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==Rice Bioengineering==
I will be starting up my [http://www.taborlab.rice.edu/ lab] in the [http://bioe.rice.edu/ Department of Bioengineering] at [http://www.rice.edu/ Rice University] in the Fall of 2010.  I am looking to bring on creative students and postdocs with experience in molecular biology, evolutionary biology, microbiology, developmental biology, biophysics and chemical engineering.  Research will focus on engineering multicellular behaviors.  If you are interested in joining the lab, please email me.
== Background ==
== Background ==
*I received my B.A. studying Biology and [http://www.cm.utexas.edu/ Biochemistry] from the [http://www.utexas.edu/ University of Texas] in 2001.  I studied evolutionary biology in the lab of [http://www.zo.utexas.edu/faculty/antisense/ Jim Bull] for two years during that time.   
*I was recently a Postdoctoral Fellow in the Voigt lab at UCSF.
 
*I received my Ph.D. in May 2006 from the University of Texas, studying the design and evolution of Synthetic Biological systems under Andy Ellington.   


*I received my Ph.D. in May 2006 from the University of Texas, studying the design and evolution of synthetic biological systems under [http://ellingtonlab.org/ Andy Ellington].   
*I received my B.A. studying Biology and Biochemistry from the University of Texas in 2001.  I also studied Evolutionary Biology in the laboratory of Jim Bull for two years during that time.   


*I am currently a postdoc in the [http://www.voigtlab.ucsf.edu/ Voigt lab] at [http://www.ucsf.edu/ UCSF].




== Research Interests ==  
http://openwetware.org/images/8/81/Jtabor.jpg
== Research ==  


===Synthetic Biology===
===Synthetic Biology===
My primary interests include the forward design and programming of novel cellular behaviors ([http://en.wikipedia.org/wiki/Synthetic_biology synthetic biology]) using genetic regulation strategies at both the canonical protein/DNA interaction level (e.g. controlling [http://openwetware.org/wiki/Adventures POPS]; Endy, ''Nature'', 2005) and at the level of riboregulation (e.g. [http://openwetware.org/images/b/b7/Bayer.pdf Bayer and Smolke], ''Nature Biotechnology'' 2005).
I am interested in programming the behaviors of cells and organisms using synthetic genetic circuits.
[[Image:Darwin.JPG|thumb|right|250px|Real intelligent designers use evolution.     Bacterial photo: Aaron Chevalier]]


====Bacterial Photography====
====Bacterial Photography====
I was heavily involved with a group at the University of Texas which has designed and built a "[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html bacterial photography]" system in which a community of ''E.coli'' act as a biological film capable of capturing and permanently recapitulating any light image (see figure below).  This work was enabled by the design of an incredible chimeric light responsive genetic element from the [http://www.voigtlab.ucsf.edu/ Voigt lab] at [http://www.ucsf.edu/ UCSF].  Basically, Anselm Levskaya and Chris Voigt rewired a phytochrome protein from ''Synechocystis'' which normally changes conformation in response to light and transduces this into a change in gene expression in that organism to control an osmo-responsive genetic regulatory system in ''E.coli''.  In order to retain the functionality of the phytochrome protein, the metabolism of ''E.coli'' had to be re-engineered to produce a ringed organic compound, phycocyanobilin (PCB).  This work had previously been done in the [http://www.mcb.ucdavis.edu/faculty-labs/lagarias/main.html Lagarias lab] at [http://www.ucdavis.edu/index.html UC-Davis] (Gambetta and Lagarias, ''PNAS'', 2001).  The result is a synthetic genetic signal transduction cascade in E.coli that is strongly responsive to light in the 660nm (red) range. The applications of the fine spatial control in gene expression afforded by light approach boundless.  Also, check out Nature's [http://openwetware.org/images/9/9d/Year_in_photos_2005.pdf 2005 Year in Pictures]
I was involved with a group that designed a "[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html bacterial photography]" system in which a community of ''E.coli'' act as a biological film capable of genetically "printing" an image of light.  This was accomplished by rewiring an osmo-responsive signal transduction system in E.coli to respond to red light.  The light sensor was then used to control the expression of black pigment, such that dark areas of a projected image result in dark areas on the bacterial plate and light areas result in light areas.  Over the entire population, the image is printed at a theoretical resolution of over 100 Megapixels per square inch. This is due to relatively small size of bacteria (1x3 microns).


