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Items: 1 to 50 of 94

1.

A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides.

Corts AD, Thomason LC, Gill RT, Gralnick JA.

Sci Rep. 2019 Jan 10;9(1):39. doi: 10.1038/s41598-018-37025-4.

2.

Deep scanning lysine metabolism in Escherichia coli.

Bassalo MC, Garst AD, Choudhury A, Grau WC, Oh EJ, Spindler E, Lipscomb T, Gill RT.

Mol Syst Biol. 2018 Nov 26;14(11):e8371. doi: 10.15252/msb.20188371.

3.

Genomic Deoxyxylulose Phosphate Reductoisomerase (DXR) Mutations Conferring Resistance to the Antimalarial Drug Fosmidomycin in E. coli.

Pines G, Oh EJ, Bassalo MC, Choudhury A, Garst AD, Fankhauser RG, Eckert CA, Gill RT.

ACS Synth Biol. 2018 Nov 21. doi: 10.1021/acssynbio.8b00219. [Epub ahead of print]

PMID:
30462485
4.

Rational Control of Calcium Carbonate Precipitation by Engineered Escherichia coli.

Liang L, Heveran C, Liu R, Gill RT, Nagarajan A, Cameron J, Hubler M, Srubar WV 3rd, Cook SM.

ACS Synth Biol. 2018 Nov 16;7(11):2497-2506. doi: 10.1021/acssynbio.8b00194. Epub 2018 Nov 6.

PMID:
30384588
5.

Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production.

Liu R, Liang L, Choudhury A, Garst AD, Eckert CA, Oh EJ, Winkler J, Gill RT.

Metab Eng. 2018 Jul 17;51:50-58. doi: 10.1016/j.ymben.2018.07.007. [Epub ahead of print]

PMID:
30030154
6.

CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes.

Tarasava K, Oh EJ, Eckert CA, Gill RT.

Biotechnol J. 2018 Sep;13(9):e1700586. doi: 10.1002/biot.201700586. Epub 2018 Jul 12. Review.

PMID:
29917318
7.

Dynamic Management of Codon Compression for Saturation Mutagenesis.

Pines G, Gill RT.

Methods Mol Biol. 2018;1772:171-189. doi: 10.1007/978-1-4939-7795-6_9.

PMID:
29754228
8.

Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production.

Liu R, Liang L, Choudhury A, Bassalo MC, Garst AD, Tarasava K, Gill RT.

Metab Eng. 2018 May;47:303-313. doi: 10.1016/j.ymben.2018.04.007. Epub 2018 Apr 14.

PMID:
29665411
9.

Combinatorial pathway engineering using type I-E CRISPR interference.

Tarasava K, Liu R, Garst A, Gill RT.

Biotechnol Bioeng. 2018 Jul;115(7):1878-1883. doi: 10.1002/bit.26589. Epub 2018 Mar 30.

PMID:
29537074
10.

Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering.

Liu R, Liang L, Garst AD, Choudhury A, Nogué VSI, Beckham GT, Gill RT.

Metab Eng. 2018 May;47:10-20. doi: 10.1016/j.ymben.2018.02.007. Epub 2018 Mar 29.

PMID:
29477855
11.

Renewable acrylonitrile production.

Karp EM, Eaton TR, Sànchez I Nogué V, Vorotnikov V, Biddy MJ, Tan ECD, Brandner DG, Cywar RM, Liu R, Manker LP, Michener WE, Gilhespy M, Skoufa Z, Watson MJ, Fruchey OS, Vardon DR, Gill RT, Bratis AD, Beckham GT.

Science. 2017 Dec 8;358(6368):1307-1310. doi: 10.1126/science.aan1059.

PMID:
29217572
12.

Refactoring the Genetic Code for Increased Evolvability.

Pines G, Winkler JD, Pines A, Gill RT.

MBio. 2017 Nov 14;8(6). pii: e01654-17. doi: 10.1128/mBio.01654-17.

