Publications
Citations
Preprints
2023
- Coupling chemistry and biology for the synthesis of advanced bioproducts:
Chainani, Y., Bonnanzio, G., Tyo, K.E. and Broadbelt, L.J., 2023. Coupling chemistry and biology for the synthesis of advanced bioproducts. Current Opinion in Biotechnology, 84, p.102992. -
Pickaxe: a Python library for the prediction of novel metabolic reactions:
Shebek, K.M., Strutz, J., Broadbelt, L.J. and Tyo, K.E., 2023. Pickaxe: a Python library for the prediction of novel metabolic reactions. BMC bioinformatics, 24(1), pp.1-15. -
A dynamic kinetic model captures cell-free metabolism for improved butanol production:
Martin, J.P., Rasor, B.J., DeBonis, J., Karim, A.S., Jewett, M.C., Tyo, K.E. and Broadbelt, L.J., 2023. A dynamic kinetic model captures cell-free metabolism for improved butanol production. Metabolic Engineering, 76, pp.133-145.
2022
- MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics:
Strutz, J., Shebek, K.M., Broadbelt, L.J. and Tyo, K.E., 2022. MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics. Bioinformatics, 38(13), pp.3484-3487. - Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions:
Jeffryes, J.G., Lerma-Ortiz, C., Liu, F., Golubev, A., Niehaus, T.D., Elbadawi-Sidhu, M., Fiehn, O., Hanson, A.D., Tyo, K.E. and Henry, C.S., 2022. Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions. Metabolic Engineering, 69, pp.302-312.
2021
- Enabling commercial success of industrial biotechnology:
Biggs, B.W., Alper, H.S., Pfleger, B.F., Tyo, K.E., Santos, C.N., Ajikumar, P.K. and Stephanopoulos, G., 2021. Enabling commercial success of industrial biotechnology. Science, 374(6575), pp.1563-1565. - Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis:
Bhan, N., Callisto, A., Strutz, J., Glaser, J., Kalhor, R., Boyden, E.S., Church, G., Kording, K. and Tyo, K.E., 2021. Recording temporal signals with minutes resolution using enzymatic DNA synthesis. Journal of the American Chemical Society, 143(40), pp.16630-16640. - Engineering Acinetobacter baylyi ADP1 for mevalonate production from lignin-derived aromatic compounds:
Arvay, E., Biggs, B.W., Guerrero, L., Jiang, V. and Tyo, K., 2021. Engineering Acinetobacter baylyi ADP1 for mevalonate production from lignin-derived aromatic compounds. Metabolic engineering communications, 13, p.e00173. - Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation:
Fackler, N., Heijstra, B.D., Rasor, B.J., Brown, H., Martin, J., Ni, Z., Shebek, K.M., Rosin, R.R., Simpson, S.D., Tyo, K.E. and Giannone, R.J., 2021. Stepping on the gas to a circular economy: accelerating development of carbon-negative chemical production from gas fermentation. Annual review of chemical and biomolecular engineering, 12, pp.439-470.
- Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters:
Glasscock, C.J., Biggs, B.W., Lazar, J.T., Arnold, J.H., Burdette, L.A., Valdes, A., Kang, M.K., Tullman-Ercek, D., Tyo, K.E. and Lucks, J.B., 2021. Dynamic control of gene expression with riboregulated switchable feedback promoters. ACS synthetic biology, 10(5), pp.1199-1213. - Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design:
Ni, Z., Stine, A.E., Tyo, K.E. and Broadbelt, L.J., 2021. Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design. Metabolic Engineering, 65, pp.79-87.
2020
- Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1:
Biggs, B.W., Bedore, S.R., Arvay, E., Huang, S., Subramanian, H., McIntyre, E.A., Duscent-Maitland, C.V., Neidle, E.L. and Tyo, K.E.J., 2020. Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1. Nucleic acids research, 48(9), pp.5169-5182.
2019
- Model-guided mechanism discovery and parameter selection for directed evolution:
Stainbrook, S.C. and Tyo, K.E., 2019. Model-guided mechanism discovery and parameter selection for directed evolution. Applied microbiology and biotechnology, 103(23-24), pp.9697-9709. - Bayesian inference of metabolic kinetics from genome-scale multiomics data:
St. John, P.C., Strutz, J., Broadbelt, L.J., Tyo, K.E. and Bomble, Y.J., 2019. Bayesian inference of metabolic kinetics from genome-scale multiomics data. PLoS computational biology, 15(11), p.e1007424. - Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain:
Strutz, J., Martin, J., Greene, J., Broadbelt, L. and Tyo, K., 2019. Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain. Current opinion in biotechnology, 59, pp.24-30. - Chemically Inducible Chromosomal Evolution (CIChE) for Multicopy Metabolic Pathway Engineering:
Love, A.M., Biggs, B.W., Tyo, K.E. and Ajikumar, P.K., 2019. Chemically inducible chromosomal evolution (ciche) for multicopy metabolic pathway engineering. Microbial Metabolic Engineering: Methods and Protocols, pp.37-45. - Metabolic In Silico Network Expansions to Predict and Exploit Enzyme Promiscuity:
Jeffryes, J., Strutz, J., Henry, C. and Tyo, K.E., 2019. Metabolic in silico network expansions to predict and exploit enzyme promiscuity. Microbial Metabolic Engineering: Methods and Protocols, pp.11-21.