====Bacterial Edge Detector====
We recently reprogrammed the photographic bacteria to identify the edges of objects within the projected image.  In the bacterial edge detector, each cell determines whether it is located in the light, the dark, or at the boundary of light and dark.  Only those who are at a boundary produce the black pigment.  The emergent result over the entire population is the outline of the projected image.  Edge detection is a well studied serial algorithm where computation time increases linearly with the number of pixels (approximately as the square of image size).  Because the bacterial edge detector is a parallel computer, the algorithm runs in constant time regardless of image size.  This bottom-up approach highlights the parallel information processing abilities inherent to biological systems, a feature which is taken advantage of in natural systems such as metazoan development and neural networks.
 
====Multichromatic Control of Gene Expression====
We have recently expanded light regulation in ''E.coli'' such that the expression of different genes can be controlled with different [http://www.ncbi.nlm.nih.gov/pubmed/21035461 colors of light].


If you'd like to take your own pictures, check out the page on [http://openwetware.org/wiki/LightCannon how to build a light cannon].
==Publications==
*A. Tamsir, J.J. Tabor and C.A. Voigt. [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09565.html Robust multicellular computing using genetically encoded NOR gates and chemical 'wires']. ''Nature'', 2010.


[[Image:Darwin.JPG|thumb|left|250px|Real intelligent designers use evolution.     Bacterial photo: Aaron Chevalier]]
*J.J. Tabor, A. Levskaya and C.A. Voigt. [http://www.ncbi.nlm.nih.gov/pubmed/21035461 Multichromatic control of gene expression in ''E. coli'']. ''Journal of Molecular Biology'', 2010. <br>


====Edge Detector====
*J.J. Tabor, H. Salis, Z.B. Simpson, A.A. Chevalier, A. Levskaya, E.M.Marcotte, C.A. Voigt and A.D. Ellington. [http://www.cell.com/retrieve/pii/S0092867409005091 A Synthetic Genetic Edge Detection Program]. ''Cell'' '''137''' (7) 1272-81, 2009. <br>
We are currently making use of this novel behavior to build a biological edge detector. In this system, each ''E.coli'' on the lawn would compute whether it were in the light, the dark, or at the boundary of light and dark. Those cells at the light/dark boundary will express a LacZ reporter, and the result would not be a recapitulated image, but the outline of such an image. Interestingly, edge detection is an expensive serial computational problem, wherein the computation time increases quadratically with the size of the image. In our massively parallel E.coli edge detector, the edge detection problem is solved in constant time as the size of the image increases. We undertook this effort to demonstrate a scenario in which biology holds some sort of potential advantage over silicon-based computation.


====[http://parts.mit.edu/wiki/index.php/University_of_Texas_2006 2006 UT-Austin iGEM team]====
*J.J. Tabor, E.S. Groban and C.A. Voigt. Performance Characteristics for Sensors and Circuits Used to Program ''E.coli''.  In ''Systems Biology and Biotechnology of E.coli'', ed. S.Y.Lee, Springer, XXII, 2009. [http://openwetware.org/images/7/7d/Tabor_et_al_2009.pdf pdf]<br>


