Harnessing the Power of Synthetic Biology

Developing and applying synthetic biology tools to address society's most daunting challenges in human health and energy, and investigating the fundamental aspects of enzyme catalysis, cell metabolism, and gene regulation. Read More

Highlights

Synthetic Biology: Tools and Applications. (H. Zhao, ed.) Academic Press, 2013

List of Publications

164. T. Si, Y. Luo, and H. Xiao, and H. Zhao.“Utilizing an Endogenous Pathway for 1-Butanol Production in Saccharomyces cerevisiae.” Metabolic Engineering, accepted.

163. M. Wang, M. Beissner, and H. Zhao.“Aryl-aldehyde Formation in Fungal Polyketides: Discovery and Characterization of an Unprecedented Biosynthetic Mechanism.” Chemistry and Biology, accepted.

162. N. Sun and H. Zhao.“Design of a Single-chain TALEN Architecture for Genome Engineering.” Molecular Biosystems, accepted.

161. J. Liang, R. Chao, Z. Bao, N. Sun, Z. Abil, and H. Zhao.“FairyTALE: A High-throughput TAL Effector Synthesis Platform.” ACS Synthetic Biology, accepted.

160. C. A. Denard, H. Huang, M. J. Bartlett, L. Lu, Y. Tan, H. Zhao, and J. F. Hartwig.“Cooperative Tandem Catalysis by an Organometallic Complex and a Metalloenzyme.” Angewandte Chemie, accepted.

159. X. Feng and H. Zhao.“Investigating Xylose Metabolism in Recombinant Saccharomyces cerevisiae via 13C Metabolic Flux Analysis.” Microbial Cell Factories, 12:114 (2013).

158. N. Sun, Z. Bao, X. Xiong, and H. Zhao.“SunnyTALEN: a Second-generation TALEN System for Human Genome Editing.” Biotechnology and Bioengineering, accepted.

157. Y. Luo, H. Huang, J. Liang, M. Wang, L. Lu, Z. Shao, R. Cobb, and H. Zhao.“Activation and Characterization of a Cryptic Polycyclic Tetramate Macrolactam Biosynthetic Gene Cluster.” Nature Communications, 4: 2894 (2013).

156. C. A. Denard, J. Hartwig, and H. Zhao.“Multistep one-pot reactions combining biocatalysts and chemical catalysts for asymmetric synthesis.” ACS Catalysis, 3, 2856−2864 (2013)

155. R. E. Cobb, J. C. Ning, and H. Zhao.“DNA Assembly Techniques for Next Generation Combinatorial Biosynthesis of Natural Products.” Journal of Industrial Microbiology and Biotechnology, accepted.

154. S. Li, S. K. Ha, H. J. Kim, J. M. Galazka, J. H. D. Cate, and Y. S. Jin, H. Zhao.“Investigation of the Functional Role of Aldose 1-Epimerase in Engineered Cellobiose Utilization.” Journal of Biotechnology, 168, 1-6 (2013).

153. N. Sun and H. Zhao.“Seamless Gene Correction of the Sickle Cell Disease Mutation in Human Induced Pluripotent Stem Cells using TAL Effector Nucleases.” Biotechnology and Bioengineering, accepted.

152. Z. Shao, G. Rao, C. Li, Z. Abil, Y. Luo, and H. Zhao.“Refactoring the Silent Spectinabilin Biosynthetic Gene Cluster Using a Plug-and-Play Scaffold.” ACS Synthetic Biology, 2, 662-669 (2013).

151. X. Feng and H. Zhao.“Investigating Host Dependence of Xylose Utilization in Recombinant Saccharomyces cerevisiae Strains Using RNA-Seq Analysis.” Biotechnology for Biofuels, 6:96 (2013).

150. X. Feng and H. Zhao. “Investigating Glucose and Xylose Metabolism in Saccharomyces cerevisiae and Scheffersomyces stipitis via 13C Metabolic Flux Analysis.” AIChE Journal, 59, 3195-3202 (2013).

149. D. Eriksen, P.C. H. Hsieh, P. Lynn, and H. Zhao.“Directed Evolution of a Cellobiose Utilization Pathway in Saccharomyces cervisiae Through Simultaneous Engineering of Multiple Proteins.” Microbial Cell Factories, 12:61 (2013).

148. Y. Yuan and H. Zhao.“Directed Evolution of a Highly Efficient Cellobiose Utilizing Pathway in an Industrial Saccharomyces cerevisiae Strain.” Biotechnology and Bioengineering, 110, 2874-2881 (2013).

147. M. Zhang, X. Su, E.L. Ang, and H. Zhao.“Recent Advances of Biocatalyst Development in the Pharmaceutical Industry.” Pharmaceutical Bioprocessing, 1, 179-196 (2013).

146. N. Sun and H. Zhao.“Transcription Activator-like Effector Nucleases (TALENs): A Highly Efficient and Versatile Tool for Genome Editing.” Biotechnology and Bioengineering, 110, 1811-1821 (2013).

145. D. Eriksen, J. Lian, and H. Zhao.“Protein Design for Pathway Engineering.” Journal of Structural Biology, accepted.

144. G. Rao, J. K. Lee, and H. Zhao.“Directed Evolution of Phloroglucinol Synthases (PhlD) with Increased Stability for Phloroglucinol Production.” Applied Microbiology and Biotechnology, 97, 5861-5867 (2013).

