PUBLICATIONS

RSS of the lab's publications


Heterosis as a consequence of regulatory incompatibility
Rebecca H. Herbst*, Dana Bar-Zvi*, Sharon Reikhav, Ilya Soifer, Michal Breker, Ghil Jona, Eyal Shimoni, Maya Schuldiner, Avraham A. Levy and Naama Barkai
BMC Biology (2017) | PDF


The Genetic Requirements for Pentose Fermentation in Budding Yeast
Karin Mittelman & Naama Barkai
G3: Genes, Genomes, Genetics (2017) | PDF


Buffering Global Variability of Morphogen Gradients.
Benny Shilo & Naama Barkai
Developmental Cell (2017)


Lighting Up ERK Activity
Benny Shilo & Naama Barkai
Developmental Cell (2017)


Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress
Gilad Yaakov, David Lerner, Kajetan Bentele, Joseph Steinberger & Naama Barkai
Nature Ecology & Evolution (2017) | PDF


Early commitment and robust differentiation in colonic crypts.
Be?ta T?th, Shani Ben?Moshe, Avishai Gavish, Naama Barkai, Shalev Itzkovitz
Molecular Systems Biology (2017)


Model-based analysis of DNA replication profiles: Predicting replication fork velocity and initiation rate by profiling free-cycling cells
Ariel Gispan, Miri Carmi & Naama Barkai
Genome Research (2016) | PDF


Rethinking cell growth models.
Moshe Kafri*, Eyal Metzl-Raz*, Felix Jonas, Naama Barkai
FEMS Yeast Res (2016) | PDF


Dealing with Gene-Dosage Imbalance during S Phase.
Raz Bar-Ziv*, Yoav Voichek*, and Naama Barkai
Trends in Genetics(2016) | PDF


Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source.
Zvika Tamari*, Avihu Yona*, Yitzhak Pilpel and Naama Barkai
BMC Genomics (2016)


A role for Rtt109 in buffering gene-dosage imbalance during DNA replication.
Yoav Voichek*, Raz Bar-Ziv*, and Naama Barkai
Nucleus (2016) | PDF


Chromatin dynamics during DNA replication
Raz Bar-Ziv*, Yoav Voichek* and Naama Barkai
Genome Research (2016)| PDF
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Expression homeostasis during DNA replication
Yoav Voichek*, Raz Bar-Ziv* and Naama Barkai
Science (2016) | PDF
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Research Highlight in Nature Reviews Molecular Cell Biology (2016)


A WntD-Dependent Integral Feedback Loop Attenuates Variability in Drosophila Toll Signaling
Neta Rahimi*, Inna Averbukh*, Michal Haskel-Ittah*, Neta Degani*, Eyal D. Schejter, Naama Barkai, Ben-Zion Shilo
Developmental Cell (2016)| PDF


A two-step patterning process increases the robustness of periodic patterning in the fly eye
Avishai Gavish & Naama Barkai
Journal of Biology Physics (2016)| PDF


Periodic patterning of the Drosophila eye is stabilized by the diffusible activator Scabrous
Avishai Gavish, Arkadi Shwartz, Abraham Weizman, Eyal Schejter, Ben-Zion Shilo & Naama Barkai
Nature Communications(2016)| PDF


Natural Diversity in Pentose Fermentation Is Explained by Variations in Histone Deacetylases
Zvi Tamari & Naama Barkai
Cell Reports(2016)| PDF


The Cost of Protein Production
Moshe Kafri*, Eyal Metzl-Raz*, Ghil Jona, Naama Barkai
Cell Reports(2016)| PDF
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DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis.
Shay Shilo, Cathy Melamed-Bessudo, Yanniv Dorone, Naama Barkai, and Avraham A. Levy
Plant Cell(2015)| PDF


The Evolutionary Potential of Phenotypic Mutations.
Hayato Yanagida, Ariel Gispan, Noam Kadouri, Shelly Rozen, Michal Sharon, Naama Barkai, and Dan S. Tawfik
PLoS Genetics (2015)| PDF


Loss of growth homeostasis by genetic decoupling of cell division from
biomass growth: implication for size control mechanisms.

