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| {{Ellis Top}}
| | our lab website has now moved to http://tomellislab.com/ |
| '''Click the links to read our papers'''
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| <font face="trebuchet ms" style="color:#000000">We're in the lab right now working on new publications. '''Latest Update: JAN 2015'''
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| <br>
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| {| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse; width:720px" <!-- This line here formats your table for you. Change the code to change the formatting of your table.-->
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| ! || Title !! Authors !! Published !! PDF !! Screenshot
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| ! <b>Synthetic Biology</b>
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| |Using Spinach Aptamer to Correlate mRNA and Protein Levels in Escherichia coli
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| | '''Pothoulakis G''', '''Ellis T'''
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| | '''Methods in Enzymology''' v550, Jan 2015 [http://www.sciencedirect.com/science/article/pii/S0076687914000482 DOI Link]
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| | N/A
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| | [[Image:Spinachmeth.jpg|160px|right|Spinach]]
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| !
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| |How synthetic biology will reconsider natural bioluminescence and its applications
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| | '''Reeve B''', Sanderson T, '''Ellis T''', Freemont P
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| | '''Adv Biochem Eng Biotechnol.''' 2145:3-30, Sep 2014 [http://link.springer.com/chapter/10.1007%2F978-3-662-43619-6_1 DOI Link]
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| | N/A
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| | [[Image:bioluminChap.jpg|160px|right|Sc20]]
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| !
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| |Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast
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| | '''Jovicevic D''', '''Blount BA''', '''Ellis T'''
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| | '''Bioessays''', Aug 2014 [http://onlinelibrary.wiley.com/doi/10.1002/bies.201400086/abstract DOI Link]
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| | [http://openwetware.org/images/c/cf/DJSc20rev.pdf View PDF]
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| | [[Image:DJSc20.jpg|160px|right|Sc20]]
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| !
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| |GeneGuard: A Modular Plasmid System Designed for Biosafety
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| | '''Wright O''', '''Delmans M''', Stan GB, '''Ellis T'''
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| | '''ACS Synthetic Biology''', May 2014 [http://pubs.acs.org/doi/abs/10.1021/sb500234s DOI Link]
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| | [http://openwetware.org/images/3/37/GeneGuard.pdf View PDF]
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| | [[Image:GeneGuard.jpg|160px|right|GeneGuard]]
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| !
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| | The Sixth International Meeting on Synthetic Biology (SB6.0) Special Issue Editorial
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| | Cai Y & '''Ellis T'''
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| | '''ACS Synthetic Biology''', Mar 2014 [http://pubs.acs.org/doi/full/10.1021/sb500085b DOI Link]
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| | [http://openwetware.org/images/3/3c/Sb500085b.pdf View PDF]
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| | [[Image:Sb6acs3.jpg|160px|right|SB6ACS]]
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| !
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| | R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences
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| | '''Casini A''', '''Christodoulou G''', Freemont P, Baldwin GS, '''Ellis T''', Macdonald JT
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| | '''ACS Synthetic Biology''', Jan 2014 [http://pubs.acs.org/doi/abs/10.1021/sb4001323 DOI Link]
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| | [http://openwetware.org/images/c/c8/Sb4001323.pdf View PDF]
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| | [[Image:R2o.png|160px|right|R2o]]
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| !
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| | Predicting translation initiation rates for designing synthetic biology
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| | '''Reeve B, Hargest T, Gilbert C, Ellis T'''
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| | '''Front. Bioeng. Biotechnol''', Jan 2014 [http://www.frontiersin.org/Journal/10.3389/fbioe.2014.00001/abstract DOI Link]
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| | [http://www.readcube.com/articles/10.3389/fbioe.2014.00001 View PDF]
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| | [[Image:RBSrev.jpg|160px|right|Frontiers]]
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| !
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| | One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy
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| | '''Casini A''', Macdonald JT, '''De Jonghe J, Christodoulou G''', Freemont P, Baldwin GS, '''Ellis T'''
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| | '''Nucleic Acids Research''', Oct 2013 [http://nar.oxfordjournals.org/content/early/2013/10/22/nar.gkt915 DOI Link]
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| | [http://nar.oxfordjournals.org/content/early/2013/10/22/nar.gkt915.full-text-lowres.pdf View PDF]
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| | [[Image:MODAL.jpg|160px|right|NAR]]
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| !
