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List of works by Naama Barkai

'Big frog, small frog'--maintaining proportions in embryonic development: delivered on 2 July 2008 at the 33rd FEBS Congress in Athens, Greece.

scientific article published in March 2009

A Visual Framework for Classifying Determinants of Cell Size

A WntD-Dependent Integral Feedback Loop Attenuates Variability in Drosophila Toll Signaling

scientific article published in February 2016

A biological solution to a fundamental distributed computing problem

scientific article published in January 2011

A genetic signature of interspecies variations in gene expression

scientific article published on 18 June 2006

A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress

scientific article published on 27 September 2021

A repressor-decay timer for robust temporal patterning in embryonic neuroblast lineages

scientific article published on 10 December 2018

A role for Rtt109 in buffering gene-dosage imbalance during DNA replication.

scientific article

A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle

scientific article published on 04 March 2019

A two-step patterning process increases the robustness of periodic patterning in the fly eye

scientific article

A yeast hybrid provides insight into the evolution of gene expression regulation.

scientific article published in May 2009

Accumulation of <i>cis</i>- and <i>trans</i>-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species

scientific article published on 28 January 2021

Autocorrelation analysis reveals widespread spatial biases in microarray experiments

scientific article

Budding yeast escape commitment to the phosphate starvation program using gene expression noise

scientific article published on 3 October 2013

Buffering Global Variability of Morphogen Gradients

scientific article published on March 2017

Checkpoint-independent scaling of the Saccharomyces cerevisiae DNA replication program

scientific article

Chromatin dynamics during DNA replication

scientific article

Chromatin regulators as capacitors of interspecies variations in gene expression

scientific article

Common and divergent roles for members of the mouse DCX superfamily

scientific article published in May 2006

Comparative analysis indicates regulatory neofunctionalization of yeast duplicates

scientific article published in January 2007

Comparative biology: beyond sequence analysis

scientific article published on 10 August 2007

Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program

scientific article

Computational verification of protein-protein interactions by orthologous co-expression

scientific article

Conservation of Expression and Sequence of Metabolic Genes is Reflected by Activity Across Metabolic States

scientific article published on 06 July 2006

Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states

scientific article

Coordination of gene expression and growth-rate in natural populations of budding yeast

scientific article

Coordination of gene expression with growth rate: a feedback or a feed-forward strategy?

scientific article published on December 2009

Correction: Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase.

scientific article published on 28 April 2011

Correction: Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase.

scientific article

Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress.

scientific article

Creating gradients by morphogen shuttling.

scientific article published on 29 January 2013

DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis.

scientific article published on 17 September 2015

Dealing with Gene-Dosage Imbalance during S Phase.

scientific article

Defining transcription modules using large-scale gene expression data

scientific article

Developmental biology: Segmentation within scale

scientific article published on 19 December 2012

Disentangling signaling gradients generated by equivalent sources

scientific article published on 14 September 2011

Divergence and selectivity of expression-coupled histone modifications in budding yeasts

scientific article

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

scientific article

Dual role of starvation signaling in promoting growth and recovery

scientific article published on 13 December 2017

Dynamic lineage priming is driven via direct enhancer regulation by ERK

scientific article published on 06 November 2019

Dynamics of Spaetzle morphogen shuttling in the Drosophila embryo shapes gastrulation patterning

scientific article published on 12 November 2019

EGF receptor signaling - a quantitative view

scientific article published in December 2007

Early commitment and robust differentiation in colonic crypts ⬇️

scientific article published on 03 January 2017

Efficiency and specificity in microRNA biogenesis ⬇️

scientific article published on May 13, 2012

Elucidating mechanisms underlying robustness of morphogen gradients

scientific article published in August 2004

Epigenetic Control of Expression Homeostasis during Replication Is Stabilized by the Replication Checkpoint

scientific article published on 14 June 2018

Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase

scientific article

Error minimization in lateral inhibition circuits

scientific article published on 6 July 2010

Evaluating putative mechanisms of the mitotic spindle checkpoint

scientific article

Evolution of gene sequence and gene expression are not correlated in yeast.

scientific article

Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns

scientific article

Expansion-Repression Mechanism for Scaling the Dpp Activation Gradient in Drosophila Wing Imaginal Discs ⬇️

scientific article published on August 11, 2011

Expression homeostasis during DNA replication.

scientific article

Expression noise and acetylation profiles distinguish HDAC functions

scientific article

Extensive divergence of yeast stress responses through transitions between induced and constitutive activation ⬇️

scientific article published on September 19, 2011

Gene Transcription as a Limiting Factor in Protein Production and Cell Growth

scientific article published on 21 July 2020

Global shape of Toll activation is determined by wntD enhancer properties

scientific article published on 03 January 2020

Heterosis as a consequence of regulatory incompatibility

scientific article

Improved readout precision of the Bicoid morphogen gradient by early decoding

scientific article published on 3 December 2011

Increasing population growth by asymmetric segregation of a limiting resource during cell division

scientific article

Independent evolution of transcript abundance and gene regulatory dynamics

scientific article published on 22 July 2020

Inferring regulatory mechanisms from patterns of evolutionary divergence ⬇️

scientific article published on September 13, 2011

Interpreting clone-mediated perturbations of morphogen profiles.