13.

The Tolerome: A Database of Transcriptome-Level Contributions to Diverse Escherichia coli Resistance and Tolerance Phenotypes.

Erickson KE, Winkler JD, Nguyen DT, Gill RT, Chatterjee A.

ACS Synth Biol. 2017 Dec 15;6(12):2302-2315. doi: 10.1021/acssynbio.7b00235. Epub 2017 Oct 19.

PMID:
29017328
14.

ROS mediated selection for increased NADPH availability in Escherichia coli.

Reynolds TS, Courtney CM, Erickson KE, Wolfe LM, Chatterjee A, Nagpal P, Gill RT.

Biotechnol Bioeng. 2017 Nov;114(11):2685-2689. doi: 10.1002/bit.26385. Epub 2017 Aug 17.

PMID:
28710857
15.

CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli.

Liang L, Liu R, Garst AD, Lee T, Nogué VSI, Beckham GT, Gill RT.

Metab Eng. 2017 May;41:1-10. doi: 10.1016/j.ymben.2017.02.009. Epub 2017 Feb 16.

PMID:
28216108
16.

Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies.

Zeitoun RI, Pines G, Grau WC, Gill RT.

ACS Synth Biol. 2017 Apr 21;6(4):619-627. doi: 10.1021/acssynbio.6b00376. Epub 2017 Jan 24.

PMID:
28103008
17.

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering.

Garst AD, Bassalo MC, Pines G, Lynch SA, Halweg-Edwards AL, Liu R, Liang L, Wang Z, Zeitoun R, Alexander WG, Gill RT.

Nat Biotechnol. 2017 Jan;35(1):48-55. doi: 10.1038/nbt.3718. Epub 2016 Dec 12.

PMID:
27941803
18.

Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli.

Groot J, Cepress-Mclean SC, Robbins-Pianka A, Knight R, Gill RT.

Biotechnol Bioeng. 2017 Apr;114(4):885-893. doi: 10.1002/bit.26217. Epub 2016 Dec 15.

PMID:
27861733
19.

Sustainability assessment of electrokinetic bioremediation compared with alternative remediation options for a petroleum release site.

Gill RT, Thornton SF, Harbottle MJ, Smith JW.

J Environ Manage. 2016 Dec 15;184(Pt 1):120-131. doi: 10.1016/j.jenvman.2016.07.036. Epub 2016 Aug 8.

20.

The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes.

Winkler JD, Halweg-Edwards AL, Erickson KE, Choudhury A, Pines G, Gill RT.

ACS Synth Biol. 2016 Dec 16;5(12):1566-1577. Epub 2016 Aug 2.

PMID:
27438180
21.

Quantifying complexity in metabolic engineering using the LASER database.

Winkler JD, Halweg-Edwards AL, Gill RT.

Metab Eng Commun. 2016 Jul 7;3:227-233. doi: 10.1016/j.meteno.2016.07.002. eCollection 2016 Dec.

22.

A Web Interface for Codon Compression.

Halweg-Edwards AL, Pines G, Winkler JD, Pines A, Gill RT.

ACS Synth Biol. 2016 Sep 16;5(9):1021-3. doi: 10.1021/acssynbio.6b00026. Epub 2016 May 19.

PMID:
27169595
23.

Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli.

Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik VK, Arkin AP, Gill RT.

ACS Synth Biol. 2016 Jul 15;5(7):561-8. doi: 10.1021/acssynbio.5b00187. Epub 2016 Apr 22.

PMID:
27072506
24.

Directed evolution and synthetic biology applications to microbial systems.

Bassalo MC, Liu R, Gill RT.

Curr Opin Biotechnol. 2016 Jun;39:126-133. doi: 10.1016/j.copbio.2016.03.016. Epub 2016 Apr 4. Review.

PMID:
27054950
25.

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli.

Weiss SJ, Mansell TJ, Mortazavi P, Knight R, Gill RT.

