PUBLICATIONS

• Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome. BA Blount, G-OF Gowers, JCH Ho, R Ledesma-Amaro, D Jovicevic, RM McKiernan, ZX Xie, BZ Li, YJ Yuan, T Ellis. Nature Communications, May 2018. DOI link    OA paper

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• Cell-free prediction of protein expression costs for growing cells. O Borkowski, C Bricio, M Murgiano, B Rothschild-Mancinelli, GB Stan, T Ellis. Nature Communications April 2018. DOI link    Preprint Link

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• Burden-driven feedback control of gene expression. F Ceroni, A Boo, S Furini, TE Gorochowski, O Borkowski, YN Ladak, AR Awan, C Gilbert, GB Stan, T Ellis. Nature Methods April 2018. DOI link    Preprint Link

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• The challenges facing synthetic biology in eukaryotes. F Ceroni & T Ellis. Nature Reviews Molecular Cell Biology, April 2018. DOI link    Commentary

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• Construction of hybrid regulated mother-specific yeast promoters for inducible differential gene expression. G Pothoulakis, T Ellis. PLoS ONE  Mar 2018. 13(3): e0194588 DOI link    OA paper

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• Synthetic gene regulation for independent external induction of the Saccharomyces cerevisiae pseudohyphal growth phenotype. G Pothoulakis, T Ellis. Communications Biology Jan 2018. 1:7. DOI link    OA paper

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• A transatlantic perspective on 20 emerging issues in biological engineering. BC Wintle et al. eLife. Nov 2017. 6: e30247. DOI link     OA paper

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• Synthetic Genome Engineering Gets Infectious. LA Mitchell, T Ellis. Proceedings of the National Academy of Sciences, USA. Oct 2017. 114(42): 11006–11008. DOI link

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• Biosynthesis of the Antibiotic Nonribosomal Peptide Penicillin in Baker’s Yeast. AR Awan, BA Blount, DJ Bell, WM Shaw, JCH Ho, RM McKiernan, T Ellis. Nature Communications. 8, 15202, May 2017. DOI link    OA paper

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• Extracellular self-assembly of functional and tunable protein conjugates from Bacillus subtilis. C Gilbert, M Howarth, C Harwood, T Ellis, ACS Synthetic Biology. Accepted, February 2017. DOI Link    OA paper

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• Synthetic Biology in Europe. Special Issue Editorial. T Ellis, Y Cai. ACS Synthetic Biology, 5 (10), 1033-1033, October 2016. DOI Link   

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• BASIC: A Simple and Accurate Modular DNA Assembly Method. M Storch, A Casini, B Mackrow, T Ellis and GS Baldwin. Methods in Molecular Biology 1472, 79-91, September 2016. DOI Link  Book Chapter

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• Sensing the Right Time to Be Productive. F Ceroni, BA Blount, T Ellis. Cell Systems 3 (2), 116-117, August 2016. DOI Link   

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• Overloaded and stressed: whole-cell considerations for bacterial synthetic biology. O Borkowski, F Ceroni, GB Stan, T Ellis. Current Opinion in Microbiology, 33, 123-130, August 2016. DOI Link   

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• On the record with E. coli DNA. O Borkowski, C Gilbert, T Ellis. Science, 353 (6298), 444-445, July 2016. DOI Link   

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• The Geobacillus plasmid set: a modular toolkit for thermophile engineering. B Reeve, E Martinez-Klimova, J De Jonghe, DJ Leak, T Ellis. ACS Synthetic Biology,  June 2016. DOI Link   

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• Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain. M Florea, H Hagemann, G Santosa, J Abbott, CN Micklem, X Spencer-Milnes, L de Arroyo Garcia, D Paschou, C Lazenbatt, D Kong, H Chughtai, K Jensen, PS Freemont, R Kitney, B Reeve, T Ellis. Proceedings of the National Academy of Sciences, USA. June 2016. 113(24): E3431–E3440  PubMed Central OA Paper

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• GC Preps: Fast and Easy Extraction of Stable Yeast Genomic DNA. BA Blount, MRM Driessen, T Ellis. Scientific Reports, May 2016. 6: 26863   PubMed Central OA Paper

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• Biosynthesis of therapeutic natural products using synthetic biology. AR Awan, WM Shaw, T Ellis. Advanced Drug Delivery Reviews, April 2016 DOI Link   

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• A protease-based biosensor for the detection of schistosome cercariae. AJ Webb, R Kelwick, MJ Doenhoff, N Kylilis, JT MacDonald, KY Wen, C McKeown, G Baldwin, T Ellis, K Jensen, PS Freemont. Scientific Reports, April 2016. 6: 24725  PubMed Central OA Paper