2018
- High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing:
De Paz, A.M., Cybulski, T.R., Marblestone, A.H., Zamft, B.M., Church, G.M., Boyden, E.S., Kording, K.P. and Tyo, K.E.J., 2018. High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic acids research, 46(13), pp.e78-e78. - Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion:
Younger, A.K., Su, P.Y., Shepard, A.J., Udani, S.V., Cybulski, T.R., Tyo, K.E. and Leonard, J.N., 2018. Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion. Protein Engineering, Design and Selection, 31(2), pp.55-63. - Detection of a Peptide Biomarker by Engineered Yeast Receptors:
Adeniran, A., Stainbrook, S., Bostick, J.W. and Tyo, K.E., 2018. Detection of a peptide biomarker by engineered yeast receptors. ACS synthetic biology, 7(2), pp.696-705.
2017
- Predicting novel substrates for enzymes with minimal experimental effort with active learning:
Pertusi, D.A., Moura, M.E., Jeffryes, J.G., Prabhu, S., Biggs, B.W. and Tyo, K.E., 2017. Predicting novel substrates for enzymes with minimal experimental effort with active learning. Metabolic engineering, 44, pp.171-181. - Increased processivity, misincorporation, and nucleotide incorporation efficiency in Sulfolobus solfataricus Dpo4 thumb domain mutants:
Wang, L., Liang, C., Wu, J., Liu, L. and Tyo, K.E., 2017. Increased processivity, misincorporation, and nucleotide incorporation efficiency in Sulfolobus solfataricus Dpo4 thumb domain mutants. Applied and Environmental Microbiology, 83(18), pp.e01013-17. - Acceleration strategies to enhance metabolic ensemble modeling performance:
Greene, J.L., Wäechter, A., Tyo, K.E. and Broadbelt, L.J., 2017. Acceleration strategies to enhance metabolic ensemble modeling performance. Biophysical journal, 113(5), pp.1150-1162. - A glucose-sensing toggle switch for autonomous, high productivity genetic control:
Bothfeld, W., Kapov, G. and Tyo, K.E., 2017. A glucose-sensing toggle switch for autonomous, high productivity genetic control. ACS synthetic biology, 6(7), pp.1296-1304. - DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase:
Wu, J., De Paz, A., Zamft, B.M., Marblestone, A.H., Boyden, E.S., Kording, K.P. and Tyo, K.E., 2017. DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. Scientific reports, 7(1), p.4756. - Modulating and evaluating receptor promiscuity through directed evolution and modeling:
Stainbrook, S.C., Yu, J.S., Reddick, M.P., Bagheri, N. and Tyo, K.E., 2017. Modulating and evaluating receptor promiscuity through directed evolution and modeling. Protein Engineering, Design and Selection, 30(6), pp.455-465. - Nucleotide-time alignment for molecular recorders:
Cybulski, T.R., Boyden, E.S., Church, G.M., Tyo, K.E. and Kording, K.P., 2017. Nucleotide-time alignment for molecular recorders. PLoS computational biology, 13(5), p.e1005483. - CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort:
Yu, J.S., Pertusi, D.A., Adeniran, A.V. and Tyo, K.E., 2017. CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort. Bioinformatics, 33(6), pp.909-916. - Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1:
Henry, C.S., Rotman, E., Lathem, W.W., Tyo, K.E., Hauser, A.R. and Mandel, M.J., 2017. Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1. The Journal of Infectious Diseases, 215(suppl_1), pp.S37-S43.
