Published in Mol Syst Biol on January 15, 2008
Nucleosome positioning: how is it established, and why does it matter? Dev Biol (2009) 2.68
From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet (2009) 2.54
The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Res (2014) 1.52
Promoter architecture and the evolvability of gene expression. J Biol (2009) 1.47
Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol Syst Biol (2010) 1.44
Coupled evolution of transcription and mRNA degradation. PLoS Biol (2011) 1.40
Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics (2010) 1.18
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet (2013) 1.17
Chromatin regulators as capacitors of interspecies variations in gene expression. Mol Syst Biol (2010) 1.14
Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biol Evol (2010) 1.06
The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One (2011) 1.06
Contrasting genetic paths to morphological and physiological evolution. Proc Natl Acad Sci U S A (2010) 1.05
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. Genome Biol (2008) 1.02
From elements to modules: regulatory evolution in Ascomycota fungi. Curr Opin Genet Dev (2009) 1.02
Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol Cell Biol (2011) 1.01
Intersecting transcription networks constrain gene regulatory evolution. Nature (2015) 0.92
A comprehensive analysis of gene expression evolution between humans and mice. Evol Bioinform Online (2009) 0.92
Gene expression variations are predictive for stochastic noise. Nucleic Acids Res (2010) 0.89
Positive selection at high temperature reduces gene transcription in the bacteriophage ϕX174. BMC Evol Biol (2010) 0.87
Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects. Nucleic Acids Res (2010) 0.87
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Res (2009) 0.85
Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes. PLoS Genet (2014) 0.85
Integrated genome-scale prediction of detrimental mutations in transcription networks. PLoS Genet (2011) 0.84
Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast. BMC Evol Biol (2011) 0.84
Comparative gene expression between two yeast species. BMC Genomics (2013) 0.82
Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis. Genome Biol (2008) 0.82
Biophysical fitness landscapes for transcription factor binding sites. PLoS Comput Biol (2014) 0.81
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS One (2008) 0.81
A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome Biol (2014) 0.80
Nucleosome-coupled expression differences in closely-related species. BMC Genomics (2011) 0.80
Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework. PLoS Comput Biol (2014) 0.80
Combinatorial Cis-regulation in Saccharomyces Species. G3 (Bethesda) (2016) 0.79
The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins. PLoS One (2011) 0.78
Gene expression divergence is coupled to evolution of DNA structure in coding regions. PLoS Comput Biol (2011) 0.77
Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters. Genome Res (2014) 0.77
Population-genetic analysis of HvABCG31 promoter sequence in wild barley (Hordeum vulgare ssp. spontaneum). BMC Evol Biol (2012) 0.75
Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus. Genome Biol Evol (2015) 0.75
Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression. Mol Biol Evol (2016) 0.75
The relationship between gene isoform multiplicity, number of exons and protein divergence. PLoS One (2013) 0.75
Construction and evaluation of yeast expression networks by database-guided predictions. Microb Cell (2016) 0.75
Regulatory versus coding signatures of natural selection in a candidate gene involved in the adaptive divergence of whitefish species pairs (Coregonus spp.). Ecol Evol (2012) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
The role of chromatin during transcription. Cell (2007) 26.48
A genomic code for nucleosome positioning. Nature (2006) 15.38
Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science (2000) 13.20
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
The evolutionary significance of cis-regulatory mutations. Nat Rev Genet (2007) 9.35
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92
The rapid evolution of reproductive proteins. Nat Rev Genet (2002) 6.88
Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet (2003) 6.60
Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol (2002) 6.44
Nucleosome positions predicted through comparative genomics. Nat Genet (2006) 5.81
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science (2005) 5.68
Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science (2003) 5.67
Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development (1998) 4.36
Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature (2006) 4.26
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell (2003) 4.12
