Publications

All publications tracked by myNCBI

 

Greene, J.L., Waechter, A., Tyo, K.E.J., Broadbelt, L.J. (2017) Acceleration Strategies to Enhance Metabolic Ensemble Modeling Performance. Biophysical Journal 113 1150-1162.

Wang, L., Liang, C., Wu, J., Liu, L., Tyo, K.E.J. (2017) Increased processivity, misincorporation, and nucleotide efficiency in Sulfolobus solfataricus Dpo4 thumb domain mutants. Applied and Environmental Microbiology 83(18) e01013-17

Cybulski, T.R., Boyden, E.S., Church, G.M., Tyo, K.E.J., Kording, K.P. (2017) Nucleotide-time alignment for molecular recorders. PLoS Computational Biology 13(5) e1005483.

Stainbrook, S., Yu, J., Reddick, M., Bagheri, N., Tyo, K. (2017). Modulating and evaluating receptor promiscuity through directed evolution and modeling. Protein Engineering Design and Selection 30(6) 455-465.

Bothfeld, W., Kapov, G., Tyo, K., (2017). A glucose-sensing toggle switch for autonomous, high productivity genetic control. ACS Synthetic Biology 6(7) 1296-1304.

Yu, J., Pertusi, D., Adeniran, A., Tyo, K (2016). CellSort: A support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort. Bioinformatics 33(6) 909-916.

Henry, C., Rotman, E., Lathem, W., Tyo, K., Hauser M., Mandel, M. (2016). Generation and validation of the iKp1289 metabolic model for Klebsiella pneumoniae KPPR1.  Journal of Infectious Diseases 215(Supplement) S37-S43.

Wrenbeck, E., Klesmith, J., Stapleton, J., Adeniran, A., Tyo, K., Whitehead, T. (2016). Plasmid-based one-pot saturation mutagenesis. Nature Methods 13(11) 928-930.

Ozer, E., Morris, A., Krapp, F., Henry, C., Tyo, K., Lathem, W., and Hauser, A. (2016).  Draft Genome Sequence of a Multi-Drug Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source.  Genome Announcements 4 (3), e00422-16.

Sekar, K., Gentile, A. M., Bostick, J. W., & Tyo, K. E. (2016). N-Terminal-Based Targeted, Inducible Protein Degradation in Escherichia coli. PloS One,11(2), e0149746.

Moura, M., Finkle, J., Stainbrook, S., Greene, J., Broadbelt, L. J., & Tyo, K. E. (2016). Evaluating enzymatic synthesis of small molecule drugs. Metabolic Engineering, 33, 138-147.

Stine, A., Zhang, M., Ro, S., Clendennen, S., Shelton, M. C., Tyo, K. E., & Broadbelt, L. J. (2016). Exploring De Novo Metabolic Pathways from Pyruvate to Propionic Acid. Biotechnology Progress, 32 (2), 303-311.

Jeffryes, J., Colastani, R., Elbadawi-Sidhu, M., Kind, T., Niehaus, T., Broadbelt, L. J., Hanson, A., Fiehn, O., Tyo, K. E, & Henry, C. S. (2015). MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. Journal of Cheminformatics, 7(1), 1-8.

Moura, M., Pertusi, D., Lenzini, S., Bhan, N., Broadbelt, L. J., & Tyo, K. E. (2016). Characterizing and predicting carboxylic acid reductase activity for diversifying bioaldehyde production. Biotechnology and Bioengineering 33 138-147.

Sekar, K., & Tyo, K. E. (2015). Regulatory effects on central carbon metabolism from poly-3-hydroxybutryate synthesis. Metabolic Engineering. 28, 180-189.

Adeniran, A., Sherer, M., & Tyo, K. E. (2015). Yeast‐based biosensors: design and applications. FEMS Yeast Research. 15 (1), 1-15.

Rodríguez‐Limas, W. A., Tannenbaum, V., & Tyo, K. E. (2015). Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 112(2), 376-385.

Pertusi, D. A., Stine, A. E., Broadbelt, L. J., & Tyo, K. E. (2014). Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics. 31 (7), 1016-1024.

Lütke-Eversloh, T., & Tyo, K. E. (2014). Editorial overview: Cell and pathway engineering. Moving from possible to profitable: recent innovations in cell and pathway engineering. Current opinion in biotechnology, 29, v.

Tyo, K. E., Liu, Z., Magnusson, Y., Petranovic, D., & Nielsen, J. (2014). Impact of protein uptake and degradation on recombinant protein secretion in yeast. Applied Microbiology and Biotechnology, 98, 7149-7159.

Rodríguez-Limas, W. A., Sekar, K., & Tyo, K. E. (2013). Virus-like particles: The future of microbial factories and cell-free systems as platforms for vaccine development. Current Opinion in Biotechnology, 24(6), 1089-1093.

