Post Doctoral Researcher at Microsoft Research Cambridge
Scientific Advisor for The CFIDS Association of America
Objective:
Biological systems are complex, involving feedbacks across numerous processes, mechanisms and objects. Experimental analysis, by its nature, rarely captures the behaviour of the complete biological system as it divides the system into static interactions with reduced spatial dimensionality and minimal dynamics. To bridge the gap between experimental findings and the underlying system behaviour, we formalize biological findings into mathematically and algorithmically rigorous specifications, which are then compiled into reactive models with an interactive animation. We design the models to behave consistently with real biological system and thus to serve as a platform for testing novel hypothesis. Our case study is a fully executable, interactive 4D simulation (time and three dimensions of space) of pancreatic development that provides a dynamic description of the process and culminates in a structure remarkably recapitulated the unique 3D cauliflower shaped structure of the pancreas (see Setty et. al PNAS 2008). Currently we are exploring ways to model other biological systems such as Gonadogenesis of the C. elegans nematode and neural development in the mammalian brain.
Biography:
Yaki Setty is a post-doctoral researcher in the Computational Biology Group at Microsoft Research Cambridge. In 2008, he completed a Ph.D. in computational biology at the Weizmann Institute of Science, in Rehovot, Israel, under the joint supervision of Professor David Harel of the Department of Computer Science and Mathematics and Professor Irun Cohen of the Department of Immunology. Setty received a B.Sc. in computer science and mathematics from Ben Gurion University in 2000 and a M.Sc. in system biology from the Weizmann Institute of Science in 2003, under supervision of Professor Uri Alon of the Department of Molecular Cell Biology and the Department of Physics of Complex Systems.
Contact details:
Microsoft Research
7 J. J. Thomson Avenue
CB3 0FB Cambridge
United Kingdom
email: yaki.setty@microsoft.com
phone: +44 1223 479 793
fax: +44 1223 479 999
Academic Activities:
- Grant Referee for The CFIDS Association of America (2008)
- Grant Referee for WWTF Vienna Science and Technology Fund (2007)
Press:
- The virtual physiological human: The search for computing’s supermodel, Futures Magazin, 2009 (PDF).
- Modelling in four dimensions, Futures Magazin, 2009 (PDF).
- Data on science reported by Y. Setty and co-researchers. Science Letter. NewsRX. 2009. February 24, 2009 (PDF)
Also in HighBeam Research (http://www.highbeam.com/doc/1G1-194146699.html, PDF) - Times Online, July 11, 2007 (PDF).
- Setty Y., I. R. Cohen, A. E. Mayo, and D. Harel, On Using Divide and Conquer in Modeling Natural Systems, in Algorithmic Bioprocesses, Springer Verlag, 2009
- Setty Y., Cohen I.R., Dor Y., and Harel D., Four-dimensional realistic modeling of pancreatic organogenesis, in Proc Natl Acad Sci U S A, December 2008
- Harel, D., Segall, I., Kugler, H., Setty, and Y., Crafting Game-Models using Reactive System Design , in Future Play, Association for Computing Machinery, Inc., November 2008
- Setty, Y., Harel, and D., Generic Reactive Animation: Realistic Modeling of Complex Natural Systems., in FMSB, Springer, 2008
- Harel, D., Setty. Y., Efroni, S., Swerdlin, N., Cohen, and I. R., Concurrency in Biological Modeling: Behavior, Execution and Visualization, in Electron. Notes Theor. Comput. Sci., vol. 194, no. 3, pp. 119–131, Elsevier Science Publishers B. V., Amsterdam, The Netherlands, The Netherlands, 2008
- Mayo, A. E., Setty, Y., Shavit, S., Zaslaver, A., Alon, and U., Plasticity of the cis-regulatory input function of a gene, in PLoS Biol, vol. 4, no. 4, pp. e45, 2006
- Setty, Y., Mayo, A. E., Surette, M. G., Alon, and U., Detailed map of a cis-regulatory input function, in Proc Natl Acad Sci U S A, vol. 100, no. 13, pp. 7702-7, 2003
