnology
organisms
Testing
Research
2017

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

Workflow
Biological Products
Yeast
Escherichia coli
Saccharomyces cerevisiae
2016

Characterization of bacillus subtilis colony biofilms via mass spectrometry and fluorescence imaging

Si, T., Li, B., Zhang, K., Xu, Y., Zhao, H. & Sweedler, J. V., Jun 3 2016, In : Journal of Proteome Research. 15, 6, p. 1955-1962 8 p.

Research output: Contribution to journalArticle

Optical Imaging
Biofilms
Bacilli
Bacillus subtilis
Mass spectrometry
2018

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

Nucleotides
Yeast
Saccharomyces cerevisiae
Clustered Regularly Interspaced Short Palindromic Repeats
Genes

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

CRISPR-Associated Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
Nucleic Acid Repetitive Sequences
Genome
HCT116 Cells
2015

In Situ Assembly of Antifouling/Bacterial Silver Nanoparticle-Hydrogel Composites with Controlled Particle Release and Matrix Softening

Baek, K., Liang, J., Lim, W. T., Zhao, H., Kim, D. H. & Kong, H., Jul 22 2015, In : ACS Applied Materials and Interfaces. 7, 28, p. 15359-15367 9 p.

Research output: Contribution to journalArticle

Hydrogel
Silver
Hydrogels
Particles (particulate matter)
Nanoparticles
2019

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.

Research output: Contribution to journalArticle

Gene Knock-In Techniques
Ribonucleoproteins
Neoplastic Stem Cells
HEK293 Cells
DNA