An integrated view of protein evolution. Nat Rev Genet (2006) 3.86
Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol (2005) 3.62
A genetic signature of interspecies variations in gene expression. Nat Genet (2006) 3.61
Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science (2006) 3.59
Genetic properties influencing the evolvability of gene expression. Science (2007) 3.45
Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A (2005) 3.04
Rapid assessment of S. cerevisiae mating type by PCR. Trends Genet (1990) 2.75
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
A walk-through of the yeast mating pheromone response pathway. Peptides (2005) 2.47
Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A (2004) 2.09
Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol (2007) 2.04
Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol Biol Evol (2007) 1.81
Using DNA microarrays to study gene expression in closely related species. Bioinformatics (2007) 1.50
Functional tests of enhancer conservation between distantly related species. Development (2003) 1.46
Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development (2003) 1.43
How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet (2004) 1.38
Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development (2005) 1.37
A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res (2006) 1.17
Evolutionary alterations of the minimal promoter for notochord-specific Brachyury expression in ascidian embryos. Development (1999) 1.12
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol (2007) 1.08
Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence. Genome Biol (2006) 0.83
Noise in protein expression scales with natural protein abundance. Nat Genet (2006) 8.03
Revealing modular organization in the yeast transcriptional network. Nat Genet (2002) 6.73
Similarities and differences in genome-wide expression data of six organisms. PLoS Biol (2003) 4.75
Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature (2002) 4.21
Two strategies for gene regulation by promoter nucleosomes. Genome Res (2008) 4.19
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol (2003) 4.06
Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci U S A (2002) 3.78
A genetic signature of interspecies variations in gene expression. Nat Genet (2006) 3.61
Defining transcription modules using large-scale gene expression data. Bioinformatics (2004) 3.33
A yeast hybrid provides insight into the evolution of gene expression regulation. Science (2009) 3.25
Rewiring of the yeast transcriptional network through the evolution of motif usage. Science (2005) 3.10
Pre-steady-state decoding of the Bicoid morphogen gradient. PLoS Biol (2007) 2.81
Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 2.51
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol (2012) 2.49
Self-enhanced ligand degradation underlies robustness of morphogen gradients. Dev Cell (2003) 2.40
Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet (2005) 2.36
Scaling of the BMP activation gradient in Xenopus embryos. Nature (2008) 2.31
Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol (2007) 1.94
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet (2012) 1.89
Expansion-repression mechanism for scaling the Dpp activation gradient in Drosophila wing imaginal discs. Curr Biol (2011) 1.79
A biological solution to a fundamental distributed computing problem. Science (2011) 1.62
Threshold responses to morphogen gradients by zero-order ultrasensitivity. Mol Syst Biol (2005) 1.59
Promoter architecture and the evolvability of gene expression. J Biol (2009) 1.47
Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol Syst Biol (2010) 1.44
The pattern and evolution of yeast promoter bendability. Trends Genet (2007) 1.37
Elucidating mechanisms underlying robustness of morphogen gradients. Curr Opin Genet Dev (2004) 1.36
Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol (2007) 1.36
Strategy of transcription regulation in the budding yeast. PLoS One (2007) 1.30
The evolving doublecortin (DCX) superfamily. BMC Genomics (2006) 1.29
Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase. PLoS Genet (2010) 1.29
Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet (2008) 1.28
Modulation of the transcription regulatory program in yeast cells committed to sporulation. Genome Biol (2006) 1.26
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
Comparative biology: beyond sequence analysis. Curr Opin Biotechnol (2007) 1.24
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res (2011) 1.19
Scaling of morphogen gradients by an expansion-repression integral feedback control. Proc Natl Acad Sci U S A (2010) 1.19
Noise-mean relationship in mutated promoters. Genome Res (2012) 1.18
Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci U S A (2013) 1.18
