Ellis:Publications: Difference between revisions
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{{Ellis Top}} | {{Ellis Top}} | ||
'''Click the links to read our papers''' | '''Click the links to read our papers''' | ||
<font face="trebuchet ms" style="color:#000000">We're in the lab right now working on new publications. | <font face="trebuchet ms" style="color:#000000">We're in the lab right now working on new publications. '''Latest Update: AUG 2014''' | ||
<br> | <br> | ||
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! || Title !! Authors !! Published !! PDF !! Screenshot | ! || Title !! Authors !! Published !! PDF !! Screenshot | ||
|- | |- | ||
! Synthetic Biology | ! <b>Synthetic Biology</b> | ||
|Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast | |||
| '''Jovicevic D''', '''Blount BA''', '''Ellis T''' | |||
| '''Bioessays''', Aug 2014 [http://onlinelibrary.wiley.com/doi/10.1002/bies.201400086/abstract DOI Link] | |||
| [http://openwetware.org/images/c/cf/DJSc20rev.pdf View PDF] | |||
| [[Image:DJSc20.jpg|160px|right|Sc20]] | |||
|- | |||
! | |||
|GeneGuard: A Modular Plasmid System Designed for Biosafety | |||
| '''Wright O''', '''Delmans M''', Stan GB, '''Ellis T''' | |||
| '''ACS Synthetic Biology''', May 2014 [http://pubs.acs.org/doi/abs/10.1021/sb500234s DOI Link] | |||
| [http://openwetware.org/images/3/37/GeneGuard.pdf View PDF] | |||
| [[Image:GeneGuard.jpg|160px|right|GeneGuard]] | |||
|- | |||
! | |||
| The Sixth International Meeting on Synthetic Biology (SB6.0) Special Issue Editorial | |||
| Cai Y & '''Ellis T''' | |||
| '''ACS Synthetic Biology''', Mar 2014 [http://pubs.acs.org/doi/full/10.1021/sb500085b DOI Link] | |||
| [http://openwetware.org/images/3/3c/Sb500085b.pdf View PDF] | |||
| [[Image:Sb6acs3.jpg|160px|right|SB6ACS]] | |||
|- | |||
! | |||
| 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 [http://pubs.acs.org/doi/abs/10.1021/sb4001323 DOI Link] | |||
| [http://openwetware.org/images/c/c8/Sb4001323.pdf View PDF] | |||
| [[Image:R2o.png|160px|right|R2o]] | |||
|- | |||
! | |||
| Predicting translation initiation rates for designing synthetic biology | |||
| '''Reeve B, Hargest T, Gilbert C, Ellis T''' | |||
| '''Front. Bioeng. Biotechnol''', Jan 2014 [http://www.frontiersin.org/Journal/10.3389/fbioe.2014.00001/abstract DOI Link] | |||
| [http://www.readcube.com/articles/10.3389/fbioe.2014.00001 View PDF] | |||
| [[Image:RBSrev.jpg|160px|right|Frontiers]] | |||
|- | |||
! | |||
| 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 [http://nar.oxfordjournals.org/content/early/2013/10/22/nar.gkt915 DOI Link] | |||
| [http://nar.oxfordjournals.org/content/early/2013/10/22/nar.gkt915.full-text-lowres.pdf View PDF] | |||
| [[Image:MODAL.jpg|160px|right|NAR]] | |||
|- | |||
! | |||
| Modelling the burden caused by gene expression: an <i>in silico</i> investigation into the interactions between synthetic gene circuits and their chassis cell | |||
| '''Algar R, Ellis T''', Stan GB | |||
| '''arXiv Q-Bio''', Sep 2013 [http://arxiv.org/abs/1309.7798 DOI Link] | |||
| [http://arxiv.org/pdf/1309.7798v1.pdf View PDF] | |||
| [[Image:ArXivRhys.jpg|160px|right|arXiv Q-Bio]] | |||
|- | |||
! | |||
| Creation and characterization of component libraries for synthetic biology | |||
| '''Weenink T, Ellis T''' | |||
| '''Methods in Molecular Biology''', 2013, Vol 1073, Page 51 [http://dx.doi.org/10.1007/978-1-62703-625-2_6 DOI Link] | |||
| Book Chapter | |||
| [[Image:TimFig2.jpg|160px|right|Methods in Mol Biol]] | |||
|- | |||
! | |||
| 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 [http://pubs.acs.org/doi/abs/10.1021/sb400089c DOI Link] | |||
| [http://openwetware.org/images/2/2b/SpinachACS.pdf View PDF] | |||
| [[Image:SpinachACS.jpg|160px|right|ACS Syn Bio]] | |||
