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• 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 journal › Review article › peer-review

  • Synthetic biology
  • Synthetic Biology
  • Government Agencies
  • Biological systems

• Accelerated genome engineering through multiplexing

  Bao, Z., Cobb, R. E. & Zhao, H., Jan 1 2016, In: Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 8, 1, p. 5-21 17 p.

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

  • Multiplexing
  • Genes
  • Genome
  • Bioengineering
  • Gene Editing

• ACS Catalysis and the Scope of Papers Sought in Three Catalysis Subdisciplines: Biocatalysis and Enzymology, Molecular Catalysis for Organic Synthesis, and Heterogeneous Photocatalysis

  Chang, S., Fornasiero, P., Gunnoe, T. B., Jones, C. W., Linic, S., Ooi, T., Williams, R. M. & Zhao, H., Jul 1 2016, In: ACS Catalysis. 6, 7, p. 4782-4785 4 p.

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

• 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 journal › Article › peer-review

  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Yeast
  • Saccharomyces cerevisiae
  • 2,3-butylene glycol
  • Xylose

• A step through the looking glass

  Liang, Y., Ang, E. L. & Zhao, H., Sep 1 2016, In: Science China Life Sciences. 59, 9, p. 979-980 2 p.

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

• Biocatalysis for Drug Discovery and Development

  Liang, Y., Zhang, M. M., Ang, E. L. & Zhao, H., May 13 2016, Green Biocatalysis. Wiley, p. 421-455 35 p.

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

  • Biocatalysis
  • Drug Discovery
  • Drug products
  • Enzymes
  • Biocatalysts

• 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 journal › Article › peer-review

  • Fluorescence imaging
  • Bacilli
  • Biofilms
  • Mass spectrometry
  • Optical Imaging

• 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 journal › Article › peer-review

  • 3-(N-acetyl-N-hydroxy)aminopropylphosphonic acid
  • Antimalarials
  • Libraries
  • Screening
  • Organophosphonates

• Combined and iterative use of computational design and directed evolution for protein-ligand binding design

  Wang, M. & Zhao, H., May 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 139-153 15 p. (Methods in Molecular Biology; vol. 1414).

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

  • Protein Binding
  • Switch Genes
  • Ligands
  • Two-Hybrid System Techniques
  • Mutagenesis

• Construction of plasmids with tunable copy numbers in Saccharomyces cerevisiae and their applications in pathway optimization and multiplex genome integration

  Lian, J., Jin, R. & Zhao, H., Nov 1 2016, In: Biotechnology and bioengineering. 113, 11, p. 2462-2473 12 p.

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

  • Antibiotics
  • Yeast
  • Saccharomyces cerevisiae
  • Genes
  • Butenes

• 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 journal › Article › peer-review

  • Cyanobacteria
  • Mutagenesis
  • Synechococcus
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • CRISPR-Associated Protein 9

• Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae

  Wang, M., Li, S. & Zhao, H., Jan 1 2016, In: Biotechnology and bioengineering. 113, 1, p. 206-215 10 p.

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

  • Xylose
  • Metabolites
  • Yeast
  • Gene Regulatory Networks
  • Gene expression

• 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 journal › Article › peer-review

  • 5'-fluoro-5'-deoxyadenosine
  • fluorinase
  • 5'-chloro-5'-deoxyadenosine
  • Fluorination
  • Methionine

• 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

• 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

• 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

• 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

• 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)

• 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

• 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-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

• Identification and engineering of n-butanol biosensors by transcriptome analysis in yeast

  Shi, S., Ang, E. L., Tan, M. H. & Zhao, H., Jan 1 2016, Metabolic Engineering 11. AIChE, p. 458-459 2 p. (Metabolic Engineering 11).

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

• Identification of an important motif that controls the activity and specificity of sugar transporters

  Wang, M., Yu, C. & Zhao, H., Jul 1 2016, In: Biotechnology and bioengineering. 113, 7, p. 1460-1467 8 p.

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

  • Xylose
  • Sugars
  • Glucose
  • xylose-glucose
  • Facilitative Glucose Transport Proteins

• Members of the rusc protein family interact with Sufu and inhibit vertebrate hedgehog signaling

  Jin, Z., Schwend, T., Fu, J., Bao, Z., Liang, J., Zhao, H., Mei, W. & Yang, J., Nov 1 2016, In: Development (Cambridge). 143, 21, p. 3944-3955 12 p.