2016
- Plasmid-based one-pot saturation mutagenesis:
Wrenbeck, E.E., Klesmith, J.R., Stapleton, J.A., Adeniran, A., Tyo, K.E. and Whitehead, T.A., 2016. Plasmid-based one-pot saturation mutagenesis. Nature Methods, 13(11), pp.928-930. - Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source:
Ozer, E.A., Morris, A.R., Krapp, F., Henry, C.S., Tyo, K.E., Lathem, W.W. and Hauser, A.R., 2016. Draft genome sequence of a multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae isolate from a clinical source. Genome Announcements, 4(3), pp.10-1128. - Characterizing and predicting carboxylic acid reductase activity for diversifying bioaldehyde production:
Moura, M., Pertusi, D., Lenzini, S., Bhan, N., Broadbelt, L.J. and Tyo, K.E., 2016. Characterizing and predicting carboxylic acid reductase activity for diversifying bioaldehyde production. Biotechnology and Bioengineering, 113(5), pp.944-952. - Exploring De Novo metabolic pathways from pyruvate to propionic acid:
Stine, A., Zhang, M., Ro, S., Clendennen, S., Shelton, M.C., Tyo, K.E. and Broadbelt, L.J., 2016. Exploring de novo metabolic pathways from pyruvate to propionic acid. Biotechnology Progress, 32(2), pp.303-311. - N-Terminal-Based Targeted, Inducible Protein Degradation in Escherichia coli:
Sekar, K., Gentile, A.M., Bostick, J.W. and Tyo, K.E., 2016. N-terminal-based targeted, inducible protein degradation in Escherichia coli. PLoS One, 11(2), p.e0149746. - Evaluating enzymatic synthesis of small molecule drugs:
Moura, M., Finkle, J., Stainbrook, S., Greene, J., Broadbelt, L.J. and Tyo, K.E., 2016. Evaluating enzymatic synthesis of small molecule drugs. Metabolic engineering, 33, pp.138-147.
2015
- MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics:
Jeffryes, J.G., Colastani, R.L., Elbadawi-Sidhu, M., Kind, T., Niehaus, T.D., Broadbelt, L.J., Hanson, A.D., Fiehn, O., Tyo, K.E. and Henry, C.S., 2015. MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. Journal of cheminformatics, 7, pp.1-8. - Efficient searching and annotation of metabolic networks using chemical similarity:
Pertusi, D.A., Stine, A.E., Broadbelt, L.J. and Tyo, K.E., 2015. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics, 31(7), pp.1016-1024. - Regulatory effects on central carbon metabolism from poly-3-hydroxybutryate synthesis:
Sekar, K. and Tyo, K.E., 2015. Regulatory effects on central carbon metabolism from poly-3-hydroxybutryate synthesis. Metabolic Engineering, 28, pp.180-189. - Yeast-based biosensors: Design and applications:
Adeniran, A., Sherer, M. and Tyo, K.E., 2015. Yeast-based biosensors: Design and applications. FEMS yeast research, 15(1), pp.1-15. - Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae:
Rodríguez‐Limas, W.A., Tannenbaum, V. and Tyo, K.E., 2015. Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae. Biotechnology and bioengineering, 112(2), pp.376-385.
2014
- Impact of protein uptake and degradation on recombinant protein secretion in yeast:
Tyo, K.E., Liu, Z., Petranovic, D. and Nielsen, J., 2014. Impact of protein uptake and degradation on recombinant protein secretion in yeast. Applied microbiology and biotechnology, 98, pp.7149-7159
2013
- Computational tools for guided discovery and engineering of metabolic pathways:
Moura, M., Broadbelt, L. and Tyo, K., 2013. Computational tools for guided discovery and engineering of metabolic pathways. Systems Metabolic Engineering: Methods and Protocols, pp.123-147. - Statistical analysis of molecular signal recording:
Glaser, J.I., Zamft, B.M., Marblestone, A.H., Moffitt, J.R., Tyo, K., Boyden, E.S., Church, G. and Kording, K.P., 2013. Statistical analysis of molecular signal recording. PLoS computational biology, 9(7), p.e1003145. - Virus-like particles: the future of microbial factories and cell-free systems as platforms for vaccine development:
Rodríguez-Limas, W.A., Sekar, K. and 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), pp.1089-1093.
2012
- Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress:
Tyo, K.E., Liu, Z., Petranovic, D. and Nielsen, J., 2012. Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress. BMC biology, 10, pp.1-14. - Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing:
Zamft, B.M., Marblestone, A.H., Kording, K., Schmidt, D., Martin-Alarcon, D., Tyo, K., Boyden, E.S. and Church, G., 2012. Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. - Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae:
Hou, J., Tyo, K.E., Liu, Z., Petranovic, D. and Nielsen, J., 2012. Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae. FEMS yeast research, 12(5), pp.491-510. - Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae:
Liu, Z., Tyo, K.E., Martínez, J.L., Petranovic, D. and Nielsen, J., 2012. Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae. Biotechnology and bioengineering, 109(5), pp.1259-1268. - Synthetic biology: emerging methodologies to catalyze the metabolic engineering design cycle:
Smolke, C.D. and Tyo, K.E., 2012. Synthetic biology: emerging methodologies to catalyze the metabolic engineering design cycle. Metabolic Engineering, 14(3), pp.187-188. - Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae:
Hou, J., Tyo, K., Liu, Z., Petranovic, D. and Nielsen, J., 2012. Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae. Metabolic engineering, 14(2), pp.120-127.