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• Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582. M Florea, B Reeve, J Abbott, PS Freemont, T Ellis. Scientific Reports, March 2016. 6: 23635   PubMed Central OA Paper

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• Bricks and blueprints: methods and standards for DNA assembly. Casini A, Storch M, Baldwin GS, Ellis T. Nature Reviews Molecular Cell Biology, June 2015 DOI Link   

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• Quantifying cellular capacity identifies gene expression designs with reduced burden. Ceroni F, Algar R, Stan GB, Ellis T. Nature Methods, April 2015 DOI Link  

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• BASIC: a new Biopart Assembly Standard for Idempotent Cloning provides accurate, single-tier DNA assembly for synthetic biology. Storch M, Casini A, Mackrow B, Fleming T, Trewhitt H, Ellis T, Baldwin GS. ACS Synthetic Biology, March 2015 DOI Link 

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• Expression-level dependent perturbation of cell proteostasis and nuclear morphology by aggregation-prone polyglutamine proteins. Lu M, Williamson N, Boschetti C, Ellis T, Yoshimi T, Tunnacliffe A. Biotechnology and Bioengineering. April 2015 DOI Link Email to Request

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• Using Spinach Aptamer to Correlate mRNA and Protein Levels in Escherichia coli. Pothoulakis G, Ellis T. Methods in Enzymology v550, Jan 2015 DOI Link  Book Chapter

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• How synthetic biology will reconsider natural bioluminescence and its applications. Reeve B, Sanderson T, Ellis T, Freemont P. Adv Biochem Eng Biotechnol. 2145:3-30, Sep 2014 DOI Link  Book Chapter

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• Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast. Jovicevic D, Blount BA, Ellis T. Bioessays, Aug 2014 DOI Link  

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• GeneGuard: A Modular Plasmid System Designed for Biosafety. Wright O, Delmans M, Stan GB, Ellis T. ACS Synthetic Biology, May 2014 DOI Link  

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• The Sixth International Meeting on Synthetic Biology (SB6.0) Special Issue Editorial. Cai Y & Ellis T. ACS Synthetic Biology, Mar 2014 DOI Link  

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• R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences. Casini A,Christodoulou G, Freemont P, Baldwin GS, Ellis T, Macdonald JT. ACS Synthetic Biology, Jan 2014 DOI Link  

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• Predicting translation initiation rates for designing synthetic biology. Reeve B, Hargest T, Gilbert C, Ellis T. Front. Bioeng. Biotechnol, Jan 2014 DOI Link  

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• One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy. Casini A, Macdonald JT, De Jonghe J, Christodoulou G, Freemont P, Baldwin GS, Ellis T. Nucleic Acids Research, Oct 2013 DOI Link 

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• Modelling the burden caused by gene expression: an in silico investigation into the interactions between synthetic gene circuits and their chassis cell. Algar R, Ellis T, Stan GB. arXiv Q-Bio, Sep 2013 DOI Link  

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• Creation and characterization of component libraries for synthetic biology. Weenink T, Ellis T. Methods in Molecular Biology, 2013, Vol 1073, Page 51 DOI Link  Book chapter

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• Characterisation of genetic control elements for synthetic biology using the Spinach RNA aptamer. Pothoulakis G, Ceroni F, Reeve B, Ellis T. ACS Synthetic Biology, Sept 2013 DOI Link  

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• Engineering of regulated stochastic cell fate determination. Wu W, Su RQ, Ellis T, Lai YC, Wang X. PNAS USA, 2013, Vol 110, Page 10610 DOI Link  

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• Building-in Biosafety for Synthetic Biology. Wright O, Stan GB, Ellis T. Microbiology, 2013, Vol 159, Page 1221 DOI Link  

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• Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology. Blount BA, Weenink T, Vasylechko S, Ellis T. PLoS One, 2012, Vol 7, Page e33279 DOI Link  

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• Construction of synthetic regulatory networks in yeast. Blount BA, Weenink T, Ellis T. FEBS Letters, 2012, Vol 586, Page 2112 DOI Link  

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• DNA assembly for synthetic biology: from parts to pathways and beyond. Ellis T, Adie T, Baldwin GS. Integrative Biology, 2011, Vol 3, Page 109DOI Link  

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• Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Ellis T, Wang X, Collins JJ. Nature Biotechnology, 2009, Vol 27, Page 465 DOI Link  

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• Synthesis and screening of regulatory component libraries for synthetic biology. Ellis T. Nature Protocols, 2009 DOI Link  

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• Gene regulation: hacking the network on a sugar high. Ellis T, Wang X, Collins JJ. Molecular Cell, 2008, Vol 30, Page 1 DOI Link