143. J. Liang, M. McLachlan, and H. Zhao.“Orthogonal Control of Endogenous Gene Expression in Mammalian Cells Using Synthetic Ligands.” Biotechnology and Bioengineering, 110, 1419-1429 (2013). PDF

142. R. E. Cobb, Y. Luo, T. Freestone, and H. Zhao.“Drug Discovery and Development via Synthetic Biology.” In Synthetic Biology: Tools and Applications, (H. Zhao, Ed.), pp. 183-206, Elsevier, San Diego, CA, 2013.

141. D. Eriksen, S. Li, and H. Zhao.“Pathway Engineering as an Enabling Synthetic Biology Tool.” In Synthetic Biology: Tools and Applications, (H. Zhao, Ed.), pp. 43-62, Elsevier, San Diego, CA, 2013.

140. H. Zhao.“Introduction.” In Synthetic Biology: Tools and Applications, (H. Zhao, Ed.), pp. xiii, Elsevier, San Diego, CA, 2013.

139. R. E. Cobb, R. Chao, and H. Zhao.“Directed Evolution: Past, Present and Future.” AIChE Journal, 59, 1432-1440 (2013). PDF

138. B. Kim, J. Du, D. Eriksen, and H. Zhao.“Combinatorial Design of a Highly Efficient Xylose Utilization Pathway for Cellulosic Biofuels Production in Saccharomyces cerevisiae.” Applied and Environmental Microbiology, 79, 931-941 (2013). PDF

137. J. Liang, J. Ning, and H. Zhao.“Coordinated Induction of Multi-gene Pathways in Saccharomyces cerevisiae.” Nucleic Acids Research, 41, e54 (2013). PDF

136. R. E. Cobb, N. Sun, and H. Zhao.“Directed Evolution as a Powerful Synthetic Biology Tool.” Methods, 60, 81–90 (2013). PDF

135. N. Sun and H. Zhao.“A Two-plasmid Bacterial Selection System for Characterization and Engineering of Homing Endonucleases.” In Methods in Molecular Biology, Volume xxx, pp. xxx: xxx (D. Edgell, Ed.), Humana Press Inc., Totowa, NJ, xxx. accepted.

134. F. Wen and H. Zhao.“Construction and screening of an antigen-derived peptide library displayed on yeast cell surface for CD4+ T cell epitope identification.” In Methods in Molecular Biology, Volume xxx, pp. xxx: xxx (S. Twine and K. Fulton, Eds.), Humana Press Inc., Totowa, NJ, xxx. accepted.

133. Y. Yuan, J. Du, and H. Zhao.“Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering (COMPACTER).” In Methods in Molecular Biology, Volume 985, pp. 177-209 (H. Alper Ed.), Humana Press Inc., Totowa, NJ, 2013.

132. M. Jeya, T. Kim, M. Tiwari, J. Lin, H. Zhao and J.K. Lee.“A Type III Polyketide Synthase from Rhizobium etli Condenses Malonyl CoAs to a Heptaketide pyrone with Unusually High Catalytic Efficiency.” Molecular Biosystems, 8, 3103-3106 (2012).

131. S. Wen, T. Tan, and H. Zhao.“Improving the Thermostability of Lipase Lip2 from Yarrowia lipolytica.” Journal of Biotechnology, 164, 248– 253 (2012). PDF

130. M. Jeya, T. Kim, M. Tiwari, J. Li, H. Zhao and J.K. Lee.“The Botrytis cinerea Type III Polyketide Synthase Shows Unprecedented High Catalytic Efficiency.” Molecular Biosystems, 8, 2864-2867 (2012).

129. N. Sun, Z. Abil, and H. Zhao.“Recent Advances in Targeted Genome Engineering in Mammalian Systems.” Biotechnology Journal, 7, 1074-1087 (2012). PDF

128. Y. Luo, J.K. Lee, and H. Zhao. “Challenges and Opportunities in Synthetic Biology for Chemical Engineers.” Chemical Engineering Science, accepted. PDF

127. H. Lu, E. Chanco, and H. Zhao.“CmlI is an N-Oxygenase in the Biosynthesis of Chloramphenicol.” Tetrahedron, 68, 7651-7654 (2012). PDF

126. J. Du, Y. Yuan, T. Si, and H. Zhao. “Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering (COMPACTER).” Nucleic Acids Research, 40, e142 (2012). PDF

125. R. E. Cobb, T. Si, and H. Zhao. “Directed Evolution: an Evolving and Enabling Synthetic Biology Tool.” Current Opinion in Chemical Biology, 16, 285–291 (2012). PDF

124. Y. Zou, H. Zhang, J. S. Brunzelle, T. W. Johannes, R. Woodyer, J. E. Hung, N. Nair, W. A. van der Donk, H. Zhao, and S. K. Nair. “Crystal Structures of Phosphite Dehydrogenase Provide Insights into Nicotinamide Cofactor Regeneration.” Biochemistry, 51, 4263−4270, (2012).

123. J. E. Hung, E. J. Fogle, H. A. Relyea, H. D. Christman, T. W. Johannes, H. Zhao, W. W. Metcalf, and W. A. van der Donk. “Site-Directed Mutagenesis of Conserved Residues in Phosphite Dehydrogenases.” Biochemistry, 51, 4254−4262 (2012).