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| | Modelling the burden caused by gene expression: an <i>in silico</i> investigation into the interactions between synthetic gene circuits and their chassis cell
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| | '''Algar R, Ellis T''', Stan GB
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| | '''arXiv Q-Bio''', Sep 2013 [http://arxiv.org/abs/1309.7798 DOI Link]
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| | [http://arxiv.org/pdf/1309.7798v1.pdf View PDF]
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| | [[Image:ArXivRhys.jpg|160px|right|arXiv Q-Bio]]
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| !
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| | Creation and characterization of component libraries for synthetic biology
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| | '''Weenink T, Ellis T'''
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| | '''Methods in Molecular Biology''', 2013, Vol 1073, Page 51 [http://dx.doi.org/10.1007/978-1-62703-625-2_6 DOI Link]
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| | Book Chapter
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| | [[Image:TimFig2.jpg|160px|right|Methods in Mol Biol]]
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| !
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| | Characterisation of genetic control elements for synthetic biology using the Spinach RNA aptamer
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| | '''Pothoulakis G, Ceroni F, Reeve B, Ellis T'''
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| | '''ACS Synthetic Biology''', Sept 2013 [http://pubs.acs.org/doi/abs/10.1021/sb400089c DOI Link]
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| | [http://openwetware.org/images/2/2b/SpinachACS.pdf View PDF]
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| | [[Image:SpinachACS.jpg|160px|right|ACS Syn Bio]]
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| !
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| | Engineering of regulated stochastic cell fate determination
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| | Wu W, Su RQ, '''Ellis T''', Lai YC, Wang X
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| | '''PNAS USA''', 2013, Vol 110, Page 10610 [http://www.pnas.org/content/110/26/10610.abstract DOI Link]
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| | [http://openwetware.org/images/2/23/PNAS-2013-Wu-10610-5.pdf View PDF]
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| | [[Image:Stochastic.png|160px|right|PNAS USA]]
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| !
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| | Building-in Biosafety for Synthetic Biology
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| | '''Wright O''', Stan GB, '''Ellis T'''
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| | '''Microbiology''', 2013, Vol 159, Page 1221 [http://mic.sgmjournals.org/content/159/Pt_7/1221.full DOI Link]
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| | [http://openwetware.org/images/9/98/MicrobioOllie.pdf View PDF]
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| | [[Image:Biosecurity.png|160px|right|Microbiology]]
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| !
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| | Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology
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| | '''Blount BA, Weenink T, Vasylechko S, Ellis T'''
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| | '''PLoS One''', 2012, Vol 7, Page e33279 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033279 DOI Link]
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| | [http://openwetware.org/images/b/b7/TALORsPDF.pdf View PDF]
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| | [[Image:TALORs.jpg|160px|right|PLoS One]]
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| !
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| | Construction of synthetic regulatory networks in yeast
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| | '''Blount BA, Weenink T, Ellis T'''
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| | '''FEBS Letters''', 2012, Vol 586, Page 2112 [http://dx.doi.org/10.1016/j.febslet.2012.01.053 DOI Link]
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| | [http://openwetware.org/images/c/cd/FEBSEllis.pdf View PDF]
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| | [[Image:YSRNreview.jpg|160px|right|FEBS Letters]]
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| !
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| | DNA assembly for synthetic biology: from parts to pathways and beyond
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| | '''Ellis T''', Adie T, Baldwin GS
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| | '''Integrative Biology''', 2011, Vol 3, Page 109 [http://dx.doi.org/10.1039/c0ib00070a DOI Link]
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| | [http://openwetware.org/images/2/2e/EllisAssembly.pdf View PDF]
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| | [[Image:SynBioAssembly.jpg|160px|right|Integrative Biology]]
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| !
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| | Diversity-based, model-guided construction of synthetic gene networks with predicted functions
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| | '''Ellis T''', Wang X, Collins JJ
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| | '''Nature Biotechnology''', 2009, Vol 27, Page 465 [http://dx.doi.org/10.1038/nbt.1536 DOI Link]
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| | [http://openwetware.org/images/4/42/Biotech.pdf View PDF]
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| | [[Image:Biotech.jpg|160px|right|Nature Biotech]]
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| !
