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  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 journal › Article › peer-review

  Open Access

  • Genomics
  • Genes
  • Yeasts
  • Basidiomycota
  • Genome

• 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 journal › Article › peer-review

  • Biocatalysis
  • Enzymes
  • Biocatalysts
  • Catalysis

• 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

• Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster

  Luo, Y., Huang, H., Liang, J., Wang, M., Lu, L., Shao, Z., Cobb, R. E. & Zhao, H., Dec 5 2013, In: Nature communications. 4, 2894.

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

  • genes
  • Multigene Family
  • Genes
  • Chemical activation
  • activation

• 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 journal › Article › peer-review

  • Multigene Family
  • Oxazoles
  • non-ribosomal peptide synthase
  • Polyketide Synthases
  • Transcription Factors

• 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 journal › Article › peer-review

  • Taurine
  • Sulfur
  • Bacteria
  • Multigene Family
  • Genes

• 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

• 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 journal › Article › peer-review

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

• A new fluorescence complementation biosensor for detection of estrogenic compounds

  Mclachlan, M. J., Katzenellenbogen, J. A. & Zhao, H., Dec 2011, In: Biotechnology and bioengineering. 108, 12, p. 2794-2803 10 p.

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

  • Estrogens
  • Biosensing Techniques
  • Biosensors
  • Fluorescence
  • Ligands

• 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 journal › Article › peer-review

  • pyrimidine
  • Alanine
  • Nitrogen
  • Degradation
  • Bacteria

• 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 journal › Article › peer-review

  • sulfoacetaldehyde
  • Bacillus (bacteria)
  • Bacillus
  • Bacteria
  • bacterium

• 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

• Aryl-aldehyde formation in fungal polyketides: Discovery and characterization of a distinct biosynthetic mechanism

  Wang, M., Beissner, M. & Zhao, H., Feb 20 2014, In: Chemistry and Biology. 21, 2, p. 257-263 7 p.

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

  • Polyketide Synthases
  • Polyketides
  • Aldehydes
  • non-ribosomal peptide synthase
  • Aspergillus

• 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

• A single-chain TALEN architecture for genome engineering

  Sun, N. & Zhao, H., Mar 1 2014, In: Molecular BioSystems. 10, 3, p. 446-453 8 p.

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

  • Transcription Activator-Like Effector Nucleases
  • Genome
  • DNA Cleavage
  • Peptides
  • Deoxyribonuclease I

• 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

• A type III polyketide synthase from Rhizobium etli condenses malonyl CoAs to a heptaketide pyrone with unusually high catalytic efficiency

  Jeya, M., Kim, T. S., Kumar Tiwari, M., Li, J., Zhao, H. & Lee, J. K., Dec 2012, In: Molecular BioSystems. 8, 12, p. 3103-3106 4 p.

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

  • flavanone synthetase
  • Rhizobium etli
  • Pyrones
  • Malonyl Coenzyme A
  • Acetyl Coenzyme A

• 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

• 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

• Biocatalyst development by directed evolution

  Wang, M., Si, T. & Zhao, H., Jul 2012, In: Bioresource Technology. 115, p. 117-125 9 p.

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

  • Biocatalysts
  • Biocatalysis
  • organic solvent
  • Enzymes
  • mutant

• 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., 2019, In: Biochemical Journal. 476, 4, p. 733-746 14 p.

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

  • sulfoacetaldehyde
  • Short Chain Dehydrogenase-Reductases
  • Klebsiella oxytoca
  • Taurine
  • NADP

• 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 journal › Article › peer-review

  • Ketoglutaric Acids
  • Bifidobacterium
  • Pyridoxal
  • Taurine
  • Pyridoxal Phosphate

• Cell surface display of functional human MHC class II proteins: Yeast display versus insect cell display

  Wen, F., Sethi, D. K., Wucherpfennig, K. W. & Zhao, H., Sep 2011, In: Protein Engineering, Design and Selection. 24, 9, p. 701-709 9 p.

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

  • Fungal Proteins
  • Peptides
  • Yeast
  • Histocompatibility Antigens Class II
  • Insecta

• Challenges and opportunities in synthetic biology for chemical engineers

  Luo, Y., Lee, J. K. & Zhao, H., Nov 5 2013, In: Chemical Engineering Science. 103, p. 115-119 5 p.

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

  • Synthetic Biology
  • Synthetic biology
  • Engineers
  • Modularization
  • Biofuels

• Characterization and application of the Fe(ii) and α-ketoglutarate dependent hydroxylase FrbJ

  Desieno, M. A., Van Der Donk, W. A. & Zhao, H., Sep 28 2011, In: Chemical Communications. 47, 36, p. 10025-10027 3 p.

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

  • Bioassay
  • FR 33289
  • Mixed Function Oxygenases
  • Antimalarials
  • 3-(N-acetyl-N-hydroxy)aminopropylphosphonic acid

• Characterization and engineering of the adenylation domain of a NRPS-like protein: A potential biocatalyst for aldehyde generation

  Wang, M. & Zhao, H., Apr 4 2014, In: ACS Catalysis. 4, 4, p. 1219-1225 7 p.

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

  • non-ribosomal peptide synthase
  • Biocatalysts
  • Aldehydes
  • Peptides
  • Staphylococcal Protein A

• 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

• 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., Sep 2019, In: Biotechnology and bioengineering. 116, 9, p. 2330-2338 9 p.

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

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

• 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., 2019, In: Organic and Biomolecular Chemistry. 17, 6, p. 1506-1518 13 p.

