PUBLICATIONS

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We research and develop new tools and methods  that accelerate synthetic genomics and all aspects of parts-based synthetic biology. 

 

We have major projects in Baker's yeast on genome synthesis, metabolic engineering and programming sensing, signalling and circuitry. 

 

We research how gene engineering burdens the cell, and develop design strategies to mitigate this. 

 

We use synthetic biology in bacteria and yeast to grow novel patterned and functional biomaterials 

PUBLICATIONS

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  • Ellis T (2019). What is synthetic genomics anyway? The Biochemist 41 (3), 6-9

  • Det-udom R, Gilbert G, Liu L, Prakitchaiwattana C, Ellis T, Ledesma-Amaro R (2019). Towards semi-synthetic microbial communities: enhancing soy sauce fermentation properties in B. subtilis co-cultures. Microbial Cell Factories, 18 (1), 101

  • Blount BA, Ellis T (2019). Genome Construction Amends Building Codes. Nature 569 (7757), 492-494

  • McCarty NS, Shaw WM, Ellis T, Ledesma-Amaro R (2019). Rapid Assembly of gRNA Arrays via Modular Cloning in Yeast. ACS Synthetic Biology, 8 (4), 906-910

  • Shaw WM, Yamauchi H, Mead J, Gowers G-OF, Bell D Öling D, Larsson N, Wigglesworth M, Ladds G, Ellis T (2019). Engineering a model cell for rational tuning of GPCR signaling. Cell, 177 (3), 782-796. e27

  • Boo A, Ellis T, Stan GB (2019). Host-aware synthetic biology. Current Opinion in Systems Biology, March 2019

  • Ellis T (2019). Predicting how evolution will beat us. Microbial Biotechnology, 12 (1), 41

 

  • Gilbert C, Ellis T (2019). Biological Engineered Living Materials–growing functional materials with genetically-programmable properties. ACS Synthetic Biology, 8 (1), 1-15

  • Blount BA, Ellis T (2018). The Synthetic Genome Summer Course. OUP Synthetic Biology, Nov 2018

  • Walker KT, Goosens VJ, Das A, Graham AE, Ellis T (2018). Engineered cell-to-cell signalling within growing bacterial cellulose pellicles. Microbial Biotechnology, Nov 2018

  • Gorochowski TE, Ellis T (2018) Designing efficient translation. Nature Biotechnology, 36 (10) 934

  • Weenink T, Van Der Hilst J, McKiernan RM, Ellis T (2018). Design of RNA Hairpin Modules that Predictably Tune Translation in Yeast. OUP Synthetic Biology, Online Oct 2018

  • Rajakumar PD, Gowers G-OF, Suckling L, Foster A, Ellis T, Kitney RI, McClymont DW, Freemont PS. (2018). Rapid Prototyping Platform for Saccharomyces cerevisiae Using Computer-Aided Genetic Design Enabled by Parallel Software and Workcell Platform Development. SLAS Technology. Online August 2018

  • Öling D, Lawenius L, Shaw WM, Clark S, Kettleborough R, Ellis T, Larsson N, Wigglesworth M (2018). Large scale synthetic site saturation GPCR libraries reveal novel mutations that alter glucose signalling. ACS Synthetic Biology. Online August 2018
     

  • 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 

  • 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

  • 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

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

  • 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  

  • 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   

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

  • 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

  • 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    

  • 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    

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

  • 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

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

  • 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   

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

  • 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   

  • 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

  • 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

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

  • 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

  • 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

  • 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   

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

  • 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 

  • 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 

  • 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

  • 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

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

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

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

  • 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  

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

  • 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 

  • 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  

  • 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

  • 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  

  • 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  

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

  • 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  

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

  • 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  

  • 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  

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

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

PhD THESES

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Submitted: Oct 2018

Started: Oct 2014

Will Shaw

Refactoring yeast signalling pathways for tunable extracellular biosensing

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Submitted: Nov 2016

Started: Oct 2012

Tim Weenink

Expanding the regulatory repertoire available for synthetic genetic circuits in S. cerevisiae

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Submitted: Mar 2016

Started: Oct 2011

Benjamin Reeve

Geobacillus thermoglucosidans as a Thermophile Chassis for Synthetic Biology

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Submitted: Dec 2014

Started: Jan 2011

Elena Martinez-Kimova

Synthetic biology approaches to the metabolic engineering of Geobacillus thermoglucosidans for isobutanol production

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Submitted: Nov 2013

Started: Oct 2010

Rhys J Algar

Understanding, characterising, and modelling the interactions between synthetic genetic circuits and their host chassis

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Submitted: April 2018

Started: Oct 2014

Charlie Gilbert

Synthetic biology approaches for engineered living materials

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Submitted: Sept 2016

Started: Oct 2012

George Pothoulakis

Organised Natural Structures using Synthetic Biology

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Submitted: Mar 2016

Started: Apr 2012

Dejana Jovicevic

Developing a Synthetic Yeast for the Expression of Heterologous Genes using SCRaMbLE

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Submitted: Sept 2014

Started: Oct 2010

Arturo Casini

Advanced DNA assembly strategies and standards for synthetic biology

CONTACT US

Tom Ellis - Professor of Synthetic Genome Engineering

Imperial College Centre for Synthetic Biology (IC-CSynB) and the Department of Bioengineering at Imperial College, London

Phone: +44-20-7594-7615

Email: t.ellis@imperial.ac.uk

Lab Address

609 Bessemer Building, Imperial College, London
South Kensington Campus, London SW7 2AZ, United Kingdom

 

Office Address

704 Bessemer Building, Imperial College, London
South Kensington Campus, London SW7 2AZ, United Kingdom