User:John Cumbers

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<font size="4">John Cumbers</font size>
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<font size="4">John Cumbers, Ph.D</font size>
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<font size="2">Department of Ecology and Evolutionary Biology<br>
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<font size="2">NASA Ames Research Center<br>
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Box G-W<br>
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Mail Stop 239-20, Bldg N239 Rm 373 <br>
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Brown University<br>
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P.O. Box 1, Moffett Field, CA 94035-0001, USA.  <br>
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Providence, RI 02912<br>
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cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088 <br>
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John underscore Cumbers at brown dot edu</font size>
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myname @ gmail . com
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</font size>
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Hello, I'm a graduate student in the [[Tatar]] lab at Brown University.
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I work at NASA Ames Research Center in Silicon Valley, California.  I helped to start NASA's program in synthetic biology and I now work at NASA in partnerships and project management.
== Research Interests ==
== Research Interests ==
<blockquote>  
<blockquote>  
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*Mechanisms of aging
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*Synthetic biology with applications to space settlement
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*Gene Regulatory networks
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*Radiation and cold tolerance in cyanobacteria
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*Predicting binding motifs
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*Mechanisms of aging  
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*CHiP chip & binding site discovery
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*Synthetic interventions in aging
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</blockquote>
</blockquote>
== Education==
== Education==
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<blockquote>M.Sc, University of Edinburgh, 2005 (Bioinformatics) <br>
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<blockquote>
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B.Sc, University of Hull, 2004  (Computer Science with Information Engineering) <br>
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Ph.D (2011) Cellular Biology, Molecular Biology and Biochemistry, Brown University, USA. <br>
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M.Sc (2005) Bioinformatics, University of Edinburgh, UK. <br>
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B.Sc (2004) Computer Science & Information Engineering, University of Hull, UK. <br>
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</blockquote>
</blockquote>
== Publications ==
== Publications ==
<blockquote>
<blockquote>
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'''Measuring the activity of BioBrick promoters using an in vivo reference standard'''<br>
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''Journal of Biological Engineering,'' 2009 March 20;3:4<br>
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[[Jason_Kelly | Jason R Kelly]], Adam J Rubin, Caroline M Ajo-Franklin, John Cumbers, Michael J. Czar, Kim de Mora, Aaron L Glieberman, Dileep D Monie, [[Drew Endy]]<br>
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[http://www.jbioleng.org/content/3/1/4 URL] [http://www.jbioleng.org/content/pdf/1754-1611-3-4.pdf PDF reprint] <br><br>
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'''Drosophila Germ Line Modulation of Insulin Signaling and Lifespan'''  <br>
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Flatt, T., Min, K., D’Alterio, C., Villa-Cuesta, E., Cumbers, J., Lehmann,R., Jones, D.L., Tatar,M.,<br>
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PNAS April 29, 2008 vol. 105 no. 17 6368-6373. <br><br>
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'''Progress toward construction and modelling of a tri-stable toggle switch in E. coli'''  <br>
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Lohmueller, J.; Neretti, N.; Hickey, B.; Kaka, A.; Gao, A.; Lemon, J.; Lattanzi, V.; Goldstein, P.; <br>
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Tam, L.K.; Schmidt, M.; Brodsky, A.S.; Haberstroh, K.; Morgan, J.; Palmore, T.; Wessel, G.;
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Jaklenec, A.; Urabe, H.; Gagnon, J.; Cumbers <br>
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IET Synthetic Biology, 2007. <br><br>
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'''Annual Report for the American Federation for Aging Research.''' <br>
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2006 (Front Cover: Insulin vesicles in the fruit fly brain, confocal microscopy, Left) <br><br>
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==Conference posters and abstracts==
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BioSysBio 2007: Conference in Systems Biology,
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Bioinformatics and Synthetic Biology Manchester, UK.
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11-13 January 2007. Abstracts. Editor.
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BMC Syst Biol. 2007;1 Suppl 1:P1-S15.
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Constructing a insulin sensitive cell, second international
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conference on synthetic biology (2.0). Poster
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UC Berkeley. 2006
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Computational Analysis of Insulin in the Ageing Fruit Fly
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Cumbers, J., and Armstrong, J.D.
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Abstract from BioSysBio 2005: Bioinformatics and Systems Biology Conference, Edinburgh, UK,
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BMC Bioinformatics 2005, 6(Suppl 3):P9 doi:10.1186/1471-2105-6-S3-P9
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BioSysBio: Bioinformatics and Systems Biology Conference. Edinburgh, UK. 14-15 July 2005. Abstracts.
BioSysBio: Bioinformatics and Systems Biology Conference. Edinburgh, UK. 14-15 July 2005. Abstracts.
[http://www.biomedcentral.com/content/files/pdf/1471-2105-6-S3-full.pdf BMC Bioinformatics. 2005 Sep 9;6 Suppl 3:P21-29, S1-15.]  
[http://www.biomedcentral.com/content/files/pdf/1471-2105-6-S3-full.pdf BMC Bioinformatics. 2005 Sep 9;6 Suppl 3:P21-29, S1-15.]  
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</blockquote>
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== Collaborations ==
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==[[Cumbers:Software | Software]]==
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*[[Cumbers:ideas/FOXO phospholocator | Engineering a FOXO Phospholocator]]
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==[[Cumbers:Science mutterings | Science mutterings]]==
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*[[Cumbers:ideas/Modeling insulin sensitivity | Modeling insulin sensitivity ]]
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==[[Cumbers:OWW mutterings | OWW mutterings]]==
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==[[Cumbers:General mutterings | General mutterings]]==
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== Protocols ==
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==[[Cumbers:Protocols| protocols]]==
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*[[Tatar:protocols:Drosophila ChIp on chip|Drosophila ChIp on chip]]
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== OWW News ==
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*[[Novel uses of OpenWetWare]]
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*[[Cumbers:tests| other tests]]
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*[[Cumbers:front page tests | front page tests]]
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*[[cumbers:lab highlights tests|lab highlights tests]]
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*[[cumbers:tests|Frappr mapper]]
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== Brown iGEM ==
== Brown iGEM ==
*[http://parts2.mit.edu/wiki/index.php/Brown Brown iGEM team]
*[http://parts2.mit.edu/wiki/index.php/Brown Brown iGEM team]
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== Other ==
 