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| | Synthesis and screening of regulatory component libraries for synthetic biology
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| | '''Ellis T'''
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| | '''Nature Protocols''', 2009 [http://www.nature.com/protocolexchange/protocols/561 DOI Link]
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| | [http://openwetware.org/images/9/94/Protocol.pdf View PDF]
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| | [[Image:ProtocolTom.jpg|160px|right|Nature Protocols]]
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| !
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| | Gene regulation: hacking the network on a sugar high
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| | '''Ellis T''', Wang X, Collins JJ
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| | '''Molecular Cell''', 2008, Vol 30, Page 1 [http://dx.doi.org/10.1016/j.molcel.2008.03.005 DOI Link]
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| | [http://openwetware.org/images/1/12/MolCell.pdf View PDF]
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| | [[Image:Mol_Cell.jpg|160px|right|Mol Cell]]
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| ! <b>DNA-Binding</b>
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| | An Extended PBD-Polyamide Conjugate with Selectivity for the ICB2 Transcription Factor Binding Site
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| | Brucoli F, Hawkins RM, James CH, Jackson PJM, Wells G, Jenkins TC, '''Ellis T''', Kotecha M, Hochhauser D, Hartley JA, Howard PW, Thurston DE
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| | '''J Med Chem''', 2013, Vol 56, Page 6339 [http://pubs.acs.org/doi/abs/10.1021/jm4001852 DOI Link]
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| | [http://openwetware.org/images/d/dd/PBDJMC.pdf View PDF]
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| | [[Image:PBDJMC.jpg|160px|right|J Med Chem]]
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| !
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| | Novel C8-linked pyrrolobenzodiazepine (PBD)-heterocycle conjugates that recognize DNA sequences containing an inverted CCAAT box
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| | Brucoli F, Hawkins RM, James CH, Wells G, Jenkins TC, '''Ellis T''', Hartley JA, Howard PW, Thurston DE
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| | '''Bioorg Med Chem Letters''', 2011, Vol 21, Page 3780 [http://dx.doi.org/10.1016/j.bmcl.2011.04.054 DOI Link ]
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| | [http://openwetware.org/images/7/7d/PBDpaper.pdf View PDF]
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| | [[Image:PBDfootprint.jpg|160px|right|Bioorg Med Chem Lett]]
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| !
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| | Molecular recognition of DNA by rigid [N]-polynorbornane derived bifunctional intercalators: synthesis and evaluation of their binding properties
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| | Van Vliet LD, '''Ellis T''', Foley PJ, Liu L, Pfeffer FM, Russell RA, Warrener RN, Hollfelder F, Waring MJ
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| | '''Journal of Medicinal Chemistry''', 2007, Vol 50, Page 2326 [http://dx.doi.org/10.1021/jm0613020 DOI Link]
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| | [http://openwetware.org/images/b/bd/MOLRAC.pdf View PDF]
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| | [[Image:MOLRAC.jpg|160px|right|J Med Chem]]
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| !
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| | A 96-well DNase I footprinting screen for drug-DNA interactions
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| | '''Ellis T''', Evans DA, Martin CR, Hartley JA
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| | '''Nucleic Acids Research''', 2007, Vol 35 [http://dx.doi.org/10.1093/nar/gkm467 DOI Link]
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| | [http://openwetware.org/images/6/62/Footprinting.pdf View PDF]
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| | [[Image:96wellFootprint.jpg|160px|right|NAR]]
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| !
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| | Sequence-selective interaction of the minor-groove interstrand cross-linking agent SJG-136 with naked and cellular DNA: footprinting and enzyme inhibition studies
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| | Martin C, '''Ellis T''', McGurk CJ, Jenkins TC, Hartley JA, Waring MJ, Thurston DE
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| | '''Biochemistry''', 2005, Vol 44, Page 4135 [http://dx.doi.org/10.1021/bi0479813 DOI Link]
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| | [http://openwetware.org/images/1/18/SJG-136.pdf View PDF]
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| | [[Image:SJG136.jpg|160px|right|Biochemistry]]
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| !
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| | DNase I footprinting of small molecule binding sites on DNA
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| | Bailly C, Kluza J, Martin C, '''Ellis T''', Waring MJ
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| | '''Methods in Molecular Biology''', 2005, Vol 288, Page 319 [http://dx.doi.org/10.1385/1-59259-823-4:319 DOI Link]
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| | Book Chapter
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| | [[Image:DNaseI.jpg|160px|right|Meth Mol Biol]]
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| |}
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