Publications

2022

TS Moon. Making space for young speakers. Nature Chemical Biology, 18, 353 (2022)
https://www.nature.com/articles/s41589-022-01001-x

R Mackelprang, KP Adamala, ER Aurand, JC Diggans, AD Ellington, SW Evans, JLC Fortman, NJ Hillson, AW Hinman, FJ Isaacs, MI June, S Mamaghani, TS Moon, MJ Palmer, J Peccoud, EA Vitalis, I Hook-Barnard, D Friedman. Making Security Viral: Shifting engineering biology culture and publishing. ACS Synth. Biol. 11, 522–527 (2022)
https://pubs.acs.org/doi/10.1021/acssynbio.1c00324#.Yg-SGCLo4zp.linkedin

AG Rottinghaus, A Ferreiro, SRS Fishbein, G Dantas and TS Moon. Genetically stable CRISPR-based kill switches for engineered microbes. Nature Communications.
https://www.nature.com/articles/s41467-022-28163-5

2021

AG Rottinghaus, C Xi, MB Amrofell, H Yi and TS Moon. Engineering probiotics for specific sensing of aromatic amino acids or neurochemicals. Cell Systems.
Recommended by Faculty Opinions
https://www.sciencedirect.com/science/article/pii/S2405471221004178?dgcid=author

K Zhang, J Hodge, A Chatterjee, TS Moon and KM Parker. Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA, Environ. Sci. Technol.
https://pubs.acs.org/doi/10.1021/acs.est.1c01255

DM DeLorenzo, J Diao, R Carr, Y Hu and TS Moon. An improved CRISPR interference tool to engineer Rhodococcus opacus. ACS Synth. Biol.
https://pubs.acs.org/doi/full/10.1021/acssynbio.0c00591

2020

MB Amrofell, AG Rottinghaus and TS Moon. Engineering microbial diagnostics and therapeutics with smart control. Curr. Opin. Biotechnol. 66, 11-17. (2020)
https://pubmed.ncbi.nlm.nih.gov/32563763/

K Davis and TS Moon. Tailoring microbes to upgrade lignin. Curr. Opin. Chem. Biol. 59, 23-29 (2020)
https://pubmed.ncbi.nlm.nih.gov/32388219/

K Zhang, J Wei, K Huff Hartz, M Lydy, TS Moon, M Sander and KM Parker. Analysis of RNA interference (RNAi) biopesticides: double-stranded RNA (dsRNA) extraction from agricultural soils and quantification by RT-qPCR. Environ. Sci. Technol. 54, 4893−4902 (2020)
https://pubs.acs.org/doi/10.1021/acs.est.9b07781

C Frankfater, WR Henson, A Juenger-Leif, M Foston, TS Moon, J Turk, JLF Kao, A Haas and F Hsu. Structural determination of a new peptidolipid family from Rhodococcus opacus and the pathogen Rhodococcus equi by multiple stage mass spectrometry. J. Am. Soc. Mass Spectrom. 31, 611−623 (2020)
https://pubs.acs.org/doi/abs/10.1021/jasms.9b00059

A Chatterjee, DM DeLorenzo, R Carr and TS Moon. Bioconversion of renewable feedstocks by Rhodococcus opacus. Curr. Opin. Biotechnol. 64, 10-16 (2020)
https://pubmed.ncbi.nlm.nih.gov/31580993/

2019

AG Rottinghaus, MB Amrofell and TS Moon. Biosensing in smart engineered probiotics. Biotechnol. J.
https://doi.org/10.1002/biot.201900319

DM DeLorenzo and TS Moon. Construction of genetic logic gates based on the T7 RNA polymerase expression system in Rhodococcus opacus PD630. ACS Synth. Biol. 10.1021/acssynbio.9b00213 (2019)
https://pubmed.ncbi.nlm.nih.gov/31362487/

W Anthony, RR Carr, DM DeLorenzo, T Campbell, Z Shang, M Foston, TS Moon and G Dantas. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds. Biotechnol Biofuels. 12:192. (2019)
https://rdcu.be/bM69g