|- | |||
! | |||
| Engineering of regulated stochastic cell fate determination | |||
| Wu W, Su RQ, '''Ellis T''', Lai YC, Wang X | |||
| '''PNAS USA''', 2013, Vol 110, Page 10610 [http://www.pnas.org/content/110/26/10610.abstract DOI Link] | |||
| [http://openwetware.org/images/2/23/PNAS-2013-Wu-10610-5.pdf View PDF] | |||
| [[Image:Stochastic.png|160px|right|PNAS USA]] | |||
|- | |||
! | |||
| Building-in Biosafety for Synthetic Biology | |||
| '''Wright O''', Stan GB, '''Ellis T''' | |||
| '''Microbiology''', 2013, Vol 159, Page 1221 [http://mic.sgmjournals.org/content/159/Pt_7/1221.full DOI Link] | |||
| [http://openwetware.org/images/9/98/MicrobioOllie.pdf View PDF] | |||
| [[Image:Biosecurity.png|160px|right|Microbiology]] | |||
|- | |||
! | |||
| 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 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033279 DOI Link] | |||
| [http://openwetware.org/images/b/b7/TALORsPDF.pdf View PDF] | |||
| [[Image:TALORs.jpg|160px|right|PLoS One]] | |||
|- | |||
! | |||
| Construction of synthetic regulatory networks in yeast | |||
| '''Blount BA, Weenink T, Ellis T''' | |||
| '''FEBS Letters''', 2012, Vol 586, Page 2112 [http://dx.doi.org/10.1016/j.febslet.2012.01.053 DOI Link] | |||
| [http://openwetware.org/images/c/cd/FEBSEllis.pdf View PDF] | |||
| [[Image:YSRNreview.jpg|160px|right|FEBS Letters]] | |||
|- | |||
! | |||
| DNA assembly for synthetic biology: from parts to pathways and beyond | | DNA assembly for synthetic biology: from parts to pathways and beyond | ||
| '''Ellis T''', Adie T, Baldwin GS | | '''Ellis T''', Adie T, Baldwin GS | ||
| '''Integrative | | '''Integrative Biology''', 2011, Vol 3, Page 109 [http://dx.doi.org/10.1039/c0ib00070a DOI Link] | ||
| [http://openwetware.org/images/2/2e/EllisAssembly.pdf View PDF] | | [http://openwetware.org/images/2/2e/EllisAssembly.pdf View PDF] | ||
| [[Image:SynBioAssembly.jpg|160px|right|Integrative Biology]] | | [[Image:SynBioAssembly.jpg|160px|right|Integrative Biology]] | ||
|- | |- | ||
! | |||
! | |||
| Diversity-based, model-guided construction of synthetic gene networks with predicted functions | | Diversity-based, model-guided construction of synthetic gene networks with predicted functions | ||
| '''Ellis T''', Wang X, Collins JJ | | '''Ellis T''', Wang X, Collins JJ | ||
| '''Nature Biotechnology''', | | '''Nature Biotechnology''', 2009, Vol 27, Page 465 [http://dx.doi.org/10.1038/nbt.1536 DOI Link] | ||
| [http://openwetware.org/images/4/42/Biotech.pdf View PDF] | | [http://openwetware.org/images/4/42/Biotech.pdf View PDF] | ||
| [[Image:Biotech.jpg|160px|right|Nature Biotech]] | | [[Image:Biotech.jpg|160px|right|Nature Biotech]] | ||
|- | |||
! | |||
| Synthesis and screening of regulatory component libraries for synthetic biology | |||
| '''Ellis T''' | |||
| '''Nature Protocols''', 2009 [http://www.nature.com/protocolexchange/protocols/561 DOI Link] | |||
| [http://openwetware.org/images/9/94/Protocol.pdf View PDF] | |||
| [[Image:ProtocolTom.jpg|160px|right|Nature Protocols]] | |||
|- | |- | ||
! | ! | ||
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| [[Image:Mol_Cell.jpg|160px|right|Mol Cell]] | | [[Image:Mol_Cell.jpg|160px|right|Mol Cell]] | ||
|- | |- | ||
! | | | ||
| | |- | ||
| '''Ellis T''' | ! <b>DNA-Binding</b> | ||
| ''' | | An Extended PBD-Polyamide Conjugate with Selectivity for the ICB2 Transcription Factor Binding Site | ||
| [http://openwetware.org/images/ | | Brucoli F, Hawkins RM, James CH, Jackson PJM, Wells G, Jenkins TC, '''Ellis T''', Kotecha M, Hochhauser D, Hartley JA, Howard PW, Thurston DE | ||
| [[Image: | | '''J Med Chem''', 2013, Vol 56, Page 6339 [http://pubs.acs.org/doi/abs/10.1021/jm4001852 DOI Link] | ||