Hannah Schmidt-Glenewinkel, Naama Barkai
Molecular Systems Biology (2014)| PDF


Sequential feedback induction stabilizes the phosphate starvation response in budding yeast.
Noam Vardi, Sagi Levy , Yonat Gurvich, Tamar Polacheck, Miri Carmi, Diego Jaitin, Ido Amit, Naama Barkai
Cell Reports (2014)| PDF


Systematic identification of cell size regulators in budding yeast.
Ilya Soifer, Naama Barkai
Molecular Systems Biology (2014)| PDF


Divergence and selectivity of expression-coupled histone modifications in budding yeasts.
Yaron Mosesson, Yoav Voichek, Naama Barkai
Plos One (2014)| PDF


Scaling morphogen gradients during tissue growth by a cell division rule
Inna Averbukh, Danny Ben-Zvi, Siddhartha Mishra, and Naama Barkai
Development (2014)| PDF


Coordination of Gene Expression and Growth-Rate in Natural Populations of Budding Yeast
Tamari Zvi, Rosin Dalia, Voichek Yoav, Barkai Naama
PLOS ONE (2014)| PDF


Scaling of dorsal-ventral patterning in the Xenopus laevis embryo.
Ben-Zvi D, Fainsod A, Shilo BZ, Barkai N.
Bioassays (2014)| PDF


Budding Yeast Escape Commitment to the Phosphate Starvation Program Using Gene Expression Noise
Vardi N, Levy S, Assaf M, Carmi M, Barkai N.
Current Biology (2013)| PDF


Increasing population growth by asymmetric segregation of a limiting resource during cell division
Avraham N, Soifer I, Carmi M, Barkai N.
Mol Syst Biol. (2013)| PDF


Disentangling signaling gradients generated by equivalent sources.
Noa Rappaport, Naama Barkai
J Biol Phys (2012)| PDF


Improved readout precision of the Bicoid morphogen gradient by early decoding.
Zvika Tamari, Naama Barkai
J Biol Phys (2012)| PDF


Creating gradients by morphogen shuttling.
Ben-Zion Shilo, Michal Haskel-Ittah, Danny Ben-Zvi, Eyal D. Schejter, Naama Barkai
Trends Genet (2013)| PDF


Developmental biology: Segmentation within scale.
Naama Barkai & Ben-Zion Shilo
Nature (2013)| PDF


Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
Anthony Gitter, Miri Carmi, Naama Barkai, Bar-Joseph Ziv
Genome Research (2013)| PDF


Self-organized shuttling: generating sharp dorsoventral polarity in the early Drosophila embryo.
Michal Haskel-Ittah, Danny Ben-Zvi, Merav Branski-Arieli, Eyal D. Schejter, Ben-Zion Shilo ,Naama Barkai1
Cell (2012)| PDF


Noise-mean relationship in mutated promoters.
Gil Hornung, Raz Bar-Ziv, Dalia Rosin, Nobuhiko Tokuriki, Dan. S. Tawfik, Moshe Oren, Naama Barkai
Genome Research (2012)| PDF


Expression Noise and Acetylation Profiles Distinguish HDAC Functions.
Leehee Weinberger, Yoav Voichek, Itay Tirosh, Gil Hornung, Ido Amit, Naama Barkai
Molecular Cell (2012)| PDF | Supplement 1 (PDF) | Supplement 2 (XLS) |See also: Making a Noisy Gene: HDACs Turn Up the Static


Efficiency and specificity in microRNA biogenesis
Omer Barad, Mati Mann, Elik Chapnik, Archana Shenoy, Robert Blelloch, Naama Barkai and Eran Hornstein
Nature Structural & Molecular Biology. (2012)| PDF


Promoter nucleosome organization shapes the evolution of gene expression
Dalia Rosin, Gil Hornung, Itay Tirosh, Ariel Gispan and Naama Barkai
PLoS Genetics. (2012)| PDF | Supplement


Nucleosome organization affects the sensitivity of gene expression to promoter mutations
Gil Hornung, Moshe Oren and Naama Barkai
Molecular Cell. (2012)| PDF | Supplement (PDF)


