Ellis:Publications: Difference between revisions

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{{Ellis Top}}
{{Ellis Top}}
'''Click the links to read our papers'''                                   


'''Latest Update: Feb 2011'''
<font face="trebuchet ms" style="color:#000000">We're in the lab right now working on new publications. '''Latest Update: JAN 2014'''
 
<font face="trebuchet ms" style="color:#000000">We're in the lab right now working on new publications.
<br>
<br>


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! || Title !! Authors !! Published !! PDF !! Screenshot  
! || Title !! Authors !! Published !! PDF !! Screenshot  
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! Synthetic Biology Reviews
! <b>Synthetic Biology</b>
| A ten slide introduction to synthetic biology
| The Sixth International Meeting on Synthetic Biology (SB6.0) Special Issue Editorial
| May 2010
| Cai Y & '''Ellis T'''
| Nature Live! at the Natural History Museum, London
| '''ACS Synthetic Biology''', Mar 2014 [http://pubs.acs.org/doi/full/10.1021/sb500085b DOI Link]
| [http://openwetware.org/images/d/d0/TomEllisNHM.pdf PDF]
| [http://openwetware.org/images/3/3c/Sb500085b.pdf View PDF]
| [[Image:TomEllisNHM.jpg|200px|right|Intro to synthetic biology]]
| [[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]]
|-
|-
! Synthetic Biology - Tom Ellis
!
| Metabolic engineering with synthetic biology
| DNA assembly for synthetic biology: from parts to pathways and beyond
| March 2010
| '''Ellis T''', Adie T, Baldwin GS
| Undergraduate synthetic biology course, Imperial College London
| '''Integrative Biology''', 2011, Vol 3, Page 109 [http://dx.doi.org/10.1039/c0ib00070a DOI Link]
| [http://openwetware.org/images/2/20/MetabolicEngineering.pdf PDF]
| [http://openwetware.org/images/2/2e/EllisAssembly.pdf View PDF]
| [[Image:MetabolicEngineering.jpg|200px|right|Metabolic engineering]]
| [[Image:SynBioAssembly.jpg|160px|right|Integrative Biology]]
|-
|-
!  
!  
| Genomic engineering and the synthetic cell
| Diversity-based, model-guided construction of synthetic gene networks with predicted functions
| March 2010
| '''Ellis T''', Wang X, Collins JJ
| Undergraduate synthetic biology course, Imperial College London
| '''Nature Biotechnology''', 2009, Vol 27, Page 465 [http://dx.doi.org/10.1038/nbt.1536 DOI Link]
| [http://openwetware.org/images/6/6d/GenomeEngineering.pdf PDF]
| [http://openwetware.org/images/4/42/Biotech.pdf View PDF]
| [[Image:GenomeEngineering.jpg|200px|right|Genome engineering]]
| [[Image:Biotech.jpg|160px|right|Nature Biotech]]
|-
|-
!  
!  
| Synthesis and screening of regulatory component libraries for synthetic biology
| Synthesis and screening of regulatory component libraries for synthetic biology
| Ellis T (April 2009)
| '''Ellis T'''
| Nature Protocols 2009 Apr 23. doi:10.1038/nprot.2009.79 [http://www.natureprotocols.com/2009/04/23/synthesis_and_screening_of_reg.php Link]
| '''Nature Protocols''', 2009 [http://www.nature.com/protocolexchange/protocols/561 DOI Link]
| [http://openwetware.org/images/9/92/ICL09.pdf PDF]
| [http://openwetware.org/images/9/94/Protocol.pdf View PDF]
| [[Image:ICL09.jpg|200px|right|Imperial Interview]]
| [[Image:ProtocolTom.jpg|160px|right|Nature Protocols]]
|-
!
| Gene regulation: hacking the network on a sugar high
| '''Ellis T''', Wang X, Collins JJ
| '''Molecular Cell''', 2008, Vol 30, Page 1 [http://dx.doi.org/10.1016/j.molcel.2008.03.005 DOI Link]
| [http://openwetware.org/images/1/12/MolCell.pdf View PDF]
| [[Image:Mol_Cell.jpg|160px|right|Mol Cell]]
|-
|-
|
|
|-
|-
! Previous Publications - Tom Ellis  
! <b>DNA-Binding</b>
| Exploiting diversity in synthesis to fast-track synthetic biology
| An Extended PBD-Polyamide Conjugate with Selectivity for the ICB2 Transcription Factor Binding Site
| April 2009
| Brucoli F, Hawkins RM, James CH, Jackson PJM, Wells G, Jenkins TC, '''Ellis T''', Kotecha M, Hochhauser D, Hartley JA, Howard PW, Thurston DE
| Advances in Synthetic Biology Conference, London 2009
| '''J Med Chem''', 2013, Vol 56, Page 6339 [http://pubs.acs.org/doi/abs/10.1021/jm4001852 DOI Link]
| [http://openwetware.org/images/8/8c/AdvancesLondon.pdf PDF]
| [http://openwetware.org/images/d/dd/PBDJMC.pdf View PDF]
| [[Image:AdvancesLondon.jpg|200px|right|Conference London 2009]]
| [[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
| 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 [http://dx.doi.org/10.1021/jm0613020 DOI Link]
| [http://openwetware.org/images/b/bd/MOLRAC.pdf View PDF]
| [[Image:MOLRAC.jpg|160px|right|J Med Chem]]
|-
!
| 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 [http://dx.doi.org/10.1093/nar/gkm467 DOI Link]
| [http://openwetware.org/images/6/62/Footprinting.pdf View PDF]
| [[Image:96wellFootprint.jpg|160px|right|NAR]]
|-
!
| 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 [http://dx.doi.org/10.1021/bi0479813 DOI Link]
| [http://openwetware.org/images/1/18/SJG-136.pdf View PDF]
| [[Image:SJG136.jpg|160px|right|Biochemistry]]
|-
|-
!  
!  
| Developing chassis fit for purpose
| DNase I footprinting of small molecule binding sites on DNA
| March 2010
| Bailly C, Kluza J, Martin C, '''Ellis T''', Waring MJ
| Grand Challenges workshop at Imperial College London
| '''Methods in Molecular Biology''', 2005, Vol 288, Page 319 [http://dx.doi.org/10.1385/1-59259-823-4:319 DOI Link]
| [http://openwetware.org/images/b/bb/Chassis.pdf PDF]
| Book Chapter
| [[Image:Chassis.png|200px|right|E.coli as a chassis]]
| [[Image:DNaseI.jpg|160px|right|Meth Mol Biol]]
|}
|}
<br>
'''Method Paper''' - Ellis T. ''Synthesis and screening of regulatory component libraries for synthetic biology'' Nature Protocols 2009 Apr 23. doi:10.1038/nprot.2009.79 [http://www.natureprotocols.com/2009/04/23/synthesis_and_screening_of_reg.php Link]
<br>

