Nadav Kashtan
I am a postdoc at the group of Uri Alon at the Weizmann Institute of Science, Israel.
My Research interests
Evolution and Ecology
I'm interested in simple questions about evolution such as:
what is the origin of modularity in biological systems? How can evolutionary theory explain the observed speed of evolution in nature?
What determines the number of species in a given ecosystem?
I study the impact of varying environments on the design of evolved organisms, populations and species.
We found that modularly varying environments lead to the rapid spontaneous evolution of modular structure (see Kashtan & Alon PNAS 2005 and Kashtan et. al. PNAS 2007).
In my research I use computer simulations (such as Genetic Algorithms), mathematical models and analysis of biological data.
Optimization problems
The optimization solving abilities of natural evolution are impressive. What can we learn from natural evolution that can be applied to optimization solving?
Aiming at understanding natural evolution we have found that varying environments can lead to the accelerated emergence of modular systems. Can this approach be used to accelerate optimization algorithms or to improve engineering design?
Studying RNA molecule design, we demonstrate that temporal switching between 'related' optimization goals can significantly accelerate bioengineering design (see Kashtan et. al. PNAS 2007).
Network motifs - building blocks of complex networks
To understand the structure and function of biological networks we define network motifs: patterns of interactions (subgraphs) that appear much more than expected in random networks.
Network motifs were suggested to be the building blocks of evolved and designed networks (see our papers Milo et. al. Science 2002 and 2004)
My main contribution to these series of studies was the developing of algorithms to analyze complex networks and to detect network motifs.
I'm the author of mfinder: a network motifs detection tool.
You are welcome to download mfinder
(see also mfinder Tool guide).
email:
nadav.kashtan@weizmann.ac.il
Phone: +972-8-934-4447
Academic background:
2004-2008: Ph.D. Weizmann Institute of Science (Life Sciences), Advisor: Uri Alon.
2002-2003: M.Sc. Weizmann Institute of Science (Computer Science & Math), Advisor: Uri Alon.
1994-1997: B.A. Tel-Aviv University (Computer Science)
Publications:
- Nadav Kashtan, Merav Parter, Erez Dekel, Avi E. Mayo and Uri Alon
Extinctions in heterogeneous environments and the evolution of modularity.
pdf
Evolution, 1558-5646.2009.00684 (2009).
- Nadav Kashtan*, Avi E. Mayo*, Tomer Kalisky and Uri Alon
An analytically solvable model for rapid evolution of modular structure.
pdf
PLoS Comput Biol., 5(4): e1000355(2009).
* equal contribution
- Merav Parter *,Nadav Kashtan* and Uri Alon
Facilitated variation: How evolution learns from past environments to generalize to new environments.
pdf
PLoS Comput Biol. 4(11): e1000206 (2008).
* equal contribution
- See research highlights in Nature Reviews Genetics: Something New
pdf
- Nadav Kashtan, Elad Noor and Uri Alon.
Varying environments can speed up evolution.
pdf
Proc Natl Acad Sci U S A. 104(34),13711-13716 (2007).
Merav Parter, Nadav Kashtan and Uri Alon.
Environmental variability and modularity of bacterial metabolic networks.
pdf
BMC Evol. Biol. 7,169 (2007).
Shalev Itzkovitz, Ron Milo, Nadav Kashtan Reuven Levitt, Amir Lahav and Uri Alon.
Recurring Harmonic Walks and Network Motifs in Western Music.
pdf
Advances in Complex Systems, 9,121–132 (2006).
Nadav Kashtan and Uri Alon.
From the Cover: Spontaneous evolution of modularity and network motifs.
pdf
Proc Natl Acad Sci U S A. 102(39),13773-13779 (2005).
See review in:
- Nature Reviews Genetics: The road to modularity
pdf
Shalev Itzkovitz, Reuven Levitt,Nadav Kashtan, Ron Milo and Uri Alon.
Coarse-graining and self-dissimilarity of complex networks.
pdf
Phys Rev E 71, 016127(2005).
Nadav Kashtan, Shalev Itzkovitz, Ron Milo and Uri Alon.
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
pdf
Bioinformatics, 20(11):1746-58 (2004).
Esti Yeger-Lotem, Shmuel Sattath, Nadav Kashtan, Shalev Itzkovitz, Ron Milo, Ron Y. Pinter, Uri Alon and Hanah Margalit.
Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction.
pdf
Proc Natl Acad Sci U S A. 101, 5934 (2004).
Nadav Kashtan, Shalev Itzkovitz, Ron Milo and Uri Alon.
Topological Generalizations of network motifs.
Pdf
Phys. Rev. E 70, 031909 (2004).
Ron Milo, Shalev Itzkovitz, Nadav Kashtan, Reuven Levitt, Inbal Ayzenshtat, Michal Sheffer and Uri Alon.
Super-families of evolved and designed networks.
pdf
Science 303, 1538-42 (2004).
Ron Milo, Shalev Itzkovitz, Nadav Kashtan, Reuven Levitt and Uri Alon.
Response to Comment on "Network Motifs: Simple Building Blocks of Complex Networks".
Science 20, 305,5687:1107D (2004).
Shalev Itzkovitz, Ron Milo, Nadav Kashtan, Guy Ziv and Uri Alon.
Subgraphs in random networks.
pdf
Phys. Rev. E 68, 026127 (2003).
Ron Milo, Nadav Kashtan, Shalev Itzkovitz, Mark E.J. Newman and Uri Alon.
On the uniform generation of random graphs with arbitrary degree sequences.
pdf
arXiv:cond-mat/0312028 (2003).
Ron Milo, Shen-Orr Shai, Shalev Itzkovitz, Nadav Kashtan, David Chklovskii and Uri Alon.
Network Motifs: Simple Building Blocks of Complex Networks.
pdf.
Science 25, 298, 824-7 (2002).