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

  • 3-(N-acetyl-N-hydroxy)aminopropylphosphonic acid
  • Biosynthesis
  • dimethylaniline monooxygenase (N-oxide forming)
  • biosynthesis
  • 4,6-dinitro-o-cresol

• Characterization of the N-oxygenase AurF from Streptomyces thioletus

  Chanco, E., Choi, Y. S., Sun, N., Vu, M. & Zhao, H., Oct 15 2014, In: Bioorganic and Medicinal Chemistry. 22, 20, p. 5569-5577 9 p.

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

  • 4-nitrobenzoic acid
  • Methylphenazonium Methosulfate
  • Oxygenases
  • Streptomyces
  • aureothin

• Cloning and characterization of a galactitol 2-dehydrogenase from Rhizobium legumenosarum and its application in d-tagatose production

  Jagtap, S. S., Singh, R., Kang, Y. C., Zhao, H. & Lee, J. K., May 10 2014, In: Enzyme and Microbial Technology. 58-59, p. 44-51 8 p.

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

  • galactitol 2-dehydrogenase
  • tagatose
  • Rhizobium
  • Oxidoreductases
  • Cloning

• Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae

  Sun, J., Shao, Z., Zhao, H., Nair, N., Wen, F., Xu, J. H. & Zhao, H., Aug 2012, In: Biotechnology and bioengineering. 109, 8, p. 2082-2092 11 p.

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

  • Cloning
  • Yeast
  • Saccharomyces cerevisiae
  • Organism Cloning
  • Xylans

• Cloning and characterization of a type III polyketide synthase from Aspergillus niger

  Li, J., Luo, Y., Lee, J. K. & Zhao, H., Oct 15 2011, In: Bioorganic and Medicinal Chemistry Letters. 21, 20, p. 6085-6089 5 p.

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

  • flavanone synthetase
  • Aspergillus
  • Aspergillus niger
  • Cloning
  • benzoyl-coenzyme A

• CmlI is an N-oxygenase in the biosynthesis of chloramphenicol

  Lu, H., Chanco, E. & Zhao, H., Sep 16 2012, In: Tetrahedron. 68, 37, p. 7651-7654 4 p.

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

  • Biosynthesis
  • Oxygenases
  • Chloramphenicol
  • Enzymes
  • Ferrozine

• Combinatorial design of a highly efficient xylose-utilizing pathway in Saccharomyces cerevisiae for the production of cellulosic biofuels

  Kim, B., Du, J., Eriksen, D. T. & Zhao, H., Feb 2013, In: Applied and environmental microbiology. 79, 3, p. 931-941 11 p.

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

  • Biofuels
  • Xylose
  • biofuel
  • xylose
  • biofuels

• 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

• 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

• 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

• Comparative biochemical characterization of three exolytic oligoalginate lyases from Vibrio splendidus reveals complementary substrate scope, temperature, and pH adaptations

  Jagtap, S. S., Hehemann, J. H., Polz, M. F., Lee, J. K. & Zhao, H., 2014, In: Applied and environmental microbiology. 80, 14, p. 4207-4214 8 p.

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

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

• 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

• 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

• Cooperative tandem catalysis by an organometallic complex and a metalloenzyme

  Denard, C. A., Huang, H., Bartlett, M. J., Lu, L., Tan, Y., Zhao, H. & Hartwig, J. F., Jan 7 2014, In: Angewandte Chemie - International Edition. 53, 2, p. 465-469 5 p.

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

  • Organometallics
  • Catalysis
  • Catalysts
  • Alkenes
  • Olefins

• Coordinated induction of multi-gene pathways in Saccharomyces cerevisiae

  Liang, J., Ning, J. C. & Zhao, H., Feb 2013, In: Nucleic acids research. 41, 4, p. e54

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

  • Saccharomyces cerevisiae
  • Zeaxanthins
  • Genes
  • Switch Genes
  • Biosynthetic Pathways

• 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

• 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

• 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

• Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration

  Zou, Y., Zhang, H., Brunzelle, J. S., Johannes, T. W., Woodyer, R., Hung, J. E., Nair, N., Van Der Donk, W. A., Zhao, H. & Nair, S. K., May 29 2012, In: Biochemistry. 51, 21, p. 4263-4270 8 p.

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

  • NAD phosphite oxidoreductase
  • Crystal structure
  • Niacinamide
  • Regeneration
  • NAD

• Customized optimization of metabolic pathways by combinatorial transcriptional engineering

  Du, J., Yuan, Y., Si, T., Lian, J. & Zhao, H., Oct 2012, In: Nucleic acids research. 40, 18, p. e142

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

  • Metabolic Networks and Pathways
  • Cellobiose
  • Xylose
  • Synthetic Biology
  • Metabolic Engineering

• Customized optimization of metabolic pathways by combinatorial transcriptional engineering.

  Yuan, Y., Du, J. & Zhao, H., Aug 2 2013, In: Methods in molecular biology (Clifton, N.J.). 985, p. 177-209 33 p.

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

  • Metabolic Networks and Pathways
  • Cellobiose
  • Synthetic Biology
  • Metabolic Engineering
  • Xylose

• Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains

  Lian, J., Si, T., Nair, N. U. & Zhao, H., Jul 2014, In: Metabolic Engineering. 24, p. 139-149 11 p.

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

  • Acetyl Coenzyme A
  • Butenes
  • Yeast
  • 1-Butanol
  • Saccharomyces cerevisiae