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Items: 44

1.

Model-guided mechanism discovery and parameter selection for directed evolution.

Stainbrook SC, Tyo KEJ.

Appl Microbiol Biotechnol. 2019 Nov 4. doi: 10.1007/s00253-019-10179-5. [Epub ahead of print]

PMID:
31686141
2.

Bayesian inference of metabolic kinetics from genome-scale multiomics data.

St John PC, Strutz J, Broadbelt LJ, Tyo KEJ, Bomble YJ.

PLoS Comput Biol. 2019 Nov 4;15(11):e1007424. doi: 10.1371/journal.pcbi.1007424. eCollection 2019 Nov.

3.

Chemically Inducible Chromosomal Evolution (CIChE) for Multicopy Metabolic Pathway Engineering.

Love AM, Biggs BW, Tyo KEJ, Ajikumar PK.

Methods Mol Biol. 2019;1927:37-45. doi: 10.1007/978-1-4939-9142-6_4.

PMID:
30788784
4.

Metabolic In Silico Network Expansions to Predict and Exploit Enzyme Promiscuity.

Jeffryes J, Strutz J, Henry C, Tyo KEJ.

Methods Mol Biol. 2019;1927:11-21. doi: 10.1007/978-1-4939-9142-6_2.

PMID:
30788782
5.

Correction to "Detection of a Peptide Biomarker by Engineered Yeast Receptors".

Adeniran A, Stainbrook S, Bostick JW, Tyo KEJ.

ACS Synth Biol. 2018 Aug 17;7(8):1973. doi: 10.1021/acssynbio.8b00291. Epub 2018 Jul 20. No abstract available.

6.

High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.

de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ.

Nucleic Acids Res. 2018 Jul 27;46(13):e78. doi: 10.1093/nar/gky296.

7.

Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion.

Younger AKD, Su PY, Shepard AJ, Udani SV, Cybulski TR, Tyo KEJ, Leonard JN.

Protein Eng Des Sel. 2018 Feb 1;31(2):55-63. doi: 10.1093/protein/gzy001.

8.

Detection of a Peptide Biomarker by Engineered Yeast Receptors.

Adeniran A, Stainbrook S, Bostick JW, Tyo KEJ.

ACS Synth Biol. 2018 Feb 16;7(2):696-705. doi: 10.1021/acssynbio.7b00410. Epub 2018 Feb 5. Erratum in: ACS Synth Biol. 2018 Aug 17;7(8):1973.

9.

Predicting novel substrates for enzymes with minimal experimental effort with active learning.

Pertusi DA, Moura ME, Jeffryes JG, Prabhu S, Walters Biggs B, Tyo KEJ.

Metab Eng. 2017 Nov;44:171-181. doi: 10.1016/j.ymben.2017.09.016. Epub 2017 Oct 10.

PMID:
29030274
10.

Acceleration Strategies to Enhance Metabolic Ensemble Modeling Performance.

Greene JL, Wäechter A, Tyo KEJ, Broadbelt LJ.

Biophys J. 2017 Sep 5;113(5):1150-1162. doi: 10.1016/j.bpj.2017.07.018.

11.

Increased Processivity, Misincorporation, and Nucleotide Incorporation Efficiency in Sulfolobus solfataricus Dpo4 Thumb Domain Mutants.

Wang L, Liang C, Wu J, Liu L, Tyo KEJ.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e01013-17. doi: 10.1128/AEM.01013-17. Print 2017 Sep 15.

12.

DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase.

Wu J, de Paz A, Zamft BM, Marblestone AH, Boyden ES, Kording KP, Tyo KEJ.

Sci Rep. 2017 Jul 6;7(1):4756. doi: 10.1038/s41598-017-02578-3.

13.

Nucleotide-time alignment for molecular recorders.

Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP.

PLoS Comput Biol. 2017 May 1;13(5):e1005483. doi: 10.1371/journal.pcbi.1005483. eCollection 2017 May.

14.

Modulating and evaluating receptor promiscuity through directed evolution and modeling.

Stainbrook SC, Yu JS, Reddick MP, Bagheri N, Tyo KEJ.

Protein Eng Des Sel. 2017 Jun 1;30(6):455-465. doi: 10.1093/protein/gzx018.

15.

Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1.

Henry CS, Rotman E, Lathem WW, Tyo KE, Hauser AR, Mandel MJ.