Revision as of 03:08, 22 March 2014

Click the links to read our papers

We're in the lab right now working on new publications. Latest Update: JAN 2014

Title Authors Published PDF Screenshot
Synthetic Biology 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
SB6ACS
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 DOI Link View PDF
R2o
R2o
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
Frontiers
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 DOI Link View PDF
NAR
NAR
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
arXiv Q-Bio
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 DOI Link Book Chapter
Methods in Mol Biol
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 DOI Link View PDF
ACS Syn Bio
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 DOI Link View PDF
PNAS USA
PNAS USA
Building-in Biosafety for Synthetic Biology Wright O, Stan GB, Ellis T Microbiology, 2013, Vol 159, Page 1221 DOI Link View PDF
Microbiology
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 DOI Link View PDF
PLoS One
PLoS One
Construction of synthetic regulatory networks in yeast Blount BA, Weenink T, Ellis T FEBS Letters, 2012, Vol 586, Page 2112 DOI Link View PDF
FEBS Letters
FEBS Letters
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
Integrative Biology
Integrative Biology
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
Nature Biotech
Nature Biotech
Synthesis and screening of regulatory component libraries for synthetic biology Ellis T Nature Protocols, 2009 DOI Link View PDF
Nature Protocols
Nature Protocols
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
Mol Cell
Mol Cell
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
J Med Chem
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 DOI Link View PDF
Bioorg Med Chem Lett
Bioorg Med Chem Lett
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
J Med Chem
J Med Chem
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
NAR
NAR
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
Biochemistry
Biochemistry
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
Meth Mol Biol
Meth Mol Biol
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