Ellis:Publications: Difference between revisions

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'''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.  '''Latest Update: MAR 2011'''
<font face="trebuchet ms" style="color:#000000">We're in the lab right now working on new publications.  '''Latest Update: AUG 2014'''
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! || Title !! Authors !! Published !! PDF !! Screenshot  
! || Title !! Authors !! Published !! PDF !! Screenshot  
|-
|-
! Synthetic Biology Reviews
! <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 Biolog'''y, Feb 2011, Vol 3, Page 109 [http://dx.doi.org/10.1039/c0ib00070a DOI Link]
| '''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]]
|-
|-
|
!  
|-
! Synthetic Biology by Tom Ellis
| 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''', April 2009, Vol 27, Page 465 [http://dx.doi.org/10.1038/nbt.1536 DOI Link]
| '''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]]
|-
|-
!  
!  
Line 31: Line 127:
| [[Image:Mol_Cell.jpg|160px|right|Mol Cell]]
| [[Image:Mol_Cell.jpg|160px|right|Mol Cell]]
|-
|-
!  
|
| Synthesis and screening of regulatory component libraries for synthetic biology
|-
| '''Ellis T'''
! <b>DNA-Binding</b>
| '''Nature Protocols''', April 2009 [http://dx.doi:10.1038/nprot.2009.79 DOI Link]
| An Extended PBD-Polyamide Conjugate with Selectivity for the ICB2 Transcription Factor Binding Site
| [http://openwetware.org/images/9/94/Protocol.pdf View PDF]
| 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:ProtocolTom.jpg|160px|right|Nature Protocols]]
| '''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]]
|-
|-
! Previous Publications by Tom Ellis
!  
| 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:DNaseI.jpg|160px|right|NAR]]
| [[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 PDF 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
Sc20
Sc20
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
GeneGuard
GeneGuard
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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