Published in Nucleic Acids Res on September 21, 2010
H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell (2014) 1.68
DNA methylation and transcriptional noise. Epigenetics Chromatin (2013) 1.09
The unexpected traits associated with core promoter elements. Transcription (2012) 0.95
Determinants of expression variability. Nucleic Acids Res (2014) 0.89
Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia. Genome Med (2015) 0.89
Synchronization of cell cycle of Saccharomyces cerevisiae by using a cell chip platform. Mol Cells (2011) 0.80
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. BMC Syst Biol (2012) 0.78
Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes. Genome Biol Evol (2013) 0.77
Evidence for a sexual dimorphism in gene expression noise in metazoan species. PeerJ (2015) 0.76
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Genome Biol (2017) 0.75
Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise. PLoS One (2015) 0.75
A model for aryl hydrocarbon receptor-activated gene expression shows potency and efficacy changes and predicts squelching due to competition for transcription co-activators. PLoS One (2015) 0.75
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Stochastic gene expression in a single cell. Science (2002) 34.54
Genetic dissection of transcriptional regulation in budding yeast. Science (2002) 25.01
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell (2005) 14.57
Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet (2005) 14.39
Noise in eukaryotic gene expression. Nature (2003) 13.01
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature (2006) 12.92
Engineering stability in gene networks by autoregulation. Nature (2000) 12.88
Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13
Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci U S A (2001) 12.06
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet (2003) 11.84
Gene regulation at the single-cell level. Science (2005) 11.52
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A (2005) 9.66
Noise in gene expression: origins, consequences, and control. Science (2005) 9.64
Noise propagation in gene networks. Science (2005) 8.19
Noise in protein expression scales with natural protein abundance. Nat Genet (2006) 8.03
Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J (2001) 7.03
Control, exploitation and tolerance of intracellular noise. Nature (2002) 6.81
Revealing modular organization in the yeast transcriptional network. Nat Genet (2002) 6.73
Genetic interactions between polymorphisms that affect gene expression in yeast. Nature (2005) 6.42
Identification and distinct regulation of yeast TATA box-containing genes. Cell (2004) 6.27
Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol (2005) 6.08
Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci U S A (2000) 5.95
Regulated cell-to-cell variation in a cell-fate decision system. Nature (2005) 5.68
Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics (2005) 5.08
Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci U S A (2003) 5.07
Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet (2007) 4.62
Two strategies for gene regulation by promoter nucleosomes. Genome Res (2008) 4.19
Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet (2005) 4.07
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet (2008) 3.84
MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res (2006) 3.68
A genetic signature of interspecies variations in gene expression. Nat Genet (2006) 3.61
Genetic properties influencing the evolvability of gene expression. Science (2007) 3.45
A yeast hybrid provides insight into the evolution of gene expression regulation. Science (2009) 3.25
Gene network shaping of inherent noise spectra. Nature (2006) 3.25
Chromatin decouples promoter threshold from dynamic range. Nature (2008) 3.24
Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet (2007) 2.55
The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53
Population genetic variation in genome-wide gene expression. Mol Biol Evol (2003) 2.28
Coupling and coordination in gene expression processes: a systems biology view. Nat Rev Genet (2008) 1.90
Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol (2008) 1.88
Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet (2009) 1.71
Epigenetic regulation and the variability of gene expression. Nat Genet (2008) 1.67
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet (2007) 1.53
On the relation between promoter divergence and gene expression evolution. Mol Syst Biol (2008) 1.43
Positive selection for elevated gene expression noise in yeast. Mol Syst Biol (2009) 1.30
Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet (2008) 1.28
Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol (2009) 1.20
Graded and binary responses in stochastic gene expression. Phys Biol (2004) 1.19
Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. Proc Natl Acad Sci U S A (2010) 1.08
Phenotypic variability of growing cellular populations. Proc Natl Acad Sci U S A (2007) 1.07
Gene selection algorithm by combining reliefF and mRMR. BMC Genomics (2008) 1.00
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol (2011) 2.26
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol (2009) 1.75
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol (2002) 1.59
Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res (2003) 1.48
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res (2008) 1.44