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

  • Hedgehogs
  • vertebrate
  • Vertebrates
  • family
  • protein

• 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 journal › Article › peer-review

  • 1-Butanol
  • Metabolic Engineering
  • Saccharomyces cerevisiae
  • citramalate
  • Threonine

• 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 journal › Article › peer-review

  • cetyl alcohol
  • Metabolic engineering
  • Xylose
  • Metabolic Engineering
  • Fatty Alcohols

• New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters

  Luo, Y., Enghiad, B. & Zhao, H., Feb 2016, In: Natural Product Reports. 33, 2, p. 174-182 9 p.

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

  • Multigene Family
  • Biological Products
  • Genes
  • Metabolic engineering
  • Synthetic biology

• 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 journal › Article › peer-review

  • sugar beets
  • Sugar beets
  • adipic acid
  • Catalysis
  • catalysis

• 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 journal › Article › peer-review

  • Yeast
  • Fermentation
  • Galactose
  • Saccharomyces cerevisiae
  • Ethanol

• RNAi-assisted genome evolution (RAGE) in Saccharomyces cerevisiae

  Si, T. & Zhao, H., Jan 1 2016, In: Methods in Molecular Biology. 1470, p. 183-198 16 p.

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

  • RNA Interference
  • Saccharomyces cerevisiae
  • Genome
  • Acetic Acid
  • Libraries

• 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 journal › Review article › peer-review

  • Synthetic biology
  • Synthetic Biology
  • Biological Products
  • Standardization
  • Multigene Family

• 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 journal › Article › peer-review

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

• 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 journal › Review article › peer-review

  • Biocatalysts
  • catalysts
  • Catalysis
  • Catalysts
  • catalysis

• Use of genome-editing tools to treat sickle cell disease

  Tasan, I., Jain, S. & Zhao, H., Sep 1 2016, In: Human Genetics. 135, 9, p. 1011-1028 18 p.

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

  • Gene Editing
  • Sickle Cell Anemia
  • Globins
  • CRISPR-Associated Protein 9
  • Zinc Finger Nucleases
• 2015

  Alginate lyases from alginate-degrading Vibrio splendidus 12B01 are endolytic

  Badur, A. H., Jagtap, S. S., Yalamanchili, G., Lee, J. K., Zhao, H. & Rao, C. V., Jan 1 2015, In: Applied and environmental microbiology. 81, 5, p. 1865-1873 9 p.

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

  • poly(beta-D-mannuronate) lyase
  • Vibrio splendidus
  • alginate lyase
  • Vibrio
  • alginate

• A Rewritable, Random-Access DNA-Based Storage System

  Tabatabaei Yazdi, S. M. H., Yuan, Y., Ma, J., Zhao, H. & Milenkovic, O., Sep 18 2015, In: Scientific reports. 5, 14138.

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

  • DNA
  • Information Storage and Retrieval
  • Sensitivity and Specificity

• Building biological foundries for next-generation synthetic biology

  Chao, R., Yuan, Y. B. & Zhao, H. M., Jul 24 2015, In: Science China Life Sciences. 58, 7, p. 658-665 8 p.

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

  • Synthetic biology
  • Synthetic Biology
  • synthetic biology
  • Foundries
  • Metabolites

• Chromatin architecture reorganization during stem cell differentiation

  Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V. V., Ecker, J. R., Thomson, J. A. & Ren, B., Feb 19 2015, In: Nature. 518, 7539, p. 331-336 6 p.

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

  • Chromatin
  • Cell Differentiation
  • Stem Cells
  • Human Embryonic Stem Cells
  • Cell Lineage

• 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 journal › Article › peer-review

  • Ruthenium
  • Alkenes
  • Epoxy Compounds
  • Olefins
  • Enantioselectivity

• Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening

  Li, S., Si, T., Wang, M. & Zhao, H., Dec 18 2015, In: ACS synthetic biology. 4, 12, p. 1308-1315 8 p.

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

  • Malonyl Coenzyme A
  • Metabolites
  • Yeast
  • Genetic Testing
  • Screening

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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 journal › Article › peer-review

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

• Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB)

  Zhao, H., Jan 1 2015, Synthetic Biology: Engineering, Evolution, and Design Conference 2015, SEED 2015. AIChE, p. 784-785 2 p. (Synthetic Biology: Engineering, Evolution, and Design Conference 2015, SEED 2015; vol. 2).

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

• 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 journal › Review article › peer-review

  • Enzymes
  • Stereoselectivity
  • Biocatalysis
  • Chemical reactivity
  • Protein Engineering