The Competative Advantage of a Dual Transporter System
Sagi Levy*, Moshe Kafri*, Miri Carmi and Naama Barkai
Science. (2011)| PDF | Supplement (PDF)


Extensive divergence of yeast stress responses through transitions between induced and constitutive activation
Itay Tirosh, Koon Ho Wongb, Naama Barkai and Kevin Struhl
PNAS. (2011)| PDF | Supplement (PDF)


Robust selection of sensory organ precursors by the Notch-Delta pathway
Omer Barad, Eran Hornstein and Naama Barkai
Opp in Cell Biology. (2011)| PDF


The Era of Developmental Systems Biology
Norbert Perrimon and Naama Barkai
Curr Opp in Genetics and Development. (2011)| PDF


Scaling of morphogen gradients
Danny Ben-Zvi, Ben-Zion Shilo and Naama Barkai
Curr Opp in Genetics and Development. (2011)| PDF


Improved readout precision of the Bicoid morphogen gradient by early decoding
Zvi Tamari and Naama Barkai
Journal of Biological Physics. (2011)| PDF


Disentangling signaling gradients generated by equivalent sources
Noa Rappaport and Naama Barkai
Journal of Biological Physics. (2011)| PDF


Inferring regulatory mechanisms from patterns of evolutionary divergence
Itay Tirosh and Naama Barkai
Molecular Systems Biology. (2011)| PDF


Expansion-repression mechanism for scaling the Dpp activation gradient in Drosophila wing imaginal discs
Danny Ben-Zvi, George Pyrowolakis, Naama Barkai and Ben-Zion Shilo
Current Biology. (2011)| PDF | Supplement (PDF)
see also
Dispatch:S. Restrepo and K. Basler, Morphogen Gradients: Expand and Repress, Current Biology. Oct 11; 21(19):R815-7


 

 

?         Physical aspects of precision in genetic regulation
Zvi Tamari, Naama Barkai and Itzhak Fuoxon
Journal of Biological Physics. Mar 23 37(2):213-25 (2011) | PDF

 

 

?         A biological solution to a fundamental distributed computing problem

Yehuda Afek, Noga Alon, Omer Barad, Eran Hornstein,Naama Barkai & Ziv Bar-Joseph
Science. January 14 Vol. 331 no. 6014, p. 183-185 (2011) | PDF | Supplement

see also

Editors' Choice: L. B. Ray. Computer Scientists Learn from Flies, Sci. Signal. 4, ec21 (2011)

 

 


 

 

?         Chromatin regulators as capacitors of interspecies variations in gene expression
Itay Tirosh, Sharon Reikhav,Nadejda Sigal, Yael Assia & Naama Barkai
Mol Syst Biol. Nov 30 6:435. (2010) | PDF

see also

news & views

 

 

?         Error minimization in lateral inhibition circuits
Omer Barad, Dalia Rosin, Eran Hornstein & Naama Barkai
Science Signaling. July 6 Vol. 3, Issue 129, p. ra51 (2010) | PDF | Supplement

see also

Science Signaling podcast: Interview with Naama Barkai (text/audio)

Science Signaling Cover

 

 

?         MRC1-dependent scaling of the budding yeast DNA replication timing program
Amnon Koren, Ilya Soifer & Naama Barkai
Genome Research. Jun;20(6):781-90 (2010) | PDF | Supplement

 

 

?         Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences
Itay tirosh, Nadejda Sigal & Naama Barkai
Mol Syst Biol. May 11 6:365 (2010) |PDFo:p>

see also

news & views

 

?         Widespread remodeling of mid-coding sequence nucleosomes by Isw1
Itay tirosh, Nadejda Sigal & Naama Barkai
Genome Biol. May 10 11(5):R49 (2010) | PDF

 

 

?         Scaling of morphogen gradients by an expansion-repression integral feedback control
Danny Ben-Zvi & Naama Barkai
PNAS. Apr 13 107(15):6924-9 (2010) | PDF | Supplement (PDF)

 

 


 

 

?         Promotor architecture and the evolvability of gene expression
Itay Tirosh, Naama Barkai & Kevin Verstepen
J Biol. . Dec 14 8(11):95 (2009) | PDF

 

 