GW Roell, R Carr, T Campbell, Z Shang, WR Henson, J Czajka, H Martin, F Zhang, M Foston, G Dantas, TS Moon and YJ Tang. A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630. Metab. Eng. 55, 120-130 (2019)
https://pubmed.ncbi.nlm.nih.gov/31271774/

SJ Kim, M Leong, MB Amrofell, YJ Lee and TS Moon. Modulating responses of toehold switches by an inhibitory hairpin. ACS Synth. Biol.
https://pubs.acs.org/doi/10.1021/acssynbio.8b00488

2018

WR Henson, F Hsu, G Dantas, TS Moon and M Foston. Lipid metabolism of phenol tolerant Rhodococcus opacus strains for lignin bioconversion. Biotechnol Biofuels. 11:339 (2018)
https://rdcu.be/beIuD

YJ Lee, SJ Kim, MB Amrofell and TS Moon. Establishing a multivariate model for predictable antisense RNA-mediated repression. ACS Synth. Biol.
https://pubs.acs.org/doi/10.1021/acssynbio.8b00227

WR Henson, T Campbell, D DeLorenzo, Y Gao, B Berla, SJ Kim, M Foston, TS Moon and G Dantas. Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus. Metab. Eng. 49, 69–83 (2018)
https://pubmed.ncbi.nlm.nih.gov/30059786/

DM DeLorenzo and TS Moon. Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630. Sci. Rep. 8:6019 (2018)
https://www.nature.com/articles/s41598-018-24486-w

YJ Lee, SJ Kim and TS Moon. Multilevel regulation of bacterial gene expression with the combined STAR and antisense RNA system. ACS Synth. Biol. 10.1021/acssynbio.7b00322
https://pubs.acs.org/doi/10.1021/acssynbio.7b00322

DM DeLorenzo, AG Rottinghaus, WR Henson and TS Moon. Molecular toolkit for gene expression control and genome modification in Rhodococcus opacus PD630. ACS Synth. Biol. 10.1021/acssynbio.7b00416
https://pubs.acs.org/doi/10.1021/acssynbio.7b00416

YJ Lee and TS Moon. Design rules of synthetic non-coding RNAs in bacteria. Methods.
https://www.sciencedirect.com/science/article/pii/S1046202317303389

2017

DM DeLorenzo, WR Henson and TS Moon. Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630. ACS Synth. Biol. Accepted. DOI: 10.1021/acssynbio.7b00192
http://pubs.acs.org/doi/abs/10.1021/acssynbio.7b00192

T Shopera, WR Henson and TS Moon. Dynamics of sequestration-based gene regulatory cascades. Nucleic Acids Res. DOI: 10.1093/nar/gkx465
https://academic.oup.com/nar/article/3835315/Dynamics-of-sequestration-based-gene-regulatory

T Shopera, L He, T Oyetunde, YJ Tang and TS Moon. Decoupling resource-coupled gene expression in living cells. ACS Synth. Biol. Accepted. DOI: 10.1021/acssynbio.7b00119
http://pubs.acs.org/doi/abs/10.1021/acssynbio.7b00119

TS Moon. What Is the Role of Circuit Design in the Advancement of Synthetic Biology? Cell Systems 4, 370-372 (with 8 other contributors).
http://www.cell.com/cell-systems/fulltext/S2405-4712(17)30135-7

N Wan, DM DeLorenzo, L He, L You, CM Immethun, G Wang, EEK Baidoo, W Hollinshead, JD Keasling, TS Moon and YJ Tang. Cyanobacterial carbon metabolism: fluxome plasticity and oxygen dependence. Biotechnol. Bioeng. Accepted. DOI: 10.1002/bit.26287
http://onlinelibrary.wiley.com/doi/10.1002/bit.26287/full

A Hoynes-O’Connor, T Shopera, K Hinman, JP Creamer and TS Moon. Enabling Complex Genetic Circuits to Respond to Extrinsic Environmental Signals. Biotechnol. Bioeng. Accepted. DOI: 10.1002/bit.26279
http://onlinelibrary.wiley.com/doi/10.1002/bit.26279/full