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res (2002) 1.40
Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol (2010) 1.39
Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol (2010) 1.36
Predicting DNA- and RNA-binding proteins from sequences with kernel methods. J Theor Biol (2009) 1.23
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Mol Cell Proteomics (2009) 1.15
The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment. BMC Evol Biol (2008) 1.10
Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. Proc Natl Acad Sci U S A (2010) 1.08
Evolution of an X-linked primate-specific micro RNA cluster. Mol Biol Evol (2009) 1.08
Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol (2009) 1.05
Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PLoS Genet (2012) 1.03
The cellular robustness by genetic redundancy in budding yeast. PLoS Genet (2010) 1.00
Retention of protein complex membership by ancient duplicated gene products in budding yeast. Trends Genet (2007) 0.99
Mapping the functional yeast ABC transporter interactome. Nat Chem Biol (2013) 0.98
DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res (2010) 0.98
MAID : an effect size based model for microarray data integration across laboratories and platforms. BMC Bioinformatics (2008) 0.97
Yeast split-ubiquitin-based cytosolic screening system to detect interactions between transcriptionally active proteins. Biotechniques (2007) 0.96
Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biol (2008) 0.96
Analysis of membrane protein complexes using the split-ubiquitin membrane yeast two-hybrid (MYTH) system. Methods Mol Biol (2009) 0.96
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinformatics (2010) 0.94
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res (2013) 0.93
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Res (2009) 0.92
Evolution of olfactory receptor genes in primates dominated by birth-and-death process. Genome Biol Evol (2009) 0.91
DMEAS: DNA methylation entropy analysis software. Bioinformatics (2013) 0.88
A probabilistic framework to improve microrna target prediction by incorporating proteomics data. J Bioinform Comput Biol (2009) 0.88
Reconstructing genetic networks in yeast. Nat Biotechnol (2003) 0.88
Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Res (2014) 0.88
Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs. BMC Genomics (2012) 0.88
Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects. Nucleic Acids Res (2010) 0.87
The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins (2010) 0.87
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics (2013) 0.87
Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming. BMC Genomics (2014) 0.87
miRNA regulatory variation in human evolution. Trends Genet (2012) 0.86
Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PLoS One (2013) 0.85
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. Nucleic Acids Res (2011) 0.85
A hybrid model for robust detection of transcription factor binding sites. Bioinformatics (2008) 0.84
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PLoS One (2010) 0.81
Revisiting the contribution of cis-elements to expression divergence between duplicated genes: the role of chromatin structure. Mol Biol Evol (2010) 0.81
Global robustness and identifiability of random, scale-free, and small-world networks. Ann N Y Acad Sci (2009) 0.80
Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale. Chem Rev (2007) 0.79
DNA motif elucidation using belief propagation. Nucleic Acids Res (2013) 0.79
Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships. J Proteome Res (2015) 0.78
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations. J Comput Biol (2006) 0.78
Learned random-walk kernels and empirical-map kernels for protein sequence classification. J Comput Biol (2009) 0.78
Genome-wide genotype-based risk model for survival in acute myeloid leukaemia patients with normal karyotype. Br J Haematol (2013) 0.78
Bioinformatic approach to identify chaperone pathway relationship from large-scale interaction networks. Methods Mol Biol (2011) 0.77
Accounting for structural properties and nucleotide co-variations in the quantitative prediction of binding affinities of protein-DNA interactions. Pac Symp Biocomput (2006) 0.77
Investigating the functional implications of reinforcing feedback loops in transcriptional regulatory networks. Mol Biosyst (2014) 0.77
CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks. Ann N Y Acad Sci (2007) 0.77
Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types. Brief Funct Genomics (2016) 0.77
Mitochondrial targets for pharmacological intervention in human disease. J Proteome Res (2014) 0.76
Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments. Ann N Y Acad Sci (2007) 0.76
Alternative signaling pathways: when, where and why? FEBS Lett (2005) 0.76
Characterization and evolutionary analysis of protein-protein interaction networks. Methods Mol Biol (2012) 0.76
Structural genomics: a new era for pharmaceutical research. Genome Biol (2002) 0.75
Interrogating noise in protein sequences from the perspective of protein-protein interactions prediction. J Theor Biol (2012) 0.75
Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective. Bioinformatics (2010) 0.75
Erratum: Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun (2015) 0.75
Filtering and interpreting large-scale experimental protein-protein interaction data. Methods Mol Biol (2011) 0.75