?         Coordination of gene expression with growth rate: a feedback or a feed-forward strategy?
Sagi Levy & Naama Barkai
FEBS Lett. Dec 17 583(24):3974-8 (2009) |PDF

 

 

?         Robust generation and decoding of morphogen gradients
Naama Barkai & Ben-Zion Shilo
Cold Spring Harb Perspect Biol. Nov; 1(5) (2009) | PDF

 

 

?         Scaling of the BMP activation gradient in Xenopus embryos - Reply to Francois et al
Danny Ben-Zvi, Ben-Zion Shilo, Abraham Fainsod & Naama Barkai
Nature. Sep 3;461(7260):E2 (2009) | PDF | Supplement (PDF)

 

 

?         Reverse engineering of the spindle assembly checkpoint
Andreas Doncic, Eshel Ben-Yaacov, Shmuel Einav& Naama Barkai
PLoS ONE . Aug 4;4(8): e6495 (2009) | PDF | Supplement (PDF)

 

 

?         A yeast hybrid provides insight into the evolution of gene expression regulation.
Itay Tirosh, Sharon Reikhav, Avraham A. Levy & Naama Barkai
Science. May 1 324(5927):659-62 (2009) | PDF

 

 

?         'Big frog, small frog'--maintaining proportions in embryonic development.
Danny Ben-Zvi & Naama Barkai
FEBS J . Mar 276(5):1169-207 (2009) |PDF

 

 


 

?         Scaling of the BMP activation gradient in Xenopus embryos.
Danny Ben-Zvi, Ben-Zion Shilo, Abraham Fainsod & Naama Barkai
Nature. Jun 26;453(7199):1205-11 (2008) | PDF | Supplement (PDF)

see also

N. R. Gough, Making Animals the Right Size. Sci. Signal. 1, ec240 (2008).

J. Lewis, From signals to pattern: space, time and mathematics in developmental biology, Science, 2008 Oct 17;322(5900):399-403

M. B. Zao, Leading edge: developmental biology select, Cell, Aug 8, 134(3); 372-3 (2008).

 

 

?         Two strategies for gene regulation by promoter nucleosomes.
Itay Tirosh and Naama Barkai
Genome Res. Jun 11. (2008) | PDF

 

 

?         Evolution of gene sequence and gene expression are not correlated in yeast.
Itay Tirosh and Naama Barkai
Trends Genet. Feb 2. (2008) | PDF

 

 

?         On the relation between promoter divergence and gene expression evolution.
Itay Tirosh, Adina Weinberger,Dana Bezalel, Mark Kaganovich and Naama Barkai
Mol Syst Biol. 4:159. (2008) | PDF

 

 

?         Re-examining the Stability of the Bicoid Morphogen Gradient.
Sven Bergmann, Zvi Tamari, Eyal Schejter, Ben-Zion Shilo and Naama Barkai
Cell. 132(1):15-7 (2008)4:159. (2008)
| PDF

 

 

?         Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback
Gil Hornung and Naama Barkai
PLoS Computational Biology 4(1):e8 (2008) | PDF

 


 

?         EGF receptor signaling - a quantitative view
Ben-Zion Shilo and Naama Barkai
Current Biology 17(24):R1038-41 (2007) | PDF

 

 

?         Variability and Robustness in Biomolecular Systems
Naama Barkai and Ben-Zion Shilo

Molecular Cell. 28(5):755-60 (2007) | PDF

 

 

?         Spore germination in Saccharomyces cerevisiae: Global gene expression patterns and cell cycle landmarks
Daphna Joseph-Strauss, Drora Zenvirth, Giora Simchen and Naama Barkai
Genome Biol. 8(11): R241, (2007) | PDF

 

 

?         Comparative biology: beyond sequence analysis
Itay Tirosh, Yonatan Bilu and Naama Barkai
Curr Opin Biotechnol. 18(4):371-7 (2007) | PDF

 

 

?         Autocorrelation analysis reveals widespread spatial biases in microarray experiments
Amnon Koren, Itay Tirosh and Naama Barkai
BMC Genomics. 8, 164, (2007) | PDF

 

 

