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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Deng, X., Zhironkina, O. A., Cherepanynets, V. D., Strelkova, O. S., Kireev, I. I., & Belmont, A. S. (2016). Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers. Current Biology, 26(18), 2527-2534. DOI: 10.1016/j.cub.2016.07.020
 
Choi, E. J., Kim, J. W., Kim, S. J., Seo, S. O., Lane, S., Park, Y. C., ... Seo, J. H. (2016). Enhanced production of 2,3-butanediol in pyruvate decarboxylase-deficient Saccharomyces cerevisiae through optimizing ratio of glucose/galactose. Biotechnology Journal. DOI: 10.1002/biot.201600042
 
Zhang, G. C., Kong, I. I., Wei, N., Peng, D., Turner, T. L., Sung, B. H., ... Jin, Y. S. (2016). Optimization of an acetate reduction pathway for producing cellulosic ethanol by engineered yeast. Biotechnology and Bioengineering, 113(12), 2587-2596. DOI: 10.1002/bit.26021
 
Xing, H., Hwang, K., & Lu, Y. (2016). Recent developments of liposomes as nanocarriers for theranostic applications. Theranostics, 6(9), 1336-1352. DOI: 10.7150/thno.15464
 
Sun, H., Yeo, W. L., Lim, Y. H., Chew, X., Smith, D. J., Xue, B., ... Ang, E. L. (2016). Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate. Angewandte Chemie - International Edition. DOI: 10.1002/anie.201606722
 
Cuculis, L., Abil, Z., Zhao, H., & Schroeder, C. M. (2016). TALE proteins search DNA using a rotationally decoupled mechanism. Nature Chemical Biology, 12(10), 831-837. DOI: 10.1038/nchembio.2152
 
Lian, J., Jin, R., & Zhao, H. (2016). Construction of plasmids with tunable copy numbers in Saccharomyces cerevisiae and their applications in pathway optimization and multiplex genome integration. Biotechnology and Bioengineering, 113(11), 2462-2473. DOI: 10.1002/bit.26004
 
Tajik, A., Zhang, Y., Wei, F., Sun, J., Jia, Q., Zhou, W., ... Wang, N. (2016). Transcription upregulation via force-induced direct stretching of chromatin. Nature Materials, 15(12), 1287-1296. DOI: 10.1038/nmat4729
 
Bhagi-Damodaran, A., Petrik, I., & Lu, Y. (2016). Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities. Israel Journal of Chemistry, 56(9-10), 773-790. DOI: 10.1002/ijch.201600033
 
Zhang, S., Ito, M., Skerker, J. M., Arkin, A. P., & Rao, C. V. (2016). Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation. Applied Microbiology and Biotechnology, 1-13. DOI: 10.1007/s00253-016-7815-y
 
Xia, P. F., Zhang, G. C., Liu, J. J., Kwak, S., Tsai, C. S., Kong, I. I., ... Jin, Y. S. (2016). GroE chaperonins assisted functional expression of bacterial enzymes in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 113(10), 2149-2155. DOI: 10.1002/bit.25980
 
Zhou, J., Wu, K., & Rao, C. V. (2016). Evolutionary engineering of Geobacillus thermoglucosidasius for improved ethanol production. Biotechnology and Bioengineering, 113(10), 2156-2167. DOI: 10.1002/bit.25983
 
Rutter, C. D., & Rao, C. V. (2016). Production of 1-decanol by metabolically engineered Yarrowia lipolytica. Metabolic Engineering, 38, 139-147. DOI: 10.1016/j.ymben.2016.07.011
 
Liu, J. J., Zhang, G. C., Oh, E. J., Pathanibul, P., Turner, T. L., & Jin, Y. S. (2016). Lactose fermentation by engineered Saccharomyces cerevisiae capable of fermenting cellobiose. Journal of Biotechnology, 234, 99-104. DOI: 10.1016/j.jbiotec.2016.07.018
 
Zhao, H., & Medema, M. H. (2016). Standardization for natural product synthetic biology. Natural Product Reports, 33(8), 920-924. DOI: 10.1039/c6np00030d
 
Zhang, M. M., Wang, Y., Ang, E. L., & Zhao, H. (2016). Engineering microbial hosts for production of bacterial natural products. Natural Product Reports, 33(8), 963-987. DOI: 10.1039/c6np00017g
 
Medema, M. H., & Zhao, H. (2016). Editorial: Synthetic biology and bioinformatics. Natural Product Reports, 33(8), 913-914. DOI: 10.1039/c6np90031c
 
Lian, J., & Zhao, H. (2016). Functional Reconstitution of a Pyruvate Dehydrogenase in the Cytosol of Saccharomyces cerevisiae through Lipoylation Machinery Engineering. ACS Synthetic Biology, 5(7), 689-697. DOI: 10.1021/acssynbio.6b00019
 
Wang, Y., Zhang, Z. T., Seo, S. O., Lynn, P., Lu, T., Jin, Y. S., & Blaschek, H. P. (2016). Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable "clean" Mutant Selection in Clostridium beijerinckii as an Example. ACS Synthetic Biology, 5(7), 721-732. DOI: 10.1021/acssynbio.6b00060
 