PLoS One. 2016 Jan 15;11(1):e0146916. doi: 10.1371/journal.pone.0146916. eCollection 2016.

26.

Synthesis aided design: The biological design-build-test engineering paradigm?

Gill RT, Halweg-Edwards AL, Clauset A, Way SF.

Biotechnol Bioeng. 2016 Jan;113(1):7-10. doi: 10.1002/bit.25857. Epub 2015 Nov 17. No abstract available.

PMID:
26580431
27.

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits.

Freed EF, Winkler JD, Weiss SJ, Garst AD, Mutalik VK, Arkin AP, Knight R, Gill RT.

ACS Synth Biol. 2015 Nov 20;4(11):1244-53. doi: 10.1021/acssynbio.5b00133. Epub 2015 Nov 5.

PMID:
26478262
28.

Genome scale engineering techniques for metabolic engineering.

Liu R, Bassalo MC, Zeitoun RI, Gill RT.

Metab Eng. 2015 Nov;32:143-154. doi: 10.1016/j.ymben.2015.09.013. Epub 2015 Oct 11. Review.

PMID:
26453944
29.

Complex systems in metabolic engineering.

Winkler JD, Erickson K, Choudhury A, Halweg-Edwards AL, Gill RT.

Curr Opin Biotechnol. 2015 Dec;36:107-14. doi: 10.1016/j.copbio.2015.08.002. Epub 2015 Aug 28. Review.

PMID:
26319897
30.

The emergence of commodity-scale genetic manipulation.

Halweg-Edwards AL, Grau WC, Winkler JD, Garst AD, Gill RT.

Curr Opin Chem Biol. 2015 Oct;28:150-5. doi: 10.1016/j.cbpa.2015.07.009. Epub 2015 Aug 22. Review.

PMID:
26302383
31.

Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination.

Pines G, Freed EF, Winkler JD, Gill RT.

ACS Synth Biol. 2015 Nov 20;4(11):1176-85. doi: 10.1021/acssynbio.5b00009. Epub 2015 Apr 27. Review.

PMID:
25856528
32.

Multiplexed tracking of combinatorial genomic mutations in engineered cell populations.

Zeitoun RI, Garst AD, Degen GD, Pines G, Mansell TJ, Glebes TY, Boyle NR, Gill RT.

Nat Biotechnol. 2015 Jun;33(6):631-7. doi: 10.1038/nbt.3177. Epub 2015 Mar 23.

PMID:
25798935
33.

Quantifying Impact of Chromosome Copy Number on Recombination in Escherichia coli.

Reynolds TS, Gill RT.

ACS Synth Biol. 2015 Jul 17;4(7):776-80. doi: 10.1021/sb500338g. Epub 2015 Mar 19.

PMID:
25763604
34.

CONSTRICTOR: constraint modification provides insight into design of biochemical networks.

Erickson KE, Gill RT, Chatterjee A.

PLoS One. 2014 Nov 25;9(11):e113820. doi: 10.1371/journal.pone.0113820. eCollection 2014.

35.

Codon compression algorithms for saturation mutagenesis.

Pines G, Pines A, Garst AD, Zeitoun RI, Lynch SA, Gill RT.

ACS Synth Biol. 2015 May 15;4(5):604-14. doi: 10.1021/sb500282v. Epub 2014 Oct 30.

PMID:
25303315
36.

Comparison of genome-wide selection strategies to identify furfural tolerance genes in Escherichia coli.

Glebes TY, Sandoval NR, Gillis JH, Gill RT.

Biotechnol Bioeng. 2015 Jan;112(1):129-40. doi: 10.1002/bit.25325. Epub 2014 Sep 2.

PMID:
24981318
37.

Electrokinetic-enhanced bioremediation of organic contaminants: a review of processes and environmental applications.

Gill RT, Harbottle MJ, Smith JW, Thornton SF.