?         The pattern and evolution of yeast promoter bendability
Itay Tirosh, Judith Berman and Naama Barkai
Trends in Genetics, 23(7), 318-321, (2007) | PDF

 

 

?         Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
Itay Tirosh and Naama Barkai
Genome Biology, 8, R50, (2007)
| PDF

 

?         Strategy of transcription regulation in the budding yeast
Sagi Levy, Jan Ihmels, Miri Carmi, Adina Weinberger, Gilgi Friedlander and Naama Barkai
PLoS ONE, 2(2), e250, (2007) | PDF

 

 

?         Pre-steady-state decoding of the Bicoid morphogen gradient.
Sven Bergmann, Oded Sandler, Hila Sberro, Sara Shnider, Eyal Schejter, Ben-Zion Shilo and Naama Barkai
PLoS Biology, 5(2), e46, (2007) | PDF

 

 

 


 

?         Conservation of expression and sequence of metabolic genes is reflected by their activity across metabolic states
Yonatan Bilu, Tomer Shlomi, Naama Barkai and Eytan Ruppin
PLoS Computational Biology, 2(8), e106, (2006) | PDF

 

 

?         A genetic signature of interspecies variations in gene expression
Itay Tirosh, Adina Weinberger, Miri Carmi and Naama Barkai
Nature Genetics 38, 830 - 834 (2006) | PDF | Accompanying web page

 

 

?         Noise in protein expression scales with natural protein abundance
Arren Bar-Even, Johan Paulsson, Narendra Maheshri, Miri Carmi, Erin O'Shea, Yitzhak Pilpel and Naama Barkai
Nature Genetics 38, 636 - 643 (2006)

see also Baetz and Kaern: Predictable trends in protein noise. Nature Genetics 38, 606-610 (2006) 

 

?         Noise resistance in the spindle assembly checkpoint
Andreas Doncic, Eshel Ben-Jacob and Naama Barkai
Molecular Systems Biology 2(2006)

 

 

?         Modulation of the transcription regulatory program in yeast cells committed to sporulation.
Friedlander G, Joseph-Strauss D, Carmi M, Zenvirth D, Simchen and Naama Barkai
Genome Biol. 7(3):R20 (2006)

 


 

?         Threshold responses to morphogen gradients by zero-order ultrasensitivity
Gustavo J Melen, Sagi Levy, Naama Barkai and Ben-Zion Shilo
Molecular Systems Biology 13 (2005)

 

 

?         Design of transcription factor binding sites is affected by combinatorial regulation
Yonatan Bilu and Naama Barkai
Genome Biology 6(12) (2005)

 

?         Morphogen gradient formation in a complex environment: an anomalous diffusion model.
Gil Hornung, Brian Berkowitzh and Naama Barkai
Phys. Rev. E 72 014196 (2005) | PDF | Supplement (PDF)

 

?         Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program
Jan Ihmels, Sven Bergmann, Judith Berman and Naama Barkai
PLoS Genetics 1(3) (2005)

 

?         Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage
Jan Ihmels, Sven Bergmann, Maryam Gerami-Nejad, Itai Yanai, Mark McClellan, Judith Berman and Naama Barkai
Science 309(5736):938-940 (2005) | PDF

 

?         The ups and downs of biological timers
Noa Rappaport, Shay Winter and Naama Barkai
Theor Biol Med Model. 2(1):22 (2005)

 

 

?         Evaluating putative mechanisms of the mitotic spindle checkpoint
Andreas Doncic, Eshel Ben-Jacob and Naama Barkai
PNAS 102(18):6332-6337 (2005) | PDF

 

 

?         Computational verification of protein-pretein interactions by orthologous coexpresssion
Itay Tirosh and Naama Barkai
BMC Bioinformatics 6(1):40 (2005) | PDF

 

 

?         Interpreting clone-mediated perturbations of morphogen profiles
Avigdor Eldar and Naama Barkai
Dev Biol. 278(1):203-7 (2005) | PDF

 


 

?         Elucidating mechanisms underlying robustness of morphogen gradients
Avigdor Eldar, Ben-Zion Shilo and Naama Barkai
Curr Opin Genet Dev 14(4):435-9 (2004) | PDF