Widespread remodeling of mid-coding sequence nucleosomes by Isw1. Genome Biol (2010) 1.18
The design of transcription-factor binding sites is affected by combinatorial regulation. Genome Biol (2005) 1.18
MRC1-dependent scaling of the budding yeast DNA replication timing program. Genome Res (2010) 1.18
Expression noise and acetylation profiles distinguish HDAC functions. Mol Cell (2012) 1.17
Chromatin regulators as capacitors of interspecies variations in gene expression. Mol Syst Biol (2010) 1.14
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res (2012) 1.14
Common and divergent roles for members of the mouse DCX superfamily. Cell Cycle (2006) 1.13
Evaluating putative mechanisms of the mitotic spindle checkpoint. Proc Natl Acad Sci U S A (2005) 1.12
Re-examining the stability of the Bicoid morphogen gradient. Cell (2008) 1.10
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Res (2013) 1.08
Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks. Genome Biol (2007) 1.07
The competitive advantage of a dual-transporter system. Science (2011) 1.06
Morphogen gradient formation in a complex environment: an anomalous diffusion model. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.02
Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol Cell Biol (2011) 1.01
Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput Biol (2006) 1.00
Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J Biol Chem (2007) 0.99
Coordination of gene expression with growth rate: a feedback or a feed-forward strategy? FEBS Lett (2009) 0.98
Error minimization in lateral inhibition circuits. Sci Signal (2010) 0.98
Scaling of morphogen gradients. Curr Opin Genet Dev (2011) 0.96
t-SNARE phosphorylation regulates endocytosis in yeast. Mol Biol Cell (2002) 0.96
Noise resistance in the spindle assembly checkpoint. Mol Syst Biol (2006) 0.96
Self-organized shuttling: generating sharp dorsoventral polarity in the early Drosophila embryo. Cell (2012) 0.94
Computational verification of protein-protein interactions by orthologous co-expression. BMC Bioinformatics (2005) 0.94
miR-142 orchestrates a network of actin cytoskeleton regulators during megakaryopoiesis. Elife (2014) 0.94
Extensive divergence of yeast stress responses through transitions between induced and constitutive activation. Proc Natl Acad Sci U S A (2011) 0.93
Budding yeast escape commitment to the phosphate starvation program using gene expression noise. Curr Biol (2013) 0.90
Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol (2013) 0.90
Autocorrelation analysis reveals widespread spatial biases in microarray experiments. BMC Genomics (2007) 0.86
Creating gradients by morphogen shuttling. Trends Genet (2013) 0.86
Mso1 is a novel component of the yeast exocytic SNARE complex. J Biol Chem (2005) 0.86
Efficiency and specificity in microRNA biogenesis. Nat Struct Mol Biol (2012) 0.85
Scaling morphogen gradients during tissue growth by a cell division rule. Development (2014) 0.85
Inferring regulatory mechanisms from patterns of evolutionary divergence. Mol Syst Biol (2011) 0.85
Robust selection of sensory organ precursors by the Notch-Delta pathway. Curr Opin Cell Biol (2011) 0.84
YOS9, the putative yeast homolog of a gene amplified in osteosarcomas, is involved in the endoplasmic reticulum (ER)-Golgi transport of GPI-anchored proteins. J Biol Chem (2002) 0.84
Disentangling signaling gradients generated by equivalent sources. J Biol Phys (2011) 0.83
Nucleosome organization affects the sensitivity of gene expression to promoter mutations. Mol Cell (2012) 0.82
Interpreting clone-mediated perturbations of morphogen profiles. Dev Biol (2005) 0.82
Increasing population growth by asymmetric segregation of a limiting resource during cell division. Mol Syst Biol (2013) 0.81
Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site. Genome Res (2015) 0.80
Chromatin mediation of a transcriptional memory effect in yeast. G3 (Bethesda) (2015) 0.80
Reverse engineering of the spindle assembly checkpoint. PLoS One (2009) 0.79
Checkpoint-independent scaling of the Saccharomyces cerevisiae DNA replication program. BMC Biol (2014) 0.78
Improved readout precision of the Bicoid morphogen gradient by early decoding. J Biol Phys (2011) 0.78
Scaling of dorsal-ventral patterning in the Xenopus laevis embryo. Bioessays (2013) 0.78
The ups and downs of biological timers. Theor Biol Med Model (2005) 0.77
The era of systems developmental biology. Curr Opin Genet Dev (2011) 0.77
Physical aspects of precision in genetic regulation. J Biol Phys (2010) 0.77
Promoter nucleosome organization shapes the evolution of gene expression. PLoS Genet (2012) 0.77
EGF receptor signaling - a quantitative view. Curr Biol (2007) 0.76
Developmental biology: Segmentation within scale. Nature (2012) 0.75
Corrigendum: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators. Genome Res (2017) 0.75