Wendt, K. E., Ungerer, J., Cobb, R. E., Zhao, H., & Pakrasi, H. B. (2016). CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973. Microbial Cell Factories, 15(1), [115]. DOI: 10.1186/s12934-016-0514-7
 
Zhang, H., Li, X., Su, X., Ang, E. L., Zhang, Y., & Zhao, H. (2016). Production of Adipic Acid from Sugar Beet Residue by Combined Biological and Chemical Catalysis. ChemCatChem, 8(8), 1500-1506. DOI: 10.1002/cctc.201600069
 
Zhang, J. J., Cheng, F. F., Li, J. J., Zhu, J. J., & Lu, Y. (2016). Fluorescent nanoprobes for sensing and imaging of metal ions: Recent advances and future perspectives. Nano Today, 11(3), 309-329. DOI: 10.1016/j.nantod.2016.05.010
 
Chang, S., Fornasiero, P., Gunnoe, T. B., Jones, C. W., Linic, S., Ooi, T., ... Zhao, H. (2016). ACS Catalysis and the Scope of Papers Sought in Three Catalysis Subdisciplines: Biocatalysis and Enzymology, Molecular Catalysis for Organic Synthesis, and Heterogeneous Photocatalysis. ACS Catalysis, 6(7), 4782-4785. DOI: 10.1021/acscatal.6b01749
 
Wang, Y., Zhang, Z. T., Seo, S. O., Lynn, P., Lu, T., Jin, Y. S., & Blaschek, H. P. (2016). Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9. Biotechnology and Bioengineering, 113(12), 2739-2743. DOI: 10.1002/bit.26020
 
Wang, M., Yu, C., & Zhao, H. (2016). Identification of an important motif that controls the activity and specificity of sugar transporters. Biotechnology and Bioengineering. DOI: 10.1002/bit.25926
 
Liang, Y., Ang, E. L., & Zhao, H. (2016). A step through the looking glass. Science China Life Sciences, 59(9), 979-980. DOI: 10.1007/s11427-016-0170-6
 
Xing, H., Li, J., Xu, W., Hwang, K., Wu, P., Yin, Q., ... Lu, Y. (2016). The Effects of Spacer Length and Composition on Aptamer-Mediated Cell-Specific Targeting with Nanoscale PEGylated Liposomal Doxorubicin. ChemBioChem, 1111-1117. DOI: 10.1002/cbic.201600092
 
Tasan, I., Jain, S., & Zhao, H. (2016). Use of genome-editing tools to treat sickle cell disease. Human Genetics, 135(9), 1011-1028. DOI: 10.1007/s00439-016-1688-0
 
Si, T., Li, B., Zhang, K., Xu, Y., Zhao, H., & Sweedler, J. V. (2016). Characterization of bacillus subtilis colony biofilms via mass spectrometry and fluorescence imaging. Journal of Proteome Research, 15(6), 1955-1962. DOI: 10.1021/acs.jproteome.6b00127
 
Oh, E. J., Skerker, J. M., Kim, S. R., Wei, N., Turner, T. L., Maurer, M. J., ... Jin, Y. S. (2016). Gene amplification on demand accelerates cellobiose utilization in engineered Saccharomyces cerevisiae. Applied and Environmental Microbiology, 82(12), 3631-3639. DOI: 10.1128/AEM.00410-16
 
Blanchard, A. E., Liao, C., & Lu, T. (2016). An Ecological Understanding of Quorum Sensing-Controlled Bacteriocin Synthesis. Cellular and Molecular Bioengineering, 9(3), 443-454. DOI: 10.1007/s12195-016-0447-6
 
Hwang, K., Hosseinzadeh, P., & Lu, Y. (2016). Biochemical and biophysical understanding of metal ion selectivity of DNAzymes. Inorganica Chimica Acta, 452, 12-24. DOI: 10.1016/j.ica.2016.04.017
 
Shi, S., Si, T., Liu, Z., Zhang, H., Ang, E. L., & Zhao, H. (2016). Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae. Scientific Reports, 6, [25675]. DOI: 10.1038/srep25675
 
Freestone, T. S., & Zhao, H. (2016). Combinatorial pathway engineering for optimized production of the anti-malarial FR900098. Biotechnology and Bioengineering, 113(2), 384-392. DOI: 10.1002/bit.25719
 
Quarterman, J., Skerker, J. M., Feng, X., Liu, I. Y., Zhao, H., Arkin, A. P., & Jin, Y. S. (2016). Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae. Journal of Biotechnology, 229, 13-21. DOI: 10.1016/j.jbiotec.2016.04.041
 
Liao, C., Seo, S. O., & Lu, T. (2016). System-level modeling of acetone-butanol-ethanol fermentation. FEMS Microbiology Letters, 363(9), [fnw074]. DOI: 10.1093/femsle/fnw074
 
Shenoy, A., Rao, C. V., & Schroeder, C. M. (2016). Stokes trap for multiplexed particle manipulation and assembly using fluidics. Proceedings of the National Academy of Sciences of the United States of America, 113(15), 3976-3981. DOI: 10.1073/pnas.1525162113
 