2011
- Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation:
Tyo, K.E., Nevoigt, E. and Stephanopoulos, G., 2011. Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation. In Methods in enzymology (Vol. 497, pp. 135-155). Academic Press. - Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae:
Rodríguez-Limas, W.A., Tyo, K.E., Nielsen, J., Ramírez, O.T. and Palomares, L.A., 2011. Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae. Microbial cell factories, 10(1), pp.1-10.
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Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism:
Tyo, K. E. J.; Nevoigt, E.; Stephanopoulos, G. Chapter Six – Directed Evolution of Promoters and Tandem Gene Arrays for Customizing RNA Synthesis Rates and Regulation. In Methods in Enzymology; Voigt, C., Ed.; Synthetic Biology, Part A; Academic Press, 2011; Vol. 497, pp 135–155. https://doi.org/10.1016/B978-0-12-385075-1.00006-8.
2010
- Analysis of polyhydroxybutyrate flux limitations by systematic genetic and metabolic perturbations: Tyo, K. E. J.; Fischer, C. R.; Simeon, F.; Stephanopoulos, G. Analysis of Polyhydroxybutyrate Flux Limitations by Systematic Genetic and Metabolic Perturbations. Metabolic Engineering 2010, 12 (3), 187–195. https://doi.org/10.1016/j.ymben.2009.10.005.
- Toward design-based engineering of industrial microbes: Tyo, K. E.; Kocharin, K.; Nielsen, J. Toward Design-Based Engineering of Industrial Microbes. Current Opinion in Microbiology 2010, 13 (3), 255–262. https://doi.org/10.1016/j.mib.2010.02.001.
- Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli: Ajikumar, P.K., Xiao, W.H., Tyo, K.E., Wang, Y., Simeon, F., Leonard, E., Mucha, O., Phon, T.H., Pfeifer, B. and Stephanopoulos, G., 2010. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science, 330(6000), pp.70-74.
2009
- Identification of gene disruptions for increased poly‐3‐hydroxybutyrate accumulation in Synechocystis PCC 6803: Tyo, K. E. J.; Jin, Y.-S.; Espinoza, F. A.; Stephanopoulos, G. Identification of Gene Disruptions for Increased Poly-3-Hydroxybutyrate Accumulation in Synechocystis PCC 6803. Biotechnology Progress 2009, 25 (5), 1236–1243. https://doi.org/10.1002/btpr.228.
- Stabilized gene duplication enables long-term selection-free heterologous pathway expression: Tyo, K. E. J.; Ajikumar, P. K.; Stephanopoulos, G. Stabilized Gene Duplication Enables Long-Term Selection-Free Heterologous Pathway Expression. Nat Biotechnol 2009, 27 (8), 760–765. https://doi.org/10.1038/nbt.1555.
2007
- Expanding the Metabolic Engineering Toolbox: More Options to Engineer Cells:
Tyo, K. E.; Alper, H. S.; Stephanopoulos, G. N. Expanding the Metabolic Engineering Toolbox: More Options to Engineer Cells. Trends in Biotechnology 2007, 25 (3), 132–137. https://doi.org/10.1016/j.tibtech.2007.01.003 - Terpenoids: Opportunities for Biosynthesis of Natural Product Drugs Using Engineered Microorganisms:
Ajikumar, P. K.; Tyo, K.; Carlsen, S.; Mucha, O.; Phon, T. H.; & Stephanopoulos, G. N. Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms. Molecular pharmaceutics 2007, 5(2), 167-190. https://doi.org/10.1021/mp700151b
2006
- High-Throughput Screen for Poly-3-Hydroxybutyrate in Escherichia coli and Synechocystis sp. Strain PCC6803:
Tyo, K. E.; Zhou, H.; Stephanopoulos, G. N. High-Throughput Screen for Poly-3-Hydroxybutyrate in Escherichia Coli and Synechocystis Sp. Strain PCC6803. Applied and Environmental Microbiology 2006, 72 (5), 3412–3417. https://doi.org/10.1128/AEM.72.5.3412-3417.2006
2005
- Metabolic engineering:
Raab, R. M.; Tyo, K.; Stephanopoulos, G. Metabolic Engineering. In Biotechnology for the Future; Nielsen, J., Ed.; Advances in Biochemical Engineering/Biotechnology; Springer: Berlin, Heidelberg, 2005; pp 1–17. https://doi.org/10.1007/b136411