122. R. E. Cobb and H. Zhao. “Direct Cloning of Large Genomic Sequences.” Nature Biotechnology, 30, 405-406 (2012). PDF

121. M. Tiwari, R. Singh, H. Moon, M. Jeya, H. Zhao, J. K. Lee. “Role of Conserved Gly in the Zn-dependent Medium Chain Dehydrogenase/reductase Superfamily.” Journal of Biological Chemistry, 287, 19429-19439 (2012).

120. J. Sun, F. Wen, T. Si, J. Xu, and H. Zhao. “Direct Conversion of Xylan to Ethanol by Recombinant Saccharomyces cerevisiae Strains Displaying an Engineered Minixylanosome.” Applied and Environmental Microbiology, 78, 3837-3845 (2012). PDF

119. J. Sun, Z. Shao, H. Zhao, F. Wen, H. Zhao, N. Nair, J, Xu, and H. Zhao. “Systematic Characterization of a Panel of Constitutive Promoters for Applications in Pathway Engineering in Saccharomyces cerevisiae.” Bioengineering and Biotechnology, 109, 2082-2092 (2012).  PDF

118. Z. Shao and H. Zhao. “DNA assembler: a Synthetic Biology Tool for Characterizing and Engineering Natural Product Gene Clusters.” Methods in Enzymology, 517, 203-224 (2012).

117. M. Wang, T. Si, and H. Zhao. “Biocatalyst Development by Directed Evolution.” Bioresource Technology, 115, 117–125 (2012). PDF

116. N. Sun, J. Liang, Z. Abil, and H. Zhao. “Engineered TAL Effector Nucleases (TALENs) for Use in Treatment of Sickle Cell Disease.” Molecular Biosystems, 8, 1255 – 1263 (2012). PDF

115. Z. Shao, Y. Luo, and H. Zhao. “DNA Assembler Method for Construction of Zeathanthin-producing Sacchromyces cerevisiae Strains.” In Methods in Molecular Biology, Volume 898, pp. 251-262 (J.-L. Barredo Ed.), Humana Press Inc., Totowa, NJ, 2012.

114. B. Kim, J. Du, and H. Zhao. “Strain Improvement via Evolutionary Engineering.” In Engineering Complex Phenotypes in Industrial Strains, (R. Patnaik, Ed.), John Wiley & Sons, Inc., accepted.

113. M. Tiwari, R. Singh, J. K. Lee, and H. Zhao. “Mechanistic Studies on the Flavin:NADH Reductase (PrnF) from Pseudomonas fluorescence Involved in Arylamine Oxygenation.” Biochemistry and Medicinal Chemistry Letters, 22, 1344-1347 (2012). PDF

112. N. U. Nair and H. Zhao. “Mutagenic Inverted Repeat Assisted Genome Engineering (MIRAGE) in Saccharomyces cerevisiae: Deletion of gal7.” In Methods in Molecular Biology, Volume 834, pp. 63-73 (Q. Chen, Eds.), Humana Press Inc., Totowa, NJ, 2012.

111. A. Ghosh, H. Zhao, and N. D. Price. “Genome-scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae.” PLoS ONE, 6(11): e27316 (2011) PDF

110. H. Zhao. “Highlights of Biocatalysis and Biomimetic Catalysis.” ACS Catalysis, 1, 1119-1120 (2011). PDF

109. J. Li, Y. Luo, J. Lee and H. Zhao. “Characterization of a Novel Type III Polyketide Synthase from Aspergillus niger.” Biochemistry and Medicinal Chemistry Letter, 21, 6085-6089 (2011). PDF

108. M. Wang and H. Zhao. “Microbial Synthesis of Drugs and Fuels via Synthetic Biology.” Chinese Bulletin of Life Sciences, (In Chinese), 23, 875-881 (2011).

107. M. DeSieno, W. van der Donk, and H. Zhao. “Characterization and Application of the Fe(II) and α-Ketoglutarate Dependent Hydroxylase FrbJ.” Chemical Communications , 47, 10025 – 10027 (2011). PDF

106. B. Bae, R. E. Cobb, M. DeSieno, H. Zhao, and S. Nair. “A New N-Acetyltranferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF.” Journal of Biological Chemistry , 286, 36132-36141 (2011).

105. M. McLachlan, J. A. Katzenellenbogen, and H. Zhao. “A New Fluorescence Complementation Biosensor for Detection of Estrogenic Compounds.” Bioengineering and Biotechnology , 108, 2794–2803 (2011). PDF

104. F. Wen, D. K. Sethi, K. W. Wucherpfennig, and H. Zhao. “Cell Surface Display of Functional Human MHC Class II Proteins: Yeast Display versus Insect Cell Display.” Protein Engineering Design and Selection , 24, 701-709 (2011). PDF

103. J. Du, Z. Shao, and H. Zhao. “Engineering a Microbial Factory for Synthesis of Value-added Products.” Journal of Industrial Microbiology and Biotechnology , 38, 873-890 (2011). PDF

102. B. S. Evans, Y. Chen, W. W. Metcalf, H. Zhao, and N. L. Kelleher. “Directed Evolution of the Nonribosomal Peptide Synthetase AdmK Generates New Andrimid Derivatives in vivo.” Chemistry and Biology , 18, 601-607 (2011). PDF