Glaser, J. I., Zamft, B. M., Marblestone, A. H., Moffitt, J. R., Tyo, K. E., Boyden, E. S., Church, G., Kording, K. P. (2013). Statistical analysis of molecular signal recording. PLoS Computational Biology, 9(7): e1003145. doi:10.1371/journal.pcbi.1003145.

Moura, M., Broadbelt, L., & Tyo, K. (2013). “Computational Tools for Guided Discovery and Engineering of Metabolic Pathways.” Methods in Molecular Biology: Systems Metabolic Engineering: Methods and Protocols, 985:123. Humana Press.

Zamft, B. M., Marblestone, A. H., Kording, K., Schmidt, D., Martin-Alarcon, D., Tyo, K., Boyden, E. S., & Church, G. (2012). Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. PloS ONE, 7(8), e43876. doi:10.1371/journal.pone.0043876

Hou, J., Tyo, K. E., Liu, Z., Petranovic, D., & Nielsen, J. (2012). Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiaeFEMS Yeast Research, 12(5), 491-510.

Tyo, K. E., Liu, Z., Petranovic, D., & Nielsen, J. (2012). Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress. BMC Biology, 10(1), 16.

Hou, J., Tyo, K., Liu, Z., Petranovic, D., & Nielsen, J. (2012). Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae. Metabolic Engineering, 14(2), 120-127.

Liu, Z., Tyo, K. E., Martínez, J. L., Petranovic, D., & Nielsen, J. (2012). Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 109(5), 1259-1268.

Ajikumar, P., Lim, R., Tyo, K. Chemically inducible chromosomal evolution (CIChE) for engineering lycopene production in Escherichia coli. Methods in Molecular Biology. (in press)

Rodríguez-Limas, W. A., Tyo, K. E., Nielsen, J., Ramírez, O. T., & Palomares, L. A. (2011). Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae. Microbial Cell Factories, 10(1).

Tyo, K. E., Nevoigt, E., & Stephanopoulos, G. (2011). Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation. Methods in Enzymology, 497, 135.

Petranovic, D., Tyo, K., Vemuri, G. N., & Nielsen, J. (2010). Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism. FEMS Yeast Research, 10(8), 1046-1059.

Ajikumar, P. K., Xiao, W. H., Tyo, K. E., Wang, Y., Simeon, F., Leonard, E., Wang, Y., Mucha, O., Phon, T. H., Pfiefer, B., & Stephanopoulos, G. (2010). Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science, 330 (6000), 70-74.

Tyo, K. E., Kocharin, K., & Nielsen, J. (2010). Toward design-based engineering of industrial microbes. Current Opinion in Microbiology, 13(3), 255-262.

Tyo, K. E., Ajikumar, P. K., & Stephanopoulos, G. (2009). Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nature Biotechnology, 27(8), 760-765.

Tyo, K. E., Fischer, C. R., Simeon, F., & Stephanopoulos, G. (2010). Analysis of polyhydroxybutyrate flux limitations by systematic genetic and metabolic perturbations. Metabolic Engineering, 12(3), 187-195.

Tyo, K. E., Jin, Y. S., Espinoza, F. A., & Stephanopoulos, G. (2009). Identification of gene disruptions for increased poly‐3‐hydroxybutyrate accumulation in Synechocystis PCC 6803. Biotechnology Progress, 25(5), 1236-1243.

Yu, H., Tyo, K., Alper, H., Klein‐Marcuschamer, D., & Stephanopoulos, G. (2008). A high‐throughput screen for hyaluronic acid accumulation in recombinant Escherichia coli transformed by libraries of engineered sigma factors. Biotechnology and Bioengineering, 101(4), 788-796.

Ajikumar, P., Tyo, K., Carlsen, S., Much, O., Phon, T. H., Stephanopoulos, G. (2008) Terpenoids: Biosynthesis of a versatile therapeutic class through engineered microorganisms. Molecular Pharmaceutics, 5(2), 167.

Tyo, K. E., Alper, H. S., & Stephanopoulos, G. N. (2007). Expanding the metabolic engineering toolbox: more options to engineer cells. Trends in Biotechnology, 25(3), 132-137.

Tyo, K., Zhou, H., Stephanopoulos, G. (2006) High-Throughput Screen for Poly-3-Hydroxybutryate in Escherichia coli and Synechocystis sp. Strain PCC6803. Applied and Environmental Microbiology, 72(5), 3412.

Raab, R., Tyo K., Stephanopoulos, G. (2005) Metabolic Engineering. Advances in Biochemical Engineering/Biotechnology, Springer-Verlag GmbH, 100,1.