Barkai Lab
Publications
Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences
Michal Chappleboim, Segev Naveh-Tassa, Miri Carmi, Yaakov Levy, Naama Barkai
Nucleic Acid Research (2024) I PDF
Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions
using interwoven sequence grammars
Vladimir Mindel*, Sagie Brodsky*, Aileen Cohen, Wajd Manadre, Felix Jonas, Miri Carmi, and Naama Barkai
Nucleic Acid Research (2023) | PDF
The architecture of binding cooperativity between densely bound transcription factors
Offir Lupo, Divya Krishna Kumar, Rotem Livne, Michal Chappleboim, Idan Levy, and Naama Barkai
Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA–protein binding
Felix Jonas*, Matan Vidavski, Eli Benuck, Naama Barkai^, Gilad Yaakov*^
Nucleic Acid Research (2023) | PDF
Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells
Marko Dunjić*, Felix Jonas*, Gilad Yaakov*, Roye More, Yoav Mayshar, Yoach Rais, Ayelet-Hashahar Orenbuch, Saifeng Cheng, Naama Barkai & Yonatan Stelzer
Nature Communications (2023) | PDF
Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions
Divya Krishna Kumar*, Felix Jonas*, Tamar Jana, Sagie Brodsky, Miri Carmi, Naama Barkai
The molecular grammar of protein disorder guiding genome-binding locations
Felix Jonas*, Miri Carmi*, Beniamin Krupkin*, Joseph Steinberger, Sagie Brodsky, Tamar Jana, Naama Barkai
Nucleic Acid Research (2023) | PDF
Evolution of transcription factor binding through sequence variations and turnover of binding sites
Gat Krieger*, Offir Lupo*, Patricia Wittkopp , Naama Barkai
Genome Research (2022) | PDF
Rtt109 promotes nucleosome replacement ahead of the replication fork
Felix Jonas*, Gilad Yaakov*^, Naama Barkai^
Evolution of binding preferences among whole-genome duplicated transcription factors
Tamar Gera*, Felix Jonas*, Roye More, Naama Barkai
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity
Sagie Brodsky*, Tamar Jana* , Naama Barkai
Current Opinion in Structural Biology (2021) | PDF
Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast
Gilad Yaakov*^, Felix Jonas*, Naama Barkai^
Nature Biotechnology (2021) | PDF
Rtt109 slows replication speed by histone N-terminal acetylation
Nelly Frenkel*, Felix Jonas*, Miri Carmi, Gilad Yaakov, Naama Barkai
Accumulation of cis- and trans-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species
Offir Lupo, Gat Krieger, Felix Jonas, Naama Barkai
G3: Genes, Genomes, Genetics (2021) | PDF
Speed–Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites
Tamar Jana*, Sagie Brodsky*, Naama Barkai
Trends in Genetics (2021) | PDF
Reconstituting tissue patterning
Naama Barkai, Ben-Zion Shilo
Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay
Mira Rosenthal*, Eyal Metzl-Raz*, Jérôme Bürgi, Eden Yifrach, Layla Drwesh , Amir Fadel , Yoav Peleg , Doron Rapaport, Matthias Wilmanns, Naama Barkai, Maya Schuldiner, and Einat Zalckvar
Gene Transcription as a Limiting Factor in Protein Production and Cell Growth
Eyal Metzl-Raz*, Moshe Kafri*, Gilad Yaakov* and Naama Barkai
Independent evolution of transcript abundance and gene regulatory dynamics
Gat Krieger, Offir Lupo, Avraham A. Levy and Naama Barkai
Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity
Sagie Brodsky*, Tamar Jana*, Karin Mittelman, Michal Chapal, Divya Krishna Kumar, Miri Carmi, Naama Barkai
Molecular Cell (2020) | PDF | Supplemental note
Spotlight (Trends in Genetics 2020)
Transcription Factor Binding to Replicated DNA
Raz Bar-Ziv*, Sagie Brodsky*, Michal Chapal and Naama Barkai
Global shape of Toll activation is determined by wntD enhancer properties
Neta Rahimi, Shari Carmon, Inna Averbukh, Farzaneh Khajouei, Saurabh Sinha, Eyal D. Schejter, Naama Barkai, and Ben-Zion Shilo
Resolving noise–control conflict by gene duplication
Michal Chapal, Sefi Mintzer, Sagie Brodsky, Miri Carmi, Naama Barkai