101. M. K. Tiwari, J. K. Lee, H. J. Moon, and H. Zhao. “Further Biochemical Studies on Aminopyrrolnitrin Oxygenase (PrnD).” Biochemistry and Medicinal Chemistry Letters , 21, 2873-2876 (2011). PDF

100. Z. Shao, Y. Luo, and H. Zhao. “Rapid Characterization and Engineering of Natural Product Biosynthetic Pathways via DNA Assembler.” Molecular Biosystems , 7, 1056 – 1059 (2011). PDF

99. J. Liang, Y. Luo, and H. Zhao. “Synthetic Biology: Put Synthesis in Biology.” Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 3, 7-20 (2011). PDF

98. S. Li, J. Du, J. Sun, X. Yang, J. M. Galazka, N. L. Glass, J. H. D. Cate, and H. Zhao. “Overcoming Glucose Repression in Mixed Sugar Fermentation by Co-expressing a Cellulobiose Transporter and a b-Glucosidase in Saccharomyces cerevisiae.” Molecular Biosystems , 6, 2129 – 2132 (2010). PDF

97. B. Bae, R. P. Sullivan, H. Zhao, and S. Nair. “Structure and Engineering of L-Arabinitol Dehydrogenase from Neurospora crassa.” Journal of Molecular Biology , 402, 230-240. PDF

96. J. Du, S. Li, and H. Zhao. “Cloning and Characterization of Novel Xylose Specific Transporters from Neurospora crassa and Pichia stipitis.” Molecular Biosystems , 6, 2150 – 2156 (2010). PDF

95. S. Rubin-Pitel, Y. Luo, J. K. Lee, and H. Zhao. “A Diverse Family of Type III Polyketide Synthases in Eucalyptus Species.” Molecular Biosystems , 6, 1444-1446 (2010). PDF

94. W. Tang, Z. Li, and H. Zhao. “Inverting the Enantioselectivity of P450pyr Monooxygenase by Directed Evolution.” Chemical Communications , 46, 5461-5463 (2010). PDF

93. N. U. Nair and H. Zhao. “Selective Reduction of Xylose to Xylitol from a Mixture of Hemicellulosic Sugars.” Metabolic Engineering , 12, 462–468 (2010). PDF

92. B. Kim, R. Sullivan, and H. Zhao. “Cloning and Characterization of Fungal L-Arabinitol Dehyrodenases.” Applied Microbiology and Biotechnology , 87, 1407-1414 (2010). PDF

91. N. U. Nair, C. A. Denard, and H. Zhao. “Engineering of Enzymes for Selective Catalysis.” Current Organic Chemistry , 14, 1870-1882 (2010). PDF

90. T. W. Johannes, M. A. DeSieno, B. M. Griffin, W. W. Metcalf, P. Thomas, N. L. Kelleher, and H. Zhao. “Deciphering the Late Biosynthetic Steps of Antimalarial Compound FR900098.” Chemistry and Biology , 17, 57–64 (2010). PDF

89. L. Huang, Y. Xue, Y.X. He, X. Fei, Y.B. Teng, S. Rubin-Pitel, H. Zhao, and C.Z. Zhou. “Crystal Structure and Computational Analyses Provide Insights into the Catalytic Mechanism of 2, 4-Diacetylphloroglucinol Hydrolase PhlG from Pseudomonas fluorescens.” Journal of Biological Chemistry , 285, 4603–4611, (2010).  PDF

88. F. Wen, J. Sun, and H. Zhao. “Yeast Surface Display of Trifunctional Minicellulosomes for Simultaneous and Synergistic Saccharification and Fermentation of Cellulose to Ethanol.” Applied and Environmental Microbiology, 76, 1251–1260 (2010). PDF

87. Y. Choi, T. Johannes, M. Simurdiak, Z. Shao, H. Lu, and H. Zhao. “Cloning and Heterologous Expession of the Spectinabilin Biosynthetic Gene Cluster from Streptomyces spectabilis.” Molecular Biosystems, 6, 336 – 338 (2010). PDF

86. H. Zhao and S.K. Nair. “p-Aminobenzoate N-Oxygenase.” Handbook of Metalloproteins, John Wiley & Sons, in press.

85. F. Wen, S. Rubin-Pitel, and H. Zhao. “Engineering of Therapeutic Protein.” In Protein Engineering and Design , (J. Cochran and S. Park, Eds.), pp153-177, CRC Press, Taylor & Francis Group, Boca Raton, FL, 2010.

84. N. U. Nair, W. Tang, D. Eriksen, and H. Zhao. “Industrial Applications of Enzymes as Catalysts.” In Manual of Industrial Microbiology and Biotechnology , 3rd Ed. (A. L. Demain, R. Baltz, and J. E. Davies, Eds.), pp480-494, ASM Press, Washington, DC, 2010.

83. M. DeSieno, C. Denard, and H. Zhao. “Combinatorial Biosynthesis for Drug Discovery and Development.” In Chemical Biology of Enzymes in Biotech and Pharmaceutical Applications , (W.K. Yeh, H.C. Yang, and J. R. McCarthy, Eds.), pp253-283, John Wiley & Sons, Inc., Hoboken, NJ, 2010.