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*OpenWetWare [[tips and templates]]
 
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*[[Cumbers:My Time plan | Embedding Irows into a wiki]]
 
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*[[:Category:BioSysBio Keywords|BioSysBio]].
 
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*[[Category:BioSysBio Keywords High-Throughput Experiments]]
 
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==Install tips==
 
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*[[Cumbers:BioRubyInstallTips|BioRuby]]*
 
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*[[Cumbers:Wikimedia install notes | Wikimedia install notes]]
 
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*[[Cumbers:SCnotes |SC notes]]
 
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*[[Cumbers:adding charts from excel to powerpoint | adding charts from excel to powerpoint]]
 
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Current revision


John Cumbers, Ph.D

NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373
P.O. Box 1, Moffett Field, CA 94035-0001, USA.
cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088

myname @ gmail . com

I work at NASA Ames Research Center in Silicon Valley, California. I helped to start NASA's program in synthetic biology and I now work at NASA in partnerships and project management.


Contents

Research Interests

  • Synthetic biology with applications to space settlement
  • Radiation and cold tolerance in cyanobacteria
  • Mechanisms of aging

Education

Ph.D (2011) Cellular Biology, Molecular Biology and Biochemistry, Brown University, USA.
M.Sc (2005) Bioinformatics, University of Edinburgh, UK.
B.Sc (2004) Computer Science & Information Engineering, University of Hull, UK.

Publications

Measuring the activity of BioBrick promoters using an in vivo reference standard
Journal of Biological Engineering, 2009 March 20;3:4
Jason R Kelly, Adam J Rubin, Caroline M Ajo-Franklin, John Cumbers, Michael J. Czar, Kim de Mora, Aaron L Glieberman, Dileep D Monie, Drew Endy
URL PDF reprint

Drosophila Germ Line Modulation of Insulin Signaling and Lifespan
Flatt, T., Min, K., D’Alterio, C., Villa-Cuesta, E., Cumbers, J., Lehmann,R., Jones, D.L., Tatar,M.,
PNAS April 29, 2008 vol. 105 no. 17 6368-6373.

Progress toward construction and modelling of a tri-stable toggle switch in E. coli
Lohmueller, J.; Neretti, N.; Hickey, B.; Kaka, A.; Gao, A.; Lemon, J.; Lattanzi, V.; Goldstein, P.;
Tam, L.K.; Schmidt, M.; Brodsky, A.S.; Haberstroh, K.; Morgan, J.; Palmore, T.; Wessel, G.; Jaklenec, A.; Urabe, H.; Gagnon, J.; Cumbers
IET Synthetic Biology, 2007.

Annual Report for the American Federation for Aging Research.
2006 (Front Cover: Insulin vesicles in the fruit fly brain, confocal microscopy, Left)

Conference posters and abstracts

BioSysBio 2007: Conference in Systems Biology, Bioinformatics and Synthetic Biology Manchester, UK. 11-13 January 2007. Abstracts. Editor. BMC Syst Biol. 2007;1 Suppl 1:P1-S15.


Constructing a insulin sensitive cell, second international conference on synthetic biology (2.0). Poster UC Berkeley. 2006


Computational Analysis of Insulin in the Ageing Fruit Fly Cumbers, J., and Armstrong, J.D. Abstract from BioSysBio 2005: Bioinformatics and Systems Biology Conference, Edinburgh, UK, BMC Bioinformatics 2005, 6(Suppl 3):P9 doi:10.1186/1471-2105-6-S3-P9


BioSysBio: Bioinformatics and Systems Biology Conference. Edinburgh, UK. 14-15 July 2005. Abstracts. BMC Bioinformatics. 2005 Sep 9;6 Suppl 3:P21-29, S1-15. PMID: 16219110 [PubMed - indexed for MEDLINE]

Software

Science mutterings

OWW mutterings

General mutterings

protocols

Brown iGEM

Personal tools