CM Immethun, DM DeLorenzo, CM Focht, D Gupta, CB Johnson and TS Moon. Physical, Chemical, and Metabolic State Sensors Expand the Synthetic Biology Toolbox for Synechocystis sp. PCC 6803. Biotechnol. Bioeng. Accepted. DOI: 10.1002/bit.26275
http://onlinelibrary.wiley.com/doi/10.1002/bit.26275/full

2016

A Hoynes-O’Connor and TS Moon. Development of design rules for reliable antisense RNA behavior in E. coli. ACS Synth. Biol. 5, 1441−1454 (2016)
Featured on the Cover Page
http://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00036

R Saha, D Liu, A Hoynes-O’Connor, M Liberton, J Yu, M Bhattacharyya-Pakrasi, A Balassy, F Zhang, TS Moon, CD Maranas and HB Pakrasi. Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic and Physiological Analyses. mBio. 7, e00464-16 (2016)
https://pubmed.ncbi.nlm.nih.gov/27143387/

CM Immethun, WR Henson, X Wang, D Nielsen and TS Moon. Engineering Central Metabolism for Production of Higher Alcohol-based Biofuels, Chapter 1, p1-34 in “Biotechnologies for Biofuel Production and Optimization” (CA Eckert & CT Trinh, Ed). Elsevier.
http://dx.doi.org/10.1016/B978-0-444-63475-7.00001-7

YJ Lee, A Hoynes-O’Connor, MC Leong and TS Moon. Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system. Nucleic Acids Res. DOI: 10.1093/nar/gkw056 (2016)
One of NAR Top Articles (most often accessed in July 2017)
http://nar.oxfordjournals.org/content/early/2016/02/01/nar.gkw056.full

A Yoneda, WR Henson, NK Goldner, KJ Park, KJ Forsberg, SJ Kim, MW Pesesky, M Foston, G Dantas and TS Moon. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res. DOI: 10.1093/nar/gkw055 (2016)
http://nar.oxfordjournals.org/content/early/2016/02/01/nar.gkw055.full

2015

T Shopera, WR Henson, A Ng, YJ Lee, K Ng and TS Moon. Robust, tunable genetic memory from protein sequestration combined with positive feedback. Nucleic Acids Res. DOI: 10.1093/nar/gkv936 (2015)
http://nar.oxfordjournals.org/content/early/2015/09/17/nar.gkv936.full

CM Immethun, KM Ng, DM DeLorenzo, B Waldron-Feinstein, YC Lee and TS Moon. Oxygen-Responsive Genetic Circuits Constructed in Synechocystis sp. PCC 6803. Biotechnol. Bioeng. DOI: 10.1002/bit.25722 (2015)
http://onlinelibrary.wiley.com/doi/10.1002/bit.25722/abstract

WD Hollinshead, WR Henson, Mary Abernathy, TS Moon, and YJ Tang. Rapid Metabolic Analysis of Rhodococcus opacus PD630 via parallel 13C-Metabolite Fingerprinting. Biotechnol. Bioeng. DOI: 10.1002/bit.25702 (2015)
http://onlinelibrary.wiley.com/doi/10.1002/bit.25702/abstract

A Hoynes-O’Connor and TS Moon. Programmable genetic circuits for pathway engineering. Curr. Opin. Biotechnol. 36, 115-121 (2015)
http://www.sciencedirect.com/science/article/pii/S0958166915001068

A Hoynes-O’Connor, K Hinman, L Kirchner and TS Moon. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res. 43, 6166–6179 (2015)
http://nar.oxfordjournals.org/content/43/12/6166

2014

B Thompson, TS Moon and D Nielsen. ‘Hybrid’ Processing Strategies for Expanding and Improving the Synthesis of Renewable Bioproducts, Curr. Opin. Biotechnol. 30, 17-23 (2014).
http://dx.doi.org/10.1016/j.copbio.2014.04.005

2013

D Nielsen and TS Moon. From Promise to Practice: the Role of Synthetic Biology in Green Chemistry, EMBO Reports, published online, doi:10.1038/embor.2013.178 (2013)
http://dx.doi.org/10.1038/embor.2013.178