82. W. Tang and H. Zhao. “Industrial Biotechnology: Tools and Applications.” Biotechnology Journal, 4, 1725–1739 (2009). PDF

81. N. U. Nair, Z. Shao, M. DeSieno, T. Johannes, H. Zhao, T. Lee, R.P. Sullivan, M. McLachlan, and H. Zhao. “Towards the Cost-effective Production of Antimalarial Drug FR900098 and Butanol.” Proceedings of Foundations of Systems Biology, (FOSBE), Denver, CO, 2009.

80. M. McLachlan, K. Chockalingam, K. Lai, and H. Zhao. “Directed Evolution of Orthogonal Ligand Specificities in a Single Protein Scaffold.” Angewandte Chemie International Edition , 48, 7783 –7786 (2009).  PDF

79. F. Wen, N. U. Nair, and H. Zhao. “Protein Engineering in Designing Tailored Enzymes and Microorganisms for Biofuels Production.” Current Opinion in Biotechnology , 20, 412–419 (2009). PDF

78. W. Zha, S. Rubin-Pitel, and H. Zhao. “Increasing Cellular Malonyl-CoA Level in E. coli via Metabolic Engineering.” Metabolic Engineering , 11, 192-198 (2009).  PDF

77. Z. Chen, F. Wen, N. Sun, and H. Zhao. “Directed Evolution of Homing Endonuclease with Altered Sequence Specificity.” Protein Engineering Design and Selection , 22, 249-256 (2009). PDF

76. Z. Shao, H. Zhao, and H. Zhao. “DNA Assembler, an in vivo Genetic Method for Rapid Construction of Biochemical Pathways.” Nucleic Acids Research , 37, e16 (2009). PDF

75. N. Nair and H. Zhao. “Mutagenic Inverted Repeat Assisted Genome Engineering (MIRAGE).” Nucleic Acids Research , 37, e9 (2009). PDF

74. K. M. D. Islam, M. Dilcher, C. Thurow, I. Krimmelbein, C. Vock, V. Gonzalez, H. Zhao, L. Tietze, and C. Gatz. “Directed Evolution of Estrogen Receptor Proteins with Altered Ligand-binding Specificities.” Protein Engineering Design and Selection , 22, 45-52 (2009).  PDF

73. E. Ang, J. P. Obbard, and H. Zhao. “Directed Evolution of Aniline Dioxygenase with Improved and Novel Activity.” Applied Microbiology and Biotechnology , 81, 1063–1070 (2009).  PDF

72. M. Mclachlan, R.P. Sullivan, and H. Zhao. “Directed Enzyme Evolution and High Throughput Screening.” In Biocatalysis for the Pharmaceutical Industry-Discovery, Development, and Manufacturing, (J. Tao, G., Lin, and A. Liese, Eds.) pp. 45-64, John Wiley and Sons (Asia) Pte Ltd, Singapore, 2009.  PDF

71. M. DeSieno, J. Du, and H. Zhao. “Protein Engineering of Enzymes with Altered Substrate and Cofactor Specificity. ” In Protein Engineering Handbook, (S. Lutz, U. Bornscheuer, Eds.), pp 777-796, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 2009.

70. N. Nair and H. Zhao. “Improving Proteins by Directed Evolution.” In Handbooks for Metabolic Engineering, (C. Smolke, Ed.) pp. 2.1-2.37, CRC Press, Taylor & Francis Group, Boca Raton, FL, 2009.

69. H. Zhao and W. Chen. “Chemical Biotechnology: Microbial Solutions to Global Change.” Current Opinion in Biotechnology , 19, 541–543 (2008).  PDF

68. S. Rubin-Pitel, H. Zhang, J. S. Brunzelle, T. Vu, H. Zhao, and S. Nair. “Distinct Structural Elements Dictate the Specificity of the Pentaketide Resorcylic Acid Synthase from Neurospora crassa.” Chemistry and Biology , 15, 1079-1090 (2008).  PDF

67. A. C. Eliot, B. M. Griffin, P. M. Thomas, T. W. Johannes, N. L. Kelleher, H. Zhao and W. W. Metcalf. “Cloning, Expression, and Biochemical Characterization of Streptomyces rubellomurinus Genes Required for Biosynthesis of Antimalarial Compound FR900098.” Chemistry and Biology , 765-770 (2008).  PDF

66. Z. Shao, J. A. V. Blodgett, B. T. Circello, R. Woodyer, G. Li, W. A. van der Donk, W. W. Metcalf, and H. Zhao. “Biosynthesis of 2-Hydroxyethylphosphonate, an Unexpected Intermediate Common to Multiple Phosphonate Biosynthetic Pathways.” Journal of Biological Chemistry , 23161-23168 (2008). PDF

65. Y. Choi, H. Zhang, J. S. Brunzelle, S. Nair, and H. Zhao. “In vitro Reconstitution and Structure of an Arylamine N-Oxygenase Involved in Biosynthesis of Aureothin.” Proceedings of National Academy of Sciences of the United States of America, 105, 6858-6863 (2008). PDF

64. F. Wen, O. Esteban, and H. Zhao. “Rapid Identification of CD4+ T-cell Epitopes Using Yeast Displaying Pathogen-derived Peptide Library.” Journal of Immunological Methods , 336, 37-44 (2008). PDF