Chemosphere. 2014 Jul;107:31-42. doi: 10.1016/j.chemosphere.2014.03.019. Epub 2014 Apr 9. Review.

38.

Genome-wide mapping of furfural tolerance genes in Escherichia coli.

Glebes TY, Sandoval NR, Reeder PJ, Schilling KD, Zhang M, Gill RT.

PLoS One. 2014 Jan 28;9(1):e87540. doi: 10.1371/journal.pone.0087540. eCollection 2014.

39.

Strategies for the multiplex mapping of genes to traits.

Garst A, Lynch M, Evans R, Gill RT.

Microb Cell Fact. 2013 Oct 30;12:99. doi: 10.1186/1475-2859-12-99. Review.

40.

O-antigen protects gram-negative bacteria from histone killing.

Chaput C, Spindler E, Gill RT, Zychlinsky A.

PLoS One. 2013 Aug 8;8(8):e71097. doi: 10.1371/journal.pone.0071097. eCollection 2013.

41.

Inverse metabolic engineering to improve Escherichia coli as an N-glycosylation host.

Pandhal J, Woodruff LB, Jaffe S, Desai P, Ow SY, Noirel J, Gill RT, Wright PC.

Biotechnol Bioeng. 2013 Sep;110(9):2482-93. doi: 10.1002/bit.24920. Epub 2013 May 17.

PMID:
23568537
42.

Accelerated protein engineering for chemical biotechnology via homologous recombination.

Nordwald EM, Garst A, Gill RT, Kaar JL.

Curr Opin Biotechnol. 2013 Dec;24(6):1017-22. doi: 10.1016/j.copbio.2013.03.003. Epub 2013 Mar 26. Review.

PMID:
23540421
43.

Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing.

Boyle NR, Reynolds TS, Evans R, Lynch M, Gill RT.

Biotechnol J. 2013 May;8(5):515-22. doi: 10.1002/biot.201200237. Epub 2013 Feb 22. Review.

PMID:
23436787
44.

Trackable multiplex recombineering for gene-trait mapping in E. coli.

Mansell TJ, Warner JR, Gill RT.

Methods Mol Biol. 2013;985:223-46. doi: 10.1007/978-1-62703-299-5_12.

PMID:
23417807
45.

Genome-wide identification of genes conferring energy related resistance to a synthetic antimicrobial peptide (Bac8c).

Spindler EC, Boyle NR, Hancock RE, Gill RT.

PLoS One. 2013;8(1):e55052. doi: 10.1371/journal.pone.0055052. Epub 2013 Jan 31.

46.

Engineering improved ethanol production in Escherichia coli with a genome-wide approach.

Woodruff LB, Boyle NR, Gill RT.

Metab Eng. 2013 May;17:1-11. doi: 10.1016/j.ymben.2013.01.006. Epub 2013 Jan 29.

PMID:
23376594
47.

Towards a metabolic engineering strain "commons": an Escherichia coli platform strain for ethanol production.

Woodruff LB, May BL, Warner JR, Gill RT.

Biotechnol Bioeng. 2013 May;110(5):1520-6. doi: 10.1002/bit.24840. Epub 2013 Jan 29.

PMID:
23322646
48.

Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli.

Woodruff LB, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT.

Metab Eng. 2013 Jan;15:124-33. doi: 10.1016/j.ymben.2012.10.007. Epub 2012 Nov 17.

PMID:
23164575
49.

Strategy for directing combinatorial genome engineering in Escherichia coli.

Sandoval NR, Kim JY, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, Gill RT.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10540-5. doi: 10.1073/pnas.1206299109. Epub 2012 Jun 11.

50.

Tools for genome-wide strain design and construction.

Boyle NR, Gill RT.

Curr Opin Biotechnol. 2012 Oct;23(5):666-71. doi: 10.1016/j.copbio.2012.01.012. Epub 2012 Feb 20. Review.

PMID:
22357141

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