scientific article

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

scientific article published on 11 June 2020

Iterative signature algorithm for the analysis of large-scale gene expression data

scientific article

Lighting Up ERK Activity

scientific article published in January 2017

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

scientific article published on 11 October 2012

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

scientific article published on 23 December 2014

MRC1-dependent scaling of the budding yeast DNA replication timing program

scientific article

Mechanisms of noise-resistance in genetic oscillators

scientific article

Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells

scientific article published on 27 December 2016

Modeling pattern formation: counting to two in the Drosophila egg.

scientific article

Modulation of the transcription regulatory program in yeast cells committed to sporulation

scientific article

Morphogen gradient formation in a complex environment: an anomalous diffusion model

scientific article published on 17 October 2005

Natural Diversity in Pentose Fermentation Is Explained by Variations in Histone Deacetylases

scientific article

Noise in protein expression scales with natural protein abundance

scientific article

Noise propagation and signaling sensitivity in biological networks: A role for positive feedback

scientific article published on 05 December 2007

Noise propagation and signaling sensitivity in biological networks: a role for positive feedback

scientific article

Noise resistance in the spindle assembly checkpoint

scientific article published on 16 May 2006

Noise-mean relationship in mutated promoters

scientific article

Nucleosome Organization Affects the Sensitivity of Gene Expression to Promoter Mutations ⬇️

scientific article published on March 29, 2012

On the relation between promoter divergence and gene expression evolution

scientific article published on 15 January 2008

Periodic patterning of the Drosophila eye is stabilized by the diffusible activator Scabrous.

scientific article published on 15 February 2016

Physical aspects of precision in genetic regulation

scientific article

Pre-steady-state decoding of the Bicoid morphogen gradient

scientific article

Principles of cellular resource allocation revealed by condition-dependent proteome profiling.

scientific article published on 31 August 2017

Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae

scientific article published on 30 November 2003

Promoter Nucleosome Organization Shapes the Evolution of Gene Expression ⬇️

scientific article published on March 15, 2012

Promoter architecture and the evolvability of gene expression

scientific article published on 14 December 2009

Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source

scientific article

Re-examining the stability of the Bicoid morphogen gradient

scientific article published in January 2008

Reconstituting tissue patterning

scientific article published on 01 October 2020

Resolving noise-control conflict by gene duplication

scientific article published on 22 November 2019

Rethinking cell growth models.

scientific article

Revealing modular organization in the yeast transcriptional network

scientific article published on 22 July 2002

Reverse engineering of the spindle assembly checkpoint

scientific article

Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage

scientific article published in Science

Robust generation and decoding of morphogen gradients

scientific article

Robust selection of sensory organ precursors by the Notch–Delta pathway ⬇️

scientific article published on September 29, 2011

Robustness of the BMP morphogen gradient in Drosophila embryonic patterning

scientific article published in September 2002

Saccharomyces cerevisiae Spore Germination

Scaling morphogen gradients during tissue growth by a cell division rule.

scientific article published in May 2014

Scaling of dorsal-ventral patterning in the Xenopus laevis embryo.

scientific article published on 9 December 2013

Scaling of morphogen gradients by an expansion-repression integral feedback control

scientific article

Scaling of morphogen gradients.

scientific article published on 26 August 2011

Scaling of the BMP activation gradient in Xenopus embryos

scientific article published in Nature

Self-enhanced ligand degradation underlies robustness of morphogen gradients.

scientific article

Self-organized shuttling: generating sharp dorsoventral polarity in the early Drosophila embryo.

scientific article published in August 2012

Sequential feedback induction stabilizes the phosphate starvation response in budding yeast.

scientific article published on 30 October 2014

Similarities and differences in genome-wide expression data of six organisms

scientific article

Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites

scientific article published on 05 January 2021

Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks

scientific article

Strategy of transcription regulation in the budding yeast.

scientific article

Systematic identification of cell size regulators in budding yeast

scientific article published on 19 November 2014

The Cost of Protein Production.

scientific article published on 22 December 2015

The Evolutionary Potential of Phenotypic Mutations

scientific article published on 5 August 2015

The Genetic Requirements for Pentose Fermentation in Budding Yeast

scientific article

The competitive advantage of a dual-transporter system

scientific article

The design of transcription-factor binding sites is affected by combinatorial regulation

scientific article published on 2 December 2005

The era of systems developmental biology

scientific article published on 11 November 2011

The evolving doublecortin (DCX) superfamily

scientific article

The pattern and evolution of yeast promoter bendability

scientific article published on 6 April 2007

The ups and downs of biological timers

scientific article

Threshold responses to morphogen gradients by zero-order ultrasensitivity

scientific article

Transcription Factor Binding to Replicated DNA

scientific article published on 01 March 2020

Two strategies for gene regulation by promoter nucleosomes

scientific article published on 30 April 2008

Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay

scientific article published on 17 August 2020

Variability and robustness in biomolecular systems

scientific article published on December 2007

Widespread remodeling of mid-coding sequence nucleosomes by Isw1.

scientific article published on 10 May 2010

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