J Infect Dis. 2017 Feb 15;215(suppl_1):S37-S43. doi: 10.1093/infdis/jiw465.

16.

A Glucose-Sensing Toggle Switch for Autonomous, High Productivity Genetic Control.

Bothfeld W, Kapov G, Tyo KEJ.

ACS Synth Biol. 2017 Jul 21;6(7):1296-1304. doi: 10.1021/acssynbio.6b00257. Epub 2017 Mar 30.

PMID:
28274123
17.

CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort.

Yu JS, Pertusi DA, Adeniran AV, Tyo KEJ.

Bioinformatics. 2017 Mar 15;33(6):909-916. doi: 10.1093/bioinformatics/btw710.

18.

Plasmid-based one-pot saturation mutagenesis.

Wrenbeck EE, Klesmith JR, Stapleton JA, Adeniran A, Tyo KE, Whitehead TA.

Nat Methods. 2016 Nov;13(11):928-930. doi: 10.1038/nmeth.4029. Epub 2016 Oct 10.

19.

Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source.

Ozer EA, Morris AR, Krapp F, Henry CS, Tyo KE, Lathem WW, Hauser AR.

Genome Announc. 2016 May 26;4(3). pii: e00422-16. doi: 10.1128/genomeA.00422-16.

20.

N-Terminal-Based Targeted, Inducible Protein Degradation in Escherichia coli.

Sekar K, Gentile AM, Bostick JW, Tyo KE.

PLoS One. 2016 Feb 22;11(2):e0149746. doi: 10.1371/journal.pone.0149746. eCollection 2016.

21.

Exploring De Novo metabolic pathways from pyruvate to propionic acid.

Stine A, Zhang M, Ro S, Clendennen S, Shelton MC, Tyo KE, Broadbelt LJ.

Biotechnol Prog. 2016 Mar;32(2):303-11. doi: 10.1002/btpr.2233. Epub 2016 Mar 3.

PMID:
26821575
22.

Evaluating enzymatic synthesis of small molecule drugs.

Moura M, Finkle J, Stainbrook S, Greene J, Broadbelt LJ, Tyo KEJ.

Metab Eng. 2016 Jan;33:138-147. doi: 10.1016/j.ymben.2015.11.006. Epub 2015 Dec 4.

PMID:
26655066
23.

Characterizing and predicting carboxylic acid reductase activity for diversifying bioaldehyde production.

Moura M, Pertusi D, Lenzini S, Bhan N, Broadbelt LJ, Tyo KE.

Biotechnol Bioeng. 2016 May;113(5):944-52. doi: 10.1002/bit.25860. Epub 2015 Nov 10.

PMID:
26479709
24.

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.

Jeffryes JG, Colastani RL, Elbadawi-Sidhu M, Kind T, Niehaus TD, Broadbelt LJ, Hanson AD, Fiehn O, Tyo KE, Henry CS.

J Cheminform. 2015 Aug 28;7:44. doi: 10.1186/s13321-015-0087-1. eCollection 2015.

25.

Regulatory effects on central carbon metabolism from poly-3-hydroxybutryate synthesis.

Sekar K, Tyo KEJ.

Metab Eng. 2015 Mar;28:180-189. doi: 10.1016/j.ymben.2015.01.003. Epub 2015 Jan 15.

PMID:
25598516
26.

Efficient searching and annotation of metabolic networks using chemical similarity.

Pertusi DA, Stine AE, Broadbelt LJ, Tyo KE.

Bioinformatics. 2015 Apr 1;31(7):1016-24. doi: 10.1093/bioinformatics/btu760. Epub 2014 Nov 21.

27.

Editorial overview: Cell and pathway engineering. Moving from possible to profitable: recent innovations in cell and pathway engineering.

Lütke-Eversloh T, Tyo KE.

Curr Opin Biotechnol. 2014 Oct;29:v-vii. doi: 10.1016/j.copbio.2014.08.002. Epub 2014 Aug 26. No abstract available.

PMID:
25168377
28.

Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae.

Rodríguez-Limas WA, Tannenbaum V, Tyo KE.

Biotechnol Bioeng. 2015 Feb;112(2):376-85. doi: 10.1002/bit.25360. Epub 2014 Oct 10.

PMID:
25154809
29.

Yeast-based biosensors: design and applications.

Adeniran A, Sherer M, Tyo KE.

