PUBLICATIONS

Synthetic Biology

  • 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

  • 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
  • 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

  • Synthetic Genome Engineering Gets Infectious. LA Mitchell, T EllisProceedings 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    OA paper
  • 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
  • Synthetic Biology in Europe. Special Issue Editorial. T Ellis, Y Cai. ACS Synthetic Biology, 5 (10), 1033-1033, October 2016. DOI Link   pdficon_small
  • 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   pdficon_small
  • 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   pdficon_small
  • On the record with E. coli DNA. O Borkowski, C Gilbert, T Ellis. Science, 353 (6298), 444-445, July 2016. DOI Link   pdficon_small
  • 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   pdficon_small
  • 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 PMC 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  PMC 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   pdficon_small
  • 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 PMC 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  PMC 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   pdficon_small
  • Quantifying cellular capacity identifies gene expression designs with reduced burden. Ceroni FAlgar R, Stan GB, Ellis T. Nature Methods, April 2015 DOI Link  pdficon_small
  • 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 pdficon_small
  • 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
  • Using Spinach Aptamer to Correlate mRNA and Protein Levels in Escherichia coli. Pothoulakis GEllis 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 DBlount BAEllis T. Bioessays, Aug 2014 DOI Link  pdficon_small
  • GeneGuard: A Modular Plasmid System Designed for Biosafety. Wright ODelmans M, Stan GB, Ellis T. ACS Synthetic Biology, May 2014 DOI Link  pdficon_small
  • The Sixth International Meeting on Synthetic Biology (SB6.0) Special Issue Editorial. Cai Y & Ellis T. ACS Synthetic Biology, Mar 2014 DOI Link  pdficon_small
  • 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  pdficon_small
  • Predicting translation initiation rates for designing synthetic biology. Reeve B, Hargest T, Gilbert C, Ellis T. Front. Bioeng. Biotechnol, Jan 2014 DOI Link  pdficon_small
  • 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 pdficon_small
  • 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  pdficon_small
  • 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  pdficon_small
  • 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  pdficon_small
  • Building-in Biosafety for Synthetic Biology. Wright O, Stan GB,Ellis T. Microbiology, 2013, Vol 159, Page 1221 DOI Link  pdficon_small
  • 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  pdficon_small
  • Construction of synthetic regulatory networks in yeast. Blount BA, Weenink T, Ellis T. FEBS Letters, 2012, Vol 586, Page 2112 DOI Link  pdficon_small
  • 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  pdficon_small
  • 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  pdficon_small
  • Synthesis and screening of regulatory component libraries for synthetic biology. Ellis T. Nature Protocols, 2009 DOI Link  pdficon_small
  • Gene regulation: hacking the network on a sugar high. Ellis T, Wang X, Collins JJ. Molecular Cell, 2008, Vol 30, Page 1 DOI Link  pdficon_small

DNA Binding

  • An Extended PBD-Polyamide Conjugate with Selectivity for the ICB2 Transcription Factor Binding Site. Brucoli F, Hawkins RM, James CH, Jackson PJM, Wells G, Jenkins TC, Ellis T, Kotecha M, Hochhauser D, Hartley JA, Howard PW, Thurston DE. J Med Chem, 2013, Vol 56, Page 6339 DOI Link pdficon_small
  • Novel C8-linked pyrrolobenzodiazepine (PBD)-heterocycle conjugates that recognize DNA sequences containing an inverted CCAAT box. Brucoli F, Hawkins RM, James CH, Wells G, Jenkins TC, Ellis T, Hartley JA, Howard PW, Thurston DE. Bioorg Med Chem Letters, 2011, Vol 21, Page 3780 DOI Link pdficon_small
  • Molecular recognition of DNA by rigid [N]-polynorbornane derived bifunctional intercalators: synthesis and evaluation of their binding properties. Van Vliet LD, Ellis T, Foley PJ, Liu L, Pfeffer FM, Russell RA, Warrener RN, Hollfelder F, Waring MJ. Journal of Medicinal Chemistry, 2007, Vol 50, Page 2326 DOI Link pdficon_small
  • A 96-well DNase I footprinting screen for drug-DNA interactions. Ellis T, Evans DA, Martin CR, Hartley JA. Nucleic Acids Research, 2007, Vol 35DOI Link pdficon_small
  • Sequence-selective interaction of the minor-groove interstrand cross-linking agent SJG-136 with naked and cellular DNA: footprinting and enzyme inhibition studies. Martin C, Ellis T, McGurk CJ, Jenkins TC, Hartley JA, Waring MJ, Thurston DE. Biochemistry, 2005, Vol 44, Page 4135 DOI Link pdficon_small
  • DNase I footprinting of small molecule binding sites on DNA. Bailly C, Kluza J, Martin C, Ellis T, Waring MJ. Methods in Molecular Biology, 2005, Vol 288, Page 319 DOI Link Book chapter