63. N. Nair and H. Zhao. “Evolution in Reverse: Engineering a D-Xylose-specific Xylose Reductase.” ChemBioChem, 9, 1213-1215 (2008). PDF

62. W. Zha, S. Rubin-Pitel, and H. Zhao. “Molecular Breeding of Type III Polyketide Synthases for Improved Productivity” Molecular Biosystems , 4, 246-248 (2008). PDF

61. F. Wen, M. McLachlan, and H. Zhao. “Novel and Improved Enzymes through Directed Evolution.” In Wiley Encyclopedia of Chemical Biology, John Wiley & Sons, Hoboken, NJ, 2008, DOI: 10.1002/9780470048672.wecb125. PDF

60. M. McLachlan, T. Johannes, and H. Zhao. “Further Improvement of Phosphite Dehydrogenase Thermostability by Saturation Mutagenesis.” Biotechnology and Bioengineering , 99, 268-274 (2008). PDF

59. R. P. Sullivan and H. Zhao. “Cloning and Characterization of a Highly Active L-Arabinitol Dehydrogenase from Neurospora crassa.” Applied Microbiology and Biotechnology , 77, 845–852 (2007). PDF

58. J. Lee and H. Zhao. “Identification and Characterization of a Flavin:NADH Reductase (PrnF) Involved in the Novel Two-component Arylamine Oxygenase.” Journal of Bacteriology , 189, 8556-8563 (2007). PDF

57. H. Zhao. “Directed Evolution of Novel Protein Functions.” Biotechnology and Bioengineering , 98, 313-317 (2007). PDF

56. N. Nair and H. Zhao. “Biochemical Characterization of an L-Xylulose Reductase from Neurospora crassa.” Applied and Environmental Microbiology , 73, 2001-2004 (2007).  PDF

55. E. Ang, J.P. Obbard, and H. Zhao. “Probing the Molecular Determinants of Aniline Dioxygenase Substrate Specificity.” FEBS Journal, 274, 928-939 (2007). PDF

54. R. Woodyer, G. Li, H. Zhao and W. A. van der Donk. “New Insight into the Mechanism of Methyl Transfer during the Biosynthesis of Fosfomycin.” Chemical Communications , 359-361 (2007). PDF

53. T. Johannes, R. Woodyer, and H. Zhao. “Efficient Regeneration of NADPH using an Engineered Phosphite Dehydrogenase.” Biotechnology and Bioengineering , 96, 18-26 (2007). PDF

52. H. Zhao and W. Zha. “In vitro ‘Sexual’ Evolution through the PCR-based Staggered Extension Process (StEP).” Nature Protocols , 1, 1865-1871 (2006). PDF

51. R. Woodyer, Z. Shao, P. M. Thomas, N. L. Kelleher, J. A. V. Blodgett, W. M. Metcalf, W. A. van der Donk, and H. Zhao.“Heterologous Production of Fosfomycin and Identification of the Minimal Fosfomycin Biosynthetic Cluster.” Chemistry & Biology , 13, 1171-1182 (2006). PDF

50. K. Chockalingam, J. Luba, H. S. Nick, D. N. Silverman, and H. Zhao. “Engineering and Characterization of Human Manganese Superoxide Dismutase Mutants with High Activity and Low Product Inhibition.” FEBS Journal, 273, 4853-4861 (2006). PDF

49. W. Zha, S. Rubin-Pitel, and H. Zhao. “Characterization of the Substrate Specificity of PhlD, a Type III Polyketide Synthase from Pseudomonas fluorescens.” Journal of Biological Chemistry , 281, 32036-32047 (2006). PDF

48. J. Lee, E. Ang, and H. Zhao. “Probing the Substrate Specificity of Aminopyrrolnitrin Oxygenase (PrnD) by Mutational Analysis.” Journal of Bacteriology , 188, 6179-6183 (2006). PDF

47. M. Simurdiak, J. Lee, and H. Zhao. “A New Class of Arylamine Oxygenases: Evidence that p-Aminobenzoate N-Oxygenase (AurF) is a Diiron Enzyme and Further Mechanistic Studies.” ChemBioChem, 7, 1169-1172 (2006). PDF

46. T. Johannes and H. Zhao. “Directed Evolution of Enzymes and Biosynthetic Pathways.” Current Opinion in Microbiology , 9, 261-267 (2006). PDF

45. S. Rubin-Pitel, C. M.-H. Cho, W. Chen, and H. Zhao. “Directed Evolution Tools in Bioproduct and Bioprocess Development.” In Bioprocessing for Value-Added Products from Renewable Resources: New Technologies and Applications, (S.-T. Yang, Ed.) pp. 49-72, Elsevier Science, New York, NY, 2006. PDF

44. T. Johannes, R. Woodyer, and H. Zhao. “High Throughput Screening Methods Developed for Oxidoreductases.” In Enzyme Assays: High-throughput Screening, Genetic Selection and Fingerprinting , (J.L Reymond, Ed.) Wiley VCH-Verlag Gmbh, Weinheim, Germany, Chapter 3, pp. 77-93, 2006.  PDF

43. S. Rubin-Pitel and H. Zhao. “Recent Advances in Biocatalysis by Directed Enzyme Evolution.” Combinatorial Chemistry and High Throughput Screening , 9, 247-257 (2006). PDF

42. R. Woodyer, W. A. van der Donk, and H. Zhao. “Optimizing a Biocatalyst for Improved NAD(P)H Regeneration: Directed Evolution of Phosphite Dehydrogenase.” Combinatorial Chemistry and High Throughput Screening , 9, 237-245 (2006).