BM Berla, R Saha, CM Immethun, CD Maranas, TS Moon and H Pakrasi. Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities, Front. Microbiol. 4:246 (2013)
http://www.frontiersin.org/Microbial_Physiology_and_Metabolism/10.3389/fmicb.2013.00246/abstract

K Solomon, TS Moon, B Ma, TM Sanders and KJ Prather. Tuning primary metabolism for heterologous pathway productivity, ACS Synth. Biol. 2, 126-135 (2013)
http://dx.doi.org/10.1021/sb300055e
Professor Moon is highlighted in ACS Synthetic Biology’s “Introducing Our Authors”.
http://pubs.acs.org/doi/full/10.1021/sb400018u

CM Immethun, AG Hoynes-O’Connor, A Balassy and TS Moon. Microbial Production of Isoprenoids Enabled by Synthetic Biology, Front. Microbio. 4 (75), Invited review (2013)
http://www.frontiersin.org/microbiotechnology,_ecotoxicology_and_bioremediation/10.3389/fmicb.2013.00075/abstract

2012

TS Moon, C Lou, A Tamsir, BC Stanton and CA Voigt. Genetic Programs Constructed from Layered Logic Gates in Single Cells, Nature. 491, 249-253 (2012)
https://www.nature.com/articles/nature11516

TS Moon*, D Nielsen* and KJ Prather. Sensitivity Analysis of a Proposed Model Mechanism for Newly Created Glucose 6-Oxidases, AIChE J. 58, 2303-2308 (2012)
http://dx.doi.org/10.1002/aic.12762

2011

TS Moon, EJ Clarke, ES Groban, A Tamsir, RM Clark, M Eames, T Kortemme and CA Voigt. Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli, J. Mol. Biol. 406, 215-227 (2011)
http://dx.doi.org/10.1016/j.jmb.2010.12.019

2010

SM Lippow*, TS Moon*, S Basu, S-H Yoon, X Li, B Chapman, K Robison, D Lipovšek and KJ Prather. Engineering enzyme specificity using computational design of a defined-sequence library, Chem. Biol. 17, 1306-1315 (2010)
Selected as a “Recommended” paper by faculty of 1000
http://dx.doi.org/10.1016/j.chembiol.2010.10.012

TS Moon, JE Dueber, E Shiue and KJ Prather. Use of Modular, Synthetic Scaffolds for Improved Production of Glucaric Acid in Engineered E. coli, Metab. Eng. 12, 298-305 (2010)
http://dx.doi.org/10.1016/j.ymben.2010.01.003

2009

JE Dueber, GC Wu, GR Malmirchegini, TS Moon, CJ Petzold, AV Ullal, KJ Prather and JD Keasling. Synthetic Protein Scaffolds Provide Modular Control over Metabolic Flux, Nat. Biotechnol. 27, 753-759 (2009)
http://dx.doi.org/ 10.1038/nbt.1557

TS Moon, S-H Yoon, M-J Tsang Mui Ching, A Lanza and KJ Prather. Enzymatic assay of D-glucuronate using uronate dehydrogenase, Anal. Biochem. 392, 183-185 (2009)
http://dx.doi.org/10.1016/j.ab.2009.05.032

S-H Yoon, TS Moon, P Iranpour, A Lanza and KJ Prather. Cloning and characterization of uronate dehydrogenases from two Pseudomonads and Agrobacterium tumefaciens str. C58, J. Bateriol. 191, 1565-1573 (2009)
http://dx.doi.org/10.1128/JB.00586-08

TS Moon, S-H Yoon, A Lanza, J Roy-Mayhew and KJ Prather. Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli, Appl. Environ. Microbiol. 75, 589-595 (2009)
http://dx.doi.org/10.1128/AEM.00973-08

2005

SH Kim, K Hyun, TS Moon, T Mitsumata, JS Hong, KH Ahn and SJ Lee. Morphology-rheology relationship in hyaluronate/poly(vinyl alcohol)/borax polymer blends, Polymer, 46, 7156-7163 (2005)
http://dx.doi.org/10.1016/j.polymer.2005.05.089