Published in Cell on May 18, 2007
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (2009) 8.33
Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol (2007) 8.14
Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev (2008) 5.25
Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet (2010) 4.03
Dynamics and memory of heterochromatin in living cells. Cell (2012) 3.75
RNA interference guides histone modification during the S phase of chromosomal replication. Curr Biol (2008) 2.72
A Polycomb-based switch underlying quantitative epigenetic memory. Nature (2011) 2.62
Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell (2014) 2.27
Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol (2012) 2.25
Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell (2009) 2.20
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock. Cell (2012) 2.15
Transcriptional variation in the malaria parasite Plasmodium falciparum. Genome Res (2012) 2.15
Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol (2011) 2.11
Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev (2011) 2.08
Epigenetic instability due to defective replication of structured DNA. Mol Cell (2010) 1.86
Mechanisms for the inheritance of chromatin states. Cell (2011) 1.78
High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin. Mol Cell (2009) 1.65
Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays (2013) 1.45
Spatial, temporal and interindividual epigenetic variation of functionally important DNA methylation patterns. Nucleic Acids Res (2010) 1.39
Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proc Natl Acad Sci U S A (2010) 1.38
Modeling the dynamics of transcriptional gene regulatory networks for animal development. Dev Biol (2008) 1.37
Regeneration, repair and remembering identity: the three Rs of Hox gene expression. Trends Cell Biol (2009) 1.35
Chromatin as a potential carrier of heritable information. Curr Opin Cell Biol (2010) 1.33
Making cellular memories. Cell (2010) 1.30
Epigenetic chromatin silencing: bistability and front propagation. Phys Biol (2007) 1.25
Developmental biology. Pluripotent chromatin state. Science (2009) 1.24
A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comput Biol (2011) 1.18
Ultrasensitive response motifs: basic amplifiers in molecular signalling networks. Open Biol (2013) 1.16
Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at Arabidopsis FLC. Curr Biol (2014) 1.12
The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev (2013) 1.09
Biphasic regulation of Il2 transcription in CD4+ T cells: roles for TNF-alpha receptor signaling and chromatin structure. J Immunol (2008) 1.07
Four-dimensional dynamics of MAPK information processing systems. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Inverse expression states of the BRN2 and MITF transcription factors in melanoma spheres and tumour xenografts regulate the NOTCH pathway. Oncogene (2011) 1.05
Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci U S A (2014) 1.03
Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development (2010) 1.02
Gene expression in the placenta: maternal stress and epigenetic responses. Int J Dev Biol (2010) 1.02
A dual role of H4K16 acetylation in the establishment of yeast silent chromatin. EMBO J (2011) 1.00
Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity. J Comput Sci Technol (2010) 0.98
A stochastic model of epigenetic dynamics in somatic cell reprogramming. Front Physiol (2012) 0.97
Inheritance of epigenetic chromatin silencing. J Theor Biol (2008) 0.97
Ultrasensitive gene regulation by positive feedback loops in nucleosome modification. Mol Syst Biol (2008) 0.96
Evolutionary conservation of histone modifications in mammals. Mol Biol Evol (2012) 0.93
A view on the role of epigenetics in the biology of malaria parasites. PLoS Pathog (2012) 0.92
Environmental perception and epigenetic memory: mechanistic insight through FLC. Plant J (2015) 0.92
Dissecting chromatin interactions in living cells from protein mobility maps. Chromosome Res (2011) 0.92
Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation. Proc Natl Acad Sci U S A (2014) 0.90
Corepressor protein CDYL functions as a molecular bridge between polycomb repressor complex 2 and repressive chromatin mark trimethylated histone lysine 27. J Biol Chem (2011) 0.89
Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol (2014) 0.88
Time scales in epigenetic dynamics and phenotypic heterogeneity of embryonic stem cells. PLoS Comput Biol (2013) 0.88
Vernalizing cold is registered digitally at FLC. Proc Natl Acad Sci U S A (2015) 0.88
Systems analysis of high-throughput data. Adv Exp Med Biol (2014) 0.87
A simple histone code opens many paths to epigenetics. PLoS Comput Biol (2012) 0.86
Epigenetic feedback regulation accelerates adaptation and evolution. PLoS One (2013) 0.85