41. D. Xie, Z. Shao, J. Achkar, W. Zha, J. W. Frost, and H. Zhao. “Microbial Synthesis of Triacetic Acid Lactone” Biotechnology and Bioengineering , 93, 727-736 (2006). PDF

40. J. Lee and H. Zhao. “Mechanistic Studies of an N-oxygenase that Catalyzes Arylamine Oxidation.” Angewandte Chemie International Edition , 45, 622-625 (2006). PDF

39. T. Johannes, M. Simurdiak and H. Zhao. “Biocatalysis.” In Encyclopedia of Chemical Processing , (S. Lee, Ed.) pp. 101-110, Marcel Dekker, Inc., New York, NY, 2006. PDF

38. Z. Chen and H. Zhao. “Protein Design.” In Encyclopedia of Chemical Processing , (S. Lee, Ed.) pp. 2467-2477, Marcel Dekker, Inc., New York, NY, 2006. PDF

37. Shao, Z., Ang. E. and H. Zhao. “Biomolecular Engineering.” In Encyclopedia of Chemical Processing , (S. Lee, Ed.) pp. 171-182, Marcel Dekker, Inc., New York, NY, 2006. PDF

36. Z. Chen and H. Zhao. “A Highly Sensitive Selection Method for Directed Evolution of Homing Endonucleases.” Nucleic Acids Research , 33, e154 (2005). PDF

35. J. Lee, M. Simurdiak, and H. Zhao. “Reconstitution and Characterization of Aminopyrrolnitrin Oxidase that Catalyzes Unusual Arylamine Oxidation.” Journal of Biological Chemistry , 280, 36719-36728 (2005). PDF

34. T. Johannes, R. Woodyer and H. Zhao. “Directed Evolution of a Thermostable Phosphite Dehydrogenase for NAD(P)H Regeneration.” Applied Environmental Microbiology , 71, 5728-5734 (2005). PDF

33. R. Woodyer, H. Zhao, and W. A. van der Donk. “Mechanistic Investigation of a Highly Active Phosphite Dehydrogenase Mutant and its Application for NADPH Regeneration.” FEBS Journal, 272, 3816-3827 (2005). PDF

32. Chockalingam, K. and H. Zhao. “Creating New Specific Ligand-Receptor Pairs for Transgene Regulation.” Trends in Biotechnology , 23, 333-335 (2005). PDF

31. J. Achkar, M. Xian, H. Zhao, and J.W. Frost. “Biosynthesis of Phloroglucinol.” Journal of the American Chemical Society , 127, 5332-5333 (2005). PDF

30. K. Chockalingam, Z. Chen, J.A. Katzenellenbogen, and H. Zhao. “Directed Evolution of New Specific Receptor-Ligand Pairs for Use in the Creation of Gene Switches.” Proceedings of National Academy of Sciences of the United States of America, 102, 5691-5696 (2005). PDF

29. Z. Chen and H. Zhao. “Rapid Creation of a Novel Protein Function by in vitro Co-evolution” Journal of Molecular Biology , 348, 1273-1282 (2005). PDF

28. E. Ang, H. Zhao, and J. P. Obbard. “Bioremediation of Persistent Organic Pollutants via Biomolecular Engineering” Enzyme and Microbial Technology , 37, 487-496 (2005). PDF

27. R. Woodyer, M. Simurdiak, W. van der Donk, and H. Zhao. “Heterologous Expression, Purification and Characterization of a Highly Active Xylose Reductase from Neurospora crassa.” Applied Environmental Microbiology , 71, 1642-1647 (2005). PDF

26. Z. Chen, B.S. Katzenellenbogen, J.A. Katzenellenbogen, and H. Zhao. “Directed Evolution of Human Estrogen Receptor Variants with Significantly Enhanced Androgen Specificity and Affinity.” Journal of Biological Chemistry , 279, 33855-33864 (2004). PDF

25. O. Esteban, and H. Zhao. “Directed Evolution of Soluble Single-chain Human Class II MHC Molecules on the Yeast Cell Surface.” Journal of Molecular Biology , 340, 81-95 (2004). PDF

24. W. Zha, Z. Shao, J.W. Frost, and H. Zhao. “Rational Pathway Engineering of Type I Fatty Acid Synthase Allows Biosynthesis of Triacetic Acid Lactone from D-Glucose in vivo.” Journal of the American Chemical Society , 126, 4534-4535 (2004). PDF

23. H. Zhao. “Staggered Extension Process (StEP) In vitro DNA Recombination.” Methods in Enzymology , 388, 42-49 (2004). PDF

22. R. D. Woodyer, W. Chen and H. Zhao. “Outrunning Nature: Directed Evolution of Superior Biocatalysts.” Journal of Chemical Education , 81, 126-133 (2004). PDF

