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Yaki
Setty |
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E-mail: |
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Office: |
Ziskind
304 |
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Phone: |
089342651 |
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Position: |
Since
2011: Research Fellow, Max-Planck-Institut für Informatik and Computer
Science Department, Saarbrucken, Germany |
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Since 2011: Scientific
Advisor, David Harel Group, Weizmann Institute of Science |
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Since 2009: Scientific
Advisor Chronic Fatigue and Immune
Dysfunction Syndrome Association of America |
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Previous
Position: |
Post-Doc
Researcher at Microsoft Research Cambridge UK |
Objectives:
Understanding the dynamics of stem cell population, developmental systems and
diseases over time is a key question in developmental biology research. The
dynamics of these systems and the way it develops a healthy tissue has
potential implications in regenerative medicine, tissue engineering and cancer
therapeutics. However, technical hurdles in recording multiple time point
imaging prevent existing experimental techniques from revealing the dynamics of
the development. Indeed, state-of-the-art techniques are able to record merely
a few cell divisions. In recent years, using software engineering tools, we
synthesize experimental data into computational models, a powerful yet
underutilized tool, to address dynamic aspect of the developmental process.
This approach enables to integrate previous studies of isolated subcomponents
of the process into the development as a whole. The simulations provided a
means to change parameters and analyze the development in-silico, and thereby
test hypothesis, predict unforeseen phenomena and postulate hypotheses that
could guide future experimental trials. To date, three organs from diverse
evolutionary organisms have been thus modeled: the mouse pancreas (see here), the C.
elegans gonad (see here),
and partial rodent brain development (see here).
Recently, we have utilized these principles to study the dynamics of glucose
homeostasis in healthy and diabetic in-silico subjects (see here).
Analysis and execution of the models recapitulated the development of the
organs, anticipated known experimental results and gave rise to novel testable
predictions, some of which were already been tested experimentally.
Bio
sketch:
Dr. Yaki Setty is
currently working on developing advanced techniques for analyzing the dynamics
of stem cell population, developmental systems and diseases. In 2009, Dr. Setty
was nominated as Scientific Advisor at the Chronic Fatigue and Immune
Dysfunction Syndrome Association of America, working on developing advance
technique to study Chronic Fatigue Syndrome (CFS). He did his post-doctoral
trainings as a researcher in the Computational Biology Group at Microsoft
Research Cambridge. He graduated in 2008 his 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.
Publications:
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Biological synthesis of stem cell systems: challenges, goals and
achievements. In preparation, 2011.
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In-silico study of pancreatic morphogenesis and differentiation. In
preparation, 2011
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E. Aslakson, S. Szekely, L. Bateman, S.
Vernnon and Y. Setty. Modeling Medical Histories To Optimize Patient Care: An
Object Model to Study Chronic Fatigue Syndrome Development and Treatment, In preparation, 2011
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Y. Setty, A computational approach to multi-scale modeling in
development biology. Submitted 2011
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Y. Setty, I.R. Cohen, D. Harel. Executable
Modeling of Morphogenesis: A Turing-Inspired Approach. Submitted, 2011.
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N. Bloch*, D. Sherman*, Y. Setty* and David Harel (*equal contribution) Analysis of glucose homeostasis dynamics in healthy and type-I diabetes
mellitus in-silico subjects. Under Review, Integrative Biology, 2011.
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Y. Setty, D. Dalfo, E.J.A. Hubbard, and H. Kugler. A model of stem cell
population dynamics: in-silico analysis and in-vivo validation. Development,
139, 47:56 2012.
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Y. Setty, C.C. Chen, M. Secrier, D. Kalamatianos, N. Skoblov, and S.
Emmott. How neurons migrate: A cellular decision making model of neuronal
migration. BMC Systems Biology 2011, 5:154 
.
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Y. Setty, I. R. Cohen, and D. Harel. Modeling Biology using Generic
Reactive Animation. Fundamenta Informaticae, 2010.
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Y. Setty, I. R. Cohen, Y. Dor, and D. Harel. Four-dimensional realistic
modeling of pancreatic organogenesis. Proc Natl Acad Sci U S A,
105(51):2037420379, 2008.
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D. Harel, I. Segall, H. Kugler, , and Setty Y. Crafting Game-Models
using Reactive System Design. Future Play, Association for Computing
Machinery, Inc., 9:661674, 2008.
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D. Harel, Y. Setty, S. Efroni, N. Swerdlin, , and Cohen I. R.
Concurrency in Biological Modeling: Behavior, Execution and Visualization. Electron.
Notes Theor. Comput. Sci., 194:119131, 2008.
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Y. Setty and D. Harel. Generic Reactive Animation: Realistic Modeling
of Complex Natural Systems. Lecture Notes in Bioinformatics, 5054:1
16, 2008.
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A. E. Mayo, Y. Setty, S. Shavit, A. Zaslaver, and U. Alon. Plasticity
of the cis-regulatory input function of a gene. PLoS Biol, 4(4):e45,
2006.
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Y. Setty, A. E. Mayo, M. G. Surette, and U. Alon.
Detailed map of a cis-regulatory input function. Proc Natl Acad Sci U S A, 100(13):77027707,
2003.
Press:
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Tech meets bio, Nature Medicine, 2010 (PDF,
link)
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VerticalNews, Journal of Technology and Science, 2009 (link)
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HighBeam, 2009 (link)
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In Silico Biology, Future Magazine, 2009 (PDF).
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Modeling in four dimensions, Future Magazine, 2009 (PDF).
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Times Online, July 11, 2007 (PDF).
Invited talks (highlights):
- Programing stem cells. MUNI, Ireland, April 2011
- Modeling development. INRIA, Paris, France, March 2011
- Modeling organogenesis: scaling development from
stem cells to organs. Medical
Institute South Carolina, USA, 2011
- Cellular decision-making from stem cells to
organs. Max Planck Institute Fur
Informatic, Saarbrucken Germany 2010
- Can a research network help realistic modelling
of CFS? , From Infection to
Neurometabolism: A Nexus for CFS, CFIDS meeting, Cold Spring Harbour
Sept. 2009.
- Four dimensional realistic modelling of
pancreatic organogenesis, Centre
for Clinical Epidemiology and Evaluation, UBC, Mar. 2009.
- Realistic modelling of biological systems, TechFest, Microsoft Research, US, Feb. 2009.
- Crafting Game-Models using Reactive System Design, Future Play, Canada, Nov. 2008
- Four dimensional realistic modelling of
pancreatic organogenesis, Cold
Spring Harbour, US, Dec 2008.
Academic activities
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Referee for the BMC Systems Biology (2011)
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Referee for the BMC Systems Biology (2010)
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Referee for the Bulletin of Mathematical Biology (2009)
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Grant Referee for The CFIDS Association of America (2008)
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Grant Referee for WWTF Vienna Science and Technology Fund (2007)