 
*J.J. Tabor, M. Levy, Z.B. Simpson and A.D. Ellington. Parasitism and protocells: The tragedy of the molecular commons. In ''Protocells: Bridging Nonliving and Living Matter'', eds. S. Rasmussen, M.A. Bedau, L.Chen, D.Deamer, D.C. Krakauer, N. Packer and P.F. Stadler, MIT Press, 2008. <br>
===Noise===
I am also interested in the quantitative characteristics of natural mechanisms of gene regulation and expression. Uncontrollable fluctuations in gene expression in populations of genetically identical individuals can lead to quantifiably diverse (even opposite) phenotypes within that population. It is becoming more and more obvious that biology, being evolutionarily adept as it is, has taken advantage of the noise inherent in gene expression to encode complex population level behaviors using simple genetic level specifications. For example, the virus HIV encodes a genetic amplifier in its genome, wherein a protein product of a gene results in higher transcription levels of that gene. Upon infection of a host cell, the levels of that protein product usually tend about some mean. Uncontrollable fluctuations below that mean at some critical time point result in the HIV genomes in that invaded cell going lysogenic. Fluctuations above that mean at some critical time point result in the HIV genomes in that cell going lytic. There are fitness advantages to such a bifuracted reproductive strategy, and this virus has used noise as opposed to hard-wired genetic to encode this behavior. Clearly, noise can sometimes be detrimental to cellular survival, and in certain instances biology has evolved ways to insulate, buffer or engineer away noise in gene expression as well.


*J.J. Tabor, T.S. Bayer, Z.B. Simpson, M.Levy and A.D. Ellington.  Engineering Stochasticity in Gene Expression.  ''Molecular Biosystems'', '''4''' (7) 754-61, 2008. [http://openwetware.org/images/5/56/Tabor_2008.pdf pdf] <br>


*M. Levy, J.J. Tabor and S.Wong. Taking pictures with ''E.coli'': Signal processing using synthetic biology. ''IEEE Signal Processing Magazine'', '''23''' (3), 142-144, 2006. [http://openwetware.org/images/c/cc/Levy_Tabor_Wong.pdf pdf] <br>


My recent efforts have focused on elucidating sources of noise generation and mechanisms of noise insulation in gene expression.  Check out my [http://esmane.physics.lsa.umich.edu/wl/external/ICSB/2005/20051020-umwlap001-04-tabor/real/f001.htm talk] from [http://csbi.mit.edu/icsb-2005/program/program.htm ICSB 2005].
*J.J. Tabor, M.Levy, and A.D. Ellington. Deoxyribozymes that recode sequence information. ''Nucleic Acids Research'', '''34''' (8):2166-2172, 2006. [http://openwetware.org/images/b/be/Tabor_nar_2006.pdf pdf] <br>


*J.J. Tabor, E.A. Davidson and A.D. Ellington. Developing RNA tools for engineered regulatory systems. In ''Biotechnology and Genetic Engineering Reviews'', ed. S.E. Harding, Intercept, Ltd., '''22''', 21-44, 2006. [http://openwetware.org/images/8/89/Tabor_BGER_2006.pdf pdf] <br>


*A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M.Levy, E.A. Davidson, A.Scouras, A.D. Ellington, E.M. Marcotte, and C.A. Voigt.  Engineering Escherichia coli to see light. ''Nature'', '''438''' (7067), 441-442, 2005.  [http://openwetware.org/images/5/54/Levskaya_2005.pdf pdf] <br>


*J.J. Tabor and A.D. Ellington.  Playing to Win at DNA computation.  ''Nature Biotechnology'', '''21'''(9):1013-5, 2003. [http://openwetware.org/images/a/ab/Tabor_ellington_2003.pdf pdf] <br>


==Publications==
*Jeffrey J. Tabor, Matthew Levy, Zachary B. Simpson and Andrew D. Ellington (In press). Parasitism and protocells: The tragedy of the molecular commons. In ''Protocells: Bridging Nonliving and Living Matter'', eds. S. Rasmussen, M.A. Bedau, L.Chen, D.Deamer, D.C. Krakauer, N. Packer and P.F. Stadler, MIT Press, 11/2008. <br>