Primer by Johan Hallin and Christian R. Landry | PDF
Dynamics of Spaetzle morphogen shuttling in the Drosophila embryo shapes gastrulation patterning
Neta Rahimi, Inna Averbukh, Shari Carmon, Eyal D. Schejter, Naama Barkai, Ben-Zion Shilo
Dynamic lineage priming is driven via direct enhancer regulation by ERK
William B. Hamilton, Yaron Mosesson, Rita S. Monteiro, Kristina B. Emdal, Teresa E. Knudsen, Chiara Francavilla, Naama Barkai, Jesper V. Olsen & Joshua M. Brickman
A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle
Lotte Teufel, Katja Tummler, Max Flöttmann, Andreas Herrmann, Naama Barkai & Edda Klipp
A Visual Framework for Classifying Determinants of Cell Size
Felix Jonas, Ilya Soifer, Naama Barkai
A repressor-decay timer for robust temporal patterning in embryonic Drosophila neuroblast lineages
Inna Averbukh, Sen-Lin Lai, Chris Q Doe , Naama Barkai
eLIFE (2018) | PDF
Epigenetic Control of Expression Homeostasis during Replication Is Stabilized by the Replication Checkpoint
Yoav Voichek*, Karin Mittelman*, Yulia Gordon, Raz Bar-Ziv, David Lifshitz Smit, Rom Shenhav, Naama Barkai
Molecular Cell (2018) | PDF
Molecular Cell Preview | PDF
Dual role of starvation signaling in promoting growth and recovery
Yonat Gurvich, Dena Leshkowitz, Naama Barkai
PLOS Biology (2017) | PDF
Hybrid vigor: The best of both parents, or a genomic clash?
Dana Bar-Zvi, Offir Lupo, Avraham A. Levy, Naama Barkai
Current Opinion in Systems Biology (2017) | PDF
Principles of cellular resource allocation revealed by condition-dependent proteome profiling
Eyal Metzl-Raz*, Moshe Kafri*, Gilad Yaakov*, Ilya Soifer, Yonat Gurvich, Naama Barkai
eLife (2017) | PDF
Selected for Cell Systems Call Principles of Systems Biology, No. 21 | PDF
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) | PDF
Lighting Up ERK Activity
Benny Shilo & Naama Barkai
Developmental Cell (2017) | PDF
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
Beáta Tóth, 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
Expression homeostasis during DNA replication
Yoav Voichek*, Raz Bar-Ziv* and Naama Barkai
Science (2016) | PDF
F1000Prime recommended
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
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)
Developmental biology: Segmentation within scale
Naama Barkai & Ben-Zion Shilo
Nature (2013)
Linking the signaling cascades and dynamic regulatory networks controlling stress responses
Anthony Gitter, Miri Carmi, Naama Barkai, Bar-Joseph Ziv
Genome Research (2013)
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 Barkai
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)
The Era of Developmental Systems Biology
Norbert Perrimon and Naama Barkai
Curr Opp in Genetics and Development. (2011)
Scaling of morphogen gradients
Danny Ben-Zvi, Ben-Zion Shilo and Naama Barkai
Curr Opp in Genetics and Development. (2011)
Improved readout precision of the Bicoid morphogen gradient by early decoding
Zvi Tamari and Naama Barkai
Journal of Biological Physics. (2011)
Disentangling signaling gradients generated by equivalent sources
Noa Rappaport and Naama Barkai
Journal of Biological Physics. (2011)
Inferring regulatory mechanisms from patterns of evolutionary divergence
Itay Tirosh and Naama Barkai
Molecular Systems Biology. (2011)
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)
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)
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
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).
M. B. Zao, Leading edge: developmental biology select, Cell, Aug 8, 134(3); 372-3 (2008).
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)
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
Robustness of the BMP morphogen gradient in Drosophila embryonic patterning
Avigdor Eldar, Ruslan Dorfman, Daniel Weiss, Hilary Ashe, Ben-Zion Shilo & Naama Barkai