Liu, J. J., Kong, I. I., Zhang, G. C., Jayakody, L. N., Kim, H., Xia, P. F., ... Jin, Y. S. (2016). Metabolic engineering of probiotic Saccharomyces boulardii. Applied and Environmental Microbiology, 82(8), 2280-2287. DOI: 10.1128/AEM.00057-16
 
Cao, Y., Ryser, M. D., Payne, S., Li, B., Rao, C. V., & You, L. (2016). Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria. Cell, 165(3), 620-630. DOI: 10.1016/j.cell.2016.03.006
 
Kim, J. S., Cho, D. H., Heo, P., Jung, S. C., Park, M., Oh, E. J., ... Kweon, D. H. (2016). Fumarate-mediated persistence of Escherichia coli against antibiotics. Antimicrobial Agents and Chemotherapy, 60(4), 2232-2240. DOI: 10.1128/AAC.01794-15
 
Wang, Y., Cobb, R. E., & Zhao, H. (2016). High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System. Methods in Enzymology. DOI: 10.1016/bs.mie.2016.03.014
 
Hosseinzadeh, P., Mirts, E. N., Pfister, T. D., Gao, Y. G., Mayne, C., Robinson, H., ... Lu, Y. (2016). Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions. Biochemistry, 55(10), 1494-1502. DOI: 10.1021/acs.biochem.5b01299
 
Guo, W., Sheng, J., Zhao, H., & Feng, X. (2016). Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose. Microbial Cell Factories, 15(1), [24]. DOI: 10.1186/s12934-016-0423-9
 
Luo, Y., Enghiad, B., & Zhao, H. (2016). New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters. Natural Product Reports, 33(2), 174-182. DOI: 10.1039/c5np00085h
 
Li, X., Park, A., Estrela, R., Kim, S. R., Jin, Y. S., & Cate, J. H. D. (2016). Comparison of xylose fermentation by two high-performance engineered strains of Saccharomyces cerevisiae. Biotechnology Reports, 9, 53-56. DOI: 10.1016/j.btre.2016.01.003
 
Seo, J. H., & Jin, Y. S. (2016). Editorial overview: Food biotechnology: Critical gap filler in the nexus of food, energy, and waste for a prosperous future. Current Opinion in Biotechnology, 37, 4-7. DOI: 10.1016/j.copbio.2016.01.001
 
Bao, Z., Cobb, R. E., & Zhao, H. (2016). Accelerated genome engineering through multiplexing. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 8(1), 5-21. DOI: 10.1002/wsbm.1319
 
Wang, M., Yu, C., & Zhao, H. (2016). Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization. Biotechnology and Bioengineering, 113(3), 484-491. DOI: 10.1002/bit.25724
 
Yuan, Y., Andersen, E., & Zhao, H. (2016). Flexible and Versatile Strategy for the Construction of Large Biochemical Pathways. ACS Synthetic Biology, 5(1), 46-52. DOI: 10.1021/acssynbio.5b00117
 
Mao, J., & Lu, T. (2016). Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation. Biophysical Journal, 110(1), 258-268. DOI: 10.1016/j.bpj.2015.11.033
 
Park, Y. C., Oh, E. J., Jo, J. H., Jin, Y. S., & Seo, J. H. (2016). Recent advances in biological production of sugar alcohols. Current Opinion in Biotechnology, 37, 105-113. DOI: 10.1016/j.copbio.2015.11.006
 
Jayakody, L. N., Lane, S., Kim, H., & Jin, Y. S. (2016). Mitigating health risks associated with alcoholic beverages through metabolic engineering. Current Opinion in Biotechnology, 37, 173-181. DOI: 10.1016/j.copbio.2015.12.001
 
Xu, H., Kim, S., Sorek, H., Lee, Y., Jeong, D., Kim, J., ... Jin, Y. S. (2016). PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metabolic Engineering, 34, 88-96. DOI: 10.1016/j.ymben.2015.12.007
 
Zhang, S., Skerker, J. M., Rutter, C. D., Maurer, M. J., Arkin, A. P., & Rao, C. V. (2016). Engineering Rhodosporidium toruloides for increased lipid production. Biotechnology and Bioengineering, 113(5), 1056-1066. DOI: 10.1002/bit.25864
 
Turner, T. L., Zhang, G. C., Oh, E. J., Subramaniam, V., Adiputra, A., Subramaniam, V., ... Jin, Y. S. (2016). Lactic acid production from cellobiose and xylose by engineered Saccharomyces cerevisiae. Biotechnology and Bioengineering, 113(5), 1075-1083. DOI: 10.1002/bit.25875
 
Wang, M., Li, S., & Zhao, H. (2016). Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 113(1), 206-215. DOI: 10.1002/bit.25676
 
Shi, S., Liang, Y., Zhang, M. M., Ang, E. L., & Zhao, H. (2016). A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metabolic Engineering, 33, 19-27. DOI: 10.1016/j.ymben.2015.10.011