| [http://openwetware.org/images/d/dd/PBDJMC.pdf View PDF] | |||
| [[Image:PBDJMC.jpg|160px|right|J Med Chem]] | |||
|- | |- | ||
| | ! | ||
| 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 [http://dx.doi.org/10.1016/j.bmcl.2011.04.054 DOI Link ] | |||
| [http://openwetware.org/images/7/7d/PBDpaper.pdf View PDF] | |||
| [[Image:PBDfootprint.jpg|160px|right|Bioorg Med Chem Lett]] | |||
|- | |- | ||
! | ! | ||
| Molecular recognition of DNA by rigid [N]-polynorbornane derived bifunctional intercalators: synthesis and evaluation of their binding properties | | 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 | | Van Vliet LD, '''Ellis T''', Foley PJ, Liu L, Pfeffer FM, Russell RA, Warrener RN, Hollfelder F, Waring MJ | ||
Line 52: | Line 155: | ||
| '''Nucleic Acids Research''', 2007, Vol 35 [http://dx.doi.org/10.1093/nar/gkm467 DOI Link] | | '''Nucleic Acids Research''', 2007, Vol 35 [http://dx.doi.org/10.1093/nar/gkm467 DOI Link] | ||
| [http://openwetware.org/images/6/62/Footprinting.pdf View PDF] | | [http://openwetware.org/images/6/62/Footprinting.pdf View PDF] | ||
| [[Image: | | [[Image:96wellFootprint.jpg|160px|right|NAR]] | ||
|- | |- | ||
! | ! |
Revision as of 06:41, 11 August 2014
Click the links to read our papers
We're in the lab right now working on new publications. Latest Update: AUG 2014
Title | Authors | Published | Screenshot | ||
---|---|---|---|---|---|
Synthetic Biology | Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast | Jovicevic D, Blount BA, Ellis T | Bioessays, Aug 2014 DOI Link | View PDF | |
GeneGuard: A Modular Plasmid System Designed for Biosafety | Wright O, Delmans M, Stan GB, Ellis T | ACS Synthetic Biology, May 2014 DOI Link | View PDF | ||
The Sixth International Meeting on Synthetic Biology (SB6.0) Special Issue Editorial | Cai Y & Ellis T | ACS Synthetic Biology, Mar 2014 DOI Link | View PDF | ||
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 | View PDF | ||
Predicting translation initiation rates for designing synthetic biology | Reeve B, Hargest T, Gilbert C, Ellis T | Front. Bioeng. Biotechnol, Jan 2014 DOI Link | View PDF | ||
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 | View PDF | ||
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 | View PDF | ||
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 | View PDF | ||
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 | View PDF | ||
Building-in Biosafety for Synthetic Biology | Wright O, Stan GB, Ellis T | Microbiology, 2013, Vol 159, Page 1221 DOI Link | View PDF | ||
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 | View PDF | ||
Construction of synthetic regulatory networks in yeast | Blount BA, Weenink T, Ellis T | FEBS Letters, 2012, Vol 586, Page 2112 DOI Link | View PDF | ||
DNA assembly for synthetic biology: from parts to pathways and beyond | Ellis T, Adie T, Baldwin GS | Integrative Biology, 2011, Vol 3, Page 109 DOI Link | View PDF | ||
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 | View PDF | ||
Synthesis and screening of regulatory component libraries for synthetic biology | Ellis T | Nature Protocols, 2009 DOI Link | View PDF | ||
Gene regulation: hacking the network on a sugar high | Ellis T, Wang X, Collins JJ | Molecular Cell, 2008, Vol 30, Page 1 DOI Link | View PDF | ||
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 | View PDF | |
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 | View PDF | ||
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 | View PDF | ||
A 96-well DNase I footprinting screen for drug-DNA interactions | Ellis T, Evans DA, Martin CR, Hartley JA | Nucleic Acids Research, 2007, Vol 35 DOI Link | View PDF | ||
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 | View PDF | ||
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 |