FEMS Yeast Res. 2015 Feb;15(1):1-15. Epub 2015 Jan 14. Review.

PMID:
25154658
30.

Impact of protein uptake and degradation on recombinant protein secretion in yeast.

Tyo KE, Liu Z, Magnusson Y, Petranovic D, Nielsen J.

Appl Microbiol Biotechnol. 2014 Aug;98(16):7149-59. doi: 10.1007/s00253-014-5783-7. Epub 2014 May 10.

PMID:
24816620
31.

Virus-like particles: the future of microbial factories and cell-free systems as platforms for vaccine development.

Rodríguez-Limas WA, Sekar K, Tyo KE.

Curr Opin Biotechnol. 2013 Dec;24(6):1089-93. doi: 10.1016/j.copbio.2013.02.008. Epub 2013 Mar 5. Review.

PMID:
23481378
32.

Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae.

Hou J, Tyo KE, Liu Z, Petranovic D, Nielsen J.

FEMS Yeast Res. 2012 Aug;12(5):491-510. doi: 10.1111/j.1567-1364.2012.00810.x. Epub 2012 May 17. Review.

33.

Synthetic biology: emerging methodologies to catalyze the metabolic engineering design cycle.

Smolke CD, Tyo KE.

Metab Eng. 2012 May;14(3):187-8. doi: 10.1016/j.ymben.2012.03.009. Epub 2012 Mar 23. No abstract available.

PMID:
22465683
34.

Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress.

Tyo KE, Liu Z, Petranovic D, Nielsen J.

BMC Biol. 2012 Mar 1;10:16. doi: 10.1186/1741-7007-10-16.

35.

Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae.

Liu Z, Tyo KE, Martínez JL, Petranovic D, Nielsen J.

Biotechnol Bioeng. 2012 May;109(5):1259-68. doi: 10.1002/bit.24409. Epub 2012 Jan 17.

36.

Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation.

Tyo KE, Nevoigt E, Stephanopoulos G.

Methods Enzymol. 2011;497:135-55. doi: 10.1016/B978-0-12-385075-1.00006-8.

PMID:
21601085
37.

Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae.

Rodríguez-Limas WA, Tyo KE, Nielsen J, Ramírez OT, Palomares LA.

Microb Cell Fact. 2011 May 14;10:33. doi: 10.1186/1475-2859-10-33.

38.

Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli.

Ajikumar PK, Xiao WH, Tyo KE, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G.

Science. 2010 Oct 1;330(6000):70-4. doi: 10.1126/science.1191652.

39.

Toward design-based engineering of industrial microbes.

Tyo KE, Kocharin K, Nielsen J.

Curr Opin Microbiol. 2010 Jun;13(3):255-62. doi: 10.1016/j.mib.2010.02.001. Epub 2010 Mar 11. Review.

40.

Analysis of polyhydroxybutyrate flux limitations by systematic genetic and metabolic perturbations.

Tyo KE, Fischer CR, Simeon F, Stephanopoulos G.

Metab Eng. 2010 May;12(3):187-95. doi: 10.1016/j.ymben.2009.10.005. Epub 2009 Oct 30.

PMID:
19879956
41.

Stabilized gene duplication enables long-term selection-free heterologous pathway expression.

Tyo KE, Ajikumar PK, Stephanopoulos G.

Nat Biotechnol. 2009 Aug;27(8):760-5. doi: 10.1038/nbt.1555. Epub 2009 Jul 26.

PMID:
19633654
42.

Identification of gene disruptions for increased poly-3-hydroxybutyrate accumulation in Synechocystis PCC 6803.

Tyo KE, Jin YS, Espinoza FA, Stephanopoulos G.

Biotechnol Prog. 2009 Sep-Oct;25(5):1236-43. doi: 10.1002/btpr.228.

PMID:
19606467
43.

Expanding the metabolic engineering toolbox: more options to engineer cells.

Tyo KE, Alper HS, Stephanopoulos GN.

Trends Biotechnol. 2007 Mar;25(3):132-7. Epub 2007 Jan 24. Review.

PMID:
17254656
44.

High-throughput screen for poly-3-hydroxybutyrate in Escherichia coli and Synechocystis sp. strain PCC6803.

Tyo KE, Zhou H, Stephanopoulos GN.

Appl Environ Microbiol. 2006 May;72(5):3412-7.

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