*Jeffrey J. Tabor, Travis S. Bayer, Zachary B. Simpson, Matthew Levy and Andrew D. Ellington.  Engineering Stochasticity in Gene Expression (2008).  ''Molecular Biosystems'', '''4''' (7) 754-61. [http://openwetware.org/images/5/56/Tabor_2008.pdf pdf] <br>
==Contact==


*Matthew Levy, Jeffrey J. Tabor and Stephen Wong. Taking pictures with ''E.coli'': Signal processing using synthetic biology (2006). ''IEEE Signal Processing Magazine'', '''23''' (3), 142-144. [http://openwetware.org/images/c/cc/Levy_Tabor_Wong.pdf pdf] <br>
'''Email:''' <br>
account: jeff.tabor <br>
server: gmail.com <br>


*Jeffrey J. Tabor, Matthew Levy, and Andrew D. Ellington (2006). Deoxyribozymes that recode sequence information. ''Nucleic Acids Research'', '''34''' (8):2166-2172. [http://openwetware.org/images/b/be/Tabor_nar_2006.pdf pdf] <br>
'''Phone'''<br>
Office: 713-348-8316<br>
Lab: 713-348-8404


*Jeffrey J. Tabor, Eric A. Davidson and Andrew D. Ellington (2006). Developing RNA tools for engineered regulatory systems. In ''Biotechnology and Genetic Engineering Reviews'', ed. S.E. Harding, Intercept, Ltd., '''22''', 21-44. [http://openwetware.org/images/8/89/Tabor_BGER_2006.pdf pdf] <br>
'''Mailing address:'''<br>
Rice University Bioengineering, MS-142<br>
6100 Main Street<br>
Houston, TX 77005<br>


*A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M.Levy, E.A. Davidson, A.Scouras, A.D. Ellington, E.M. Marcotte, and C.A. Voigt (2005).  Engineering Escherichia coli to see light. ''Nature'', '''438''' (7067), 441-442.  [http://openwetware.org/images/5/54/Levskaya_2005.pdf pdf] <br>
'''Shipping address:'''<br>
Rice University Bioengineering<br>
BRC 840<br>
6500 Main Street<br>
Houston, TX 77030<br>


*Jeffrey J. Tabor and Andrew D. Ellington (2003).  Playing to Win at DNA computation.  ''Nature Biotechnology'', '''21'''(9):1013-5. [http://openwetware.org/images/a/ab/Tabor_ellington_2003.pdf pdf] <br>




==Contact==
==Links==
[http://www.taborlab.rice.edu/ Tabor lab website] <br>
[http://www.microbialart.com/ Microbial art]


'''email:''' <br>
account: jeff.tabor <br>
server: gmail.com <br>
'''Shipping and mailing address:'''<br>
Byer's Hall Room 409 <br>
1700 4th Street <br>
San Francisco, CA 94158-2330 <br>
===[[Jeff Tabor/archive|archive]]===
===[[Jeff Tabor/protocols|protocols]]===
===[[Jeff Tabor/protocols|protocols]]===
===[[Jeff Tabor/Pics|other]]===
===[[Jeff Tabor/Pics|other]]===
===[[Jeff Tabor/Synthetic Biology Team Challenge|Synthetic Biology Team Challenge]]===
 


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Latest revision as of 18:50, 7 January 2011

Rice Bioengineering

I will be starting up my lab in the Department of Bioengineering at Rice University in the Fall of 2010. I am looking to bring on creative students and postdocs with experience in molecular biology, evolutionary biology, microbiology, developmental biology, biophysics and chemical engineering. Research will focus on engineering multicellular behaviors. If you are interested in joining the lab, please email me.

Background

  • I was recently a Postdoctoral Fellow in the Voigt lab at UCSF.
  • I received my Ph.D. in May 2006 from the University of Texas, studying the design and evolution of Synthetic Biological systems under Andy Ellington.
  • I received my B.A. studying Biology and Biochemistry from the University of Texas in 2001. I also studied Evolutionary Biology in the laboratory of Jim Bull for two years during that time.


http://openwetware.org/images/8/81/Jtabor.jpg

Research

Synthetic Biology

I am interested in programming the behaviors of cells and organisms using synthetic genetic circuits.