21. R. D. Woodyer, T. Johannes, and H. Zhao. “Cofactor Regeneration for Biocatalytic Applications.” In Enzyme Technology, (A. Pandey, C. Webb, C. S. Soccol, and C. Larroche, Eds.) Chapter 5, pp. 83-101, Asiatech Publishers Inc., New Delhi, India, 2004.  PDF

20. R. D. Woodyer, W. A. van der Donk and H. Zhao. “Relaxing the Nicotinamide Cofactor Specificity of Phosphite Dehydrogenase by Rational Design.” Biochemistry , 42, 11604-11614 (2003). PDF

19. H. Zhao and W. A. van der Donk. “Cofactor Regeneration for Use in Biocatalysis.” Current Opinion in Biotechnology , 14, 583-589 (2003). PDF

18. W. A. van der Donk and H. Zhao. “Recent Developments in Pyridine Nucleotide Regeneration.” Current Opinion in Biotechnology , 14, 421-426 (2003). PDF

17. J. Sun, J.A. Katzenellenbogen, H. Zhao, and B.S. Katzenellenbogen. “DNA Shuffling Method for Generating Estrogen Receptor a and b Chimeras in a Yeast System.” Biotechniques , 34, 278-288 (2003). PDF

16. Z. Chen and H. Zhao. “A Highly Efficient and Sensitive Screening Method for Trans-activation Activity of Estrogen Receptors.” Gene, 306, 127-134 (2003). PDF

15. H. Zhao. “A pH Indicator Based Screening Method for Hydrolytic Haloalkane Dehalogenase.” In Methods in Molecular Biology, Volume 230, pp. 213-221: Directed Enzyme Evolution: Screening and Selection Methods (F.H. Arnold and G. Georgiou, Eds.), Humana Press Inc., Totowa, NJ, 2003. PDF

14. O. Esteban, R. D. Woodyer, and H. Zhao. “In vitro DNA recombination by Random Priming.” In Methods in Molecular Biology , Volume 231, pp. 101-106: Directed Evolution Library Creation: Methods and Protocols, (F.H. Arnold and G. Georgiou, Eds.), Humana Press Inc., Totowa, NJ, 2003. PDF

13. W. Zha, T. Zhu, and H. Zhao. “Family Shuffling with Single-stranded DNA.” In Methods in Molecular Biology , Volume 231, pp. 93-99: Directed Evolution Library Creation: Methods and Protocols, (F.H. Arnold and G. Georgiou, Eds.), Humana Press Inc., Totowa, NJ, 2003. PDF

12. H. Zhao and W. Zha. “Evolutionary Methods for Protein Engineering.” In Enzyme Functionality: Design, Engineering and Screening , (Allan Svendsen Ed.) Chapter 15, pp. 353-373, Marcel Dekker, Inc., New York, NY, 2003.

11. H. Zhao, K. Chockalingam and Z. Chen. “Directed Evolution of Enzymes and Pathways for Industrial Biocatalysis.” Current Opinion in Biotechnology , 13, 104-110 (2002). PDF

10. F. H. Arnold, L. Giver, A. Gershenson, H. Zhao and K. Miyazaki. “Directed Evolution of Mesophilic Enzymes into Their Thermophilic Counterparts.” Annals of the New York Academy of Sciences , 870, 400-403 (1999).

9. H. Zhao and F. H. Arnold. “Directed Evolution Converts Subtilisin E into a Functional Equivalent of Thermitase.” Protein Engineering , 12, 47-53 (1999). PDF

8. H. Zhao, J. C. Moore, A. A. Volkov and F. H. Arnold. “Methods for Optimizing Industrial Enzymes by Directed Evolution.” In Manual of Industrial Microbiology and Biotechnology, 2nd Ed. (A. L. Demain and J. E. Davies, Eds.) Chapter 49, pp. 597-604, ASM Press, Washington, DC, 1999. PDF

7. H. Zhao, L. Giver, Z. Shao, J. A. Affholter and F. H. Arnold. “Molecular Evolution by Staggered Extension Process (StEP) in vitro Recombination.” Nature Biotechnology , 16, 258-261 (1998). PDF

6. Z. Shao, H. Zhao, L. Giver and F. H. Arnold. “Random-Priming In Vitro Recombination: An Effective Tool for Directed Evolution.” Nucleic Acids Research , 26, 681-683 (1998). PDF

5. H. Zhao and F. H. Arnold. “Combinatorial Protein Design: Strategies for Screening Protein Libraries.” Current Opinion in Structural Biology , 7, 480-485 (1997). PDF

4. H. Zhao and F. H. Arnold. “Functional and Non-functional Mutations Distinguished by Random Recombination of Homologous Genes.” Proceedings of National Academy of Sciences of the United States of America, 94, 7997-8000 (1997). PDF

3. H. Zhao and F. H. Arnold. “Optimization of DNA Shuffling of High Fidelity Recombination.” Nucleic Acids Research , 25, 1307-1308 (1997). PDF

2. H. Zhao, L. You and F. H. Arnold. “Strategy for the Directed Evolution of a Peptide Ligase.” Proceedings of the 13th Enzyme Engineering Conference, Annals of the New York Academy of Sciences , 799, 1-6 (1996). PDF

1. Y. Shi, H. Zhao and C. Wang. “Relative Binding Free Energy Calculations of DNA to Daunomycin and its 13-dihydro Analogue.” International Journal of Biological Macromolecules , 15, 247-251 (1993).