Design principles of biological circuits
Cells are constantly "making decisions" - monitoring their environment, modulating their metabolism and 'deciding' whether to divide, differentiate or die. For this, they use biochemical circuits composed of interacting genes and proteins. Advances over the past decades have mapped many of these circuits. Still, can we infer the underlying logic from the detailed circuit structure? Can we deduce the selection forces that shaped these circuits during evolution? What are the principles that govern the design and function of these circuits and how similar or different are they from principles that guide the design of man-made machines? The interplay between variability and robustness is a hallmark of biological computation: Biological systems are inherently noisy, yet control their behavior precisely. Research projects in our lab quantify biological variability and identify its genetic origins, examine how variability is buffered by molecular circuits and investigate whether variability can in fact be employed to improve cellular computation. We encourage a multi-disciplinary approach, combining wet-lab experiments, dynamic-system theory and computational data analysis. This is achieved through fruitful interactions between students with backgrounds in physics, biology, computer science, mathematics and chemistry.



Meyer bulding 404
Weizmann Institute of Science
Rehovot 76100
August 2014
We welcome Amir Maimon and David Lerner to the lab! Good luck with your MSc!

June 2014
The lab wishes good luck to Noam Vardi in his post-doc!

May 2014
Congratulations to Zvika, Noam and Eyal on graduating! Here's a picture from the ceremony (May 15th 2014):

May 2014
Congratulations to Inna and Danny for their amazing new paper in Development on scaling morphogen gradients during tissue growth

February 2014
Congratulations to Eyal and Yossi for handing in their M.Sc Thesis

February 2014
The Barkai Lab had a great time in Ilanit FISEB 2014! In one of the nights we went bowling...

January 2014
Congratulations to Noam Vardi on finishing his PhD! From now on - Dr. Vardi! You can read his paper from Current Biology on how yeast cells escape commitment using noise here .

January 2014
Congratulations to Zvika Tamari on finishing his PhD! Dr. Tamari!

January 2014
The Barkai lab would like to wish Mazal Tov to Noam Ohana on finishing his MSc and good luck in his future endeavors!

December 2013
Barkai lab wishes you happy holidays!

October 2013
Congratulations to the lab Vollyaball team on winning in the latest departmental tournament!

October 2013
On November the lab is going on a lab trip, to mark the departure of Ilya from the lab

October 2013
Congratulations to Noam V on his new paper in Current Biology!

September 2013
Next month Gilad will give a talk in the departmental seminar!

September 2013
The Barkai Lab wishes you a happy holiday!

August 2013
We would like to welcome Gilad Yaakov to the Barkai Lab!

August 2013
The Barkai Lab wishes good luck to Dana and Michal, our new M.Sc students!
Divergence and Selectivity of Expression-Coupled Histone Modifications in Budding Yeasts
Yaron Mosesson, Yoav Voichek, Naama Barkai
Plos Biology (2014)

Various histone modifications are widely associated with gene expression, but their functional selectivity at individual genes remains to be characterized. Here, we identify widespread differences between genome-wide patterns of two prominent marks, H3K9ac and H3K4me3, in budding yeasts. As well as characteristic gene profiles, relative modification levels vary significantly amongst genes, irrespective of expression. Interestingly, we show that these differences couple to contrasting features: higher methylation to essential, periodically expressed, ‘DPN’ (Depleted Proximal Nucleosome) genes, and higher acetylation to non-essential, responsive, ‘OPN’ (Occupied Proximal Nucleosome) genes. Thus, H3K4me3 may generally associate with expression stability, and H3K9ac, with variability. To evaluate this notion, we examine their association with expression divergence between the closely related species, S. cerevisiae and S. paradoxus. Although individually well conserved at orthologous genes, changes between modifications are mostly uncorrelated, indicating largely non-overlapping regulatory mechanisms. Notably, we find that inter-species differences in methylation, but not acetylation, are well correlated with expression changes, thereby proposing H3K4me3 as a candidate regulator of expression divergence. Taken together, our results suggest distinct evolutionary roles for...

Departments of Molecular Genetics and Physics of Complex Systems