Real intelligent designers use evolution. Bacterial photo: Aaron Chevalier

Bacterial Photography

I was involved with a group that designed a "bacterial photography" system in which a community of E.coli act as a biological film capable of genetically "printing" an image of light. This was accomplished by rewiring an osmo-responsive signal transduction system in E.coli to respond to red light. The light sensor was then used to control the expression of black pigment, such that dark areas of a projected image result in dark areas on the bacterial plate and light areas result in light areas. Over the entire population, the image is printed at a theoretical resolution of over 100 Megapixels per square inch. This is due to relatively small size of bacteria (1x3 microns).

Bacterial Edge Detector

We recently reprogrammed the photographic bacteria to identify the edges of objects within the projected image. In the bacterial edge detector, each cell determines whether it is located in the light, the dark, or at the boundary of light and dark. Only those who are at a boundary produce the black pigment. The emergent result over the entire population is the outline of the projected image. Edge detection is a well studied serial algorithm where computation time increases linearly with the number of pixels (approximately as the square of image size). Because the bacterial edge detector is a parallel computer, the algorithm runs in constant time regardless of image size. This bottom-up approach highlights the parallel information processing abilities inherent to biological systems, a feature which is taken advantage of in natural systems such as metazoan development and neural networks.

Multichromatic Control of Gene Expression

We have recently expanded light regulation in E.coli such that the expression of different genes can be controlled with different colors of light.

Publications

  • J.J. Tabor, E.S. Groban and C.A. Voigt. Performance Characteristics for Sensors and Circuits Used to Program E.coli. In Systems Biology and Biotechnology of E.coli, ed. S.Y.Lee, Springer, XXII, 2009. pdf
  • J.J. Tabor, M. Levy, Z.B. Simpson and A.D. Ellington. Parasitism and protocells: The tragedy of the molecular commons. In Protocells: Bridging Nonliving and Living Matter, eds. S. Rasmussen, M.A. Bedau, L.Chen, D.Deamer, D.C. Krakauer, N. Packer and P.F. Stadler, MIT Press, 2008.
  • J.J. Tabor, T.S. Bayer, Z.B. Simpson, M.Levy and A.D. Ellington. Engineering Stochasticity in Gene Expression. Molecular Biosystems, 4 (7) 754-61, 2008. pdf
  • M. Levy, J.J. Tabor and S.Wong. Taking pictures with E.coli: Signal processing using synthetic biology. IEEE Signal Processing Magazine, 23 (3), 142-144, 2006. pdf
  • J.J. Tabor, M.Levy, and A.D. Ellington. Deoxyribozymes that recode sequence information. Nucleic Acids Research, 34 (8):2166-2172, 2006. pdf
  • J.J. Tabor, E.A. Davidson and A.D. Ellington. Developing RNA tools for engineered regulatory systems. In Biotechnology and Genetic Engineering Reviews, ed. S.E. Harding, Intercept, Ltd., 22, 21-44, 2006. pdf
  • A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M.Levy, E.A. Davidson, A.Scouras, A.D. Ellington, E.M. Marcotte, and C.A. Voigt. Engineering Escherichia coli to see light. Nature, 438 (7067), 441-442, 2005. pdf
  • J.J. Tabor and A.D. Ellington. Playing to Win at DNA computation. Nature Biotechnology, 21(9):1013-5, 2003. pdf


Contact

Email:
account: jeff.tabor
server: gmail.com

Phone
Office: 713-348-8316
Lab: 713-348-8404

Mailing address:
Rice University Bioengineering, MS-142
6100 Main Street
Houston, TX 77005

Shipping address:
Rice University Bioengineering
BRC 840
6500 Main Street
Houston, TX 77030


Links

Tabor lab website
Microbial art

protocols

other

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