Jeff Tabor

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====Bacterial Edge Detector====
====Bacterial Edge Detector====
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We have used the bacterial photography system as a platform to program the bacterial community to solve the edges of 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 a visible black pigment.  The result is not a positive of the projected image, but only the outline of the 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).  In the massively parallel Biological edge detector, 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.
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We have 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 a visible black pigment.  The result is not a positive of the projected image, but only the outline of the 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.
    
    
==Publications==
==Publications==

Revision as of 01:38, 10 June 2009

Contents

Background

  • 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.


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
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 have 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 a visible black pigment. The result is not a positive of the projected image, but only the outline of the 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.

Publications

  • J.J. Tabor, H. Salis, Z.B. Simpson, A.A. Chevalier, A. Levskaya, E.M.Marcotte, C.A. Voigt and A.D. Ellington. A Synthetic Genetic Edge Detection Program. Cell (In press).
  • 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

Shipping and mailing address:
Byer's Hall Room 409
1700 4th Street
San Francisco, CA 94158-2330

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