Propagation of histone marks and epigenetic memory during normal and interrupted DNA replication. Cell Mol Life Sci (2011) 0.85
Understanding epigenetic changes in aging stem cells--a computational model approach. Aging Cell (2014) 0.84
Computational Epigenetics: the new scientific paradigm. Bioinformation (2010) 0.84
Dynamics of inherently bounded histone modification domains. Proc Natl Acad Sci U S A (2012) 0.83
Oncometabolic Nuclear Reprogramming of Cancer Stemness. Stem Cell Reports (2016) 0.83
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states. Nucleic Acids Res (2013) 0.83
Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes. Nucleic Acids Res (2013) 0.82
Genome-wide analysis of abnormal H3K9 acetylation in cloned mice. PLoS One (2008) 0.82
Interplay of microRNA and epigenetic regulation in the human regulatory network. Front Genet (2014) 0.82
Kinetic memory based on the enzyme-limited competition. PLoS Comput Biol (2014) 0.81
A global genome segmentation method for exploration of epigenetic patterns. PLoS One (2012) 0.80
Perspectives: using polymer modeling to understand the formation and function of nuclear compartments. Chromosome Res (2017) 0.79
The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state. PLoS Comput Biol (2013) 0.79
Nanog, Oct4 and Tet1 interplay in establishing pluripotency. Sci Rep (2016) 0.79
Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. Crit Rev Biomed Eng (2015) 0.79
Epigenetic control: slow and global, nimble and local. Genes Dev (2008) 0.78
Transcriptional interaction-assisted identification of dynamic nucleosome positioning. BMC Bioinformatics (2009) 0.78
A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types. PLoS One (2013) 0.77
Coupled positive and negative feedbacks produce diverse gene expression patterns in colonies. MBio (2015) 0.77
Morphisms of reaction networks that couple structure to function. BMC Syst Biol (2014) 0.77
Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming. Sci Rep (2015) 0.77
Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation. PLoS Comput Biol (2015) 0.77
Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3. Epigenetics Chromatin (2016) 0.77
Modeling the dynamics of bivalent histone modifications. PLoS One (2013) 0.76
Generalized nucleation and looping model for epigenetic memory of histone modifications. Proc Natl Acad Sci U S A (2016) 0.76
Noise Reduction in Complex Biological Switches. Sci Rep (2016) 0.76
Analysis of the Hox epigenetic code. World J Clin Oncol (2012) 0.76
Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design. Proc Natl Acad Sci U S A (2016) 0.76
Nucleation and spreading of a heterochromatic domain in fission yeast. Nat Commun (2016) 0.76
Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics. Nucleic Acids Res (2015) 0.75
Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny. Exp Hematol (2013) 0.75
Biological signal processing with a genetic toggle switch. PLoS One (2013) 0.75
Breaking an epigenetic chromatin switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing. PLoS One (2014) 0.75
Slow Chromatin Dynamics Allow Polycomb Target Genes to Filter Fluctuations in Transcription Factor Activity. Cell Syst (2017) 0.75
Reconciling randomness and precision. Nat Rev Mol Cell Biol (2015) 0.75
Cooperative stabilization of the SIR complex provides robust epigenetic memory in a model of SIR silencing in Saccharomyces cerevisiae. Epigenetics (2015) 0.75
Mechanistic stochastic model of histone modification pattern formation. Epigenetics Chromatin (2014) 0.75
Efficient Switches in Biology and Computer Science. PLoS Comput Biol (2017) 0.75
Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC. Proc Natl Acad Sci U S A (2016) 0.75
Stochasticity in the Genotype-Phenotype Map: Implications for the Robustness and Persistence of Bet-Hedging. Genetics (2016) 0.75
Information recovery in molecular biology: causal modelling of regulated promoter switching experiments. J Math Biol (2012) 0.75
Specificity and stability in topology of protein networks. Science (2002) 21.07
Modularity and extreme edges of the internet. Phys Rev Lett (2003) 3.34
Stability puzzles in phage lambda. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.25
Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol Cell Biol (2005) 1.98
Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Mol Cell Biol (2002) 1.84
Hierarchy measures in complex networks. Phys Rev Lett (2004) 1.76
Minimal model of spiky oscillations in NF-kappaB signaling. Proc Natl Acad Sci U S A (2006) 1.68
Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci U S A (2009) 1.60
Upstream plasticity and downstream robustness in evolution of molecular networks. BMC Evol Biol (2004) 1.36
Positioning and elongation of the fission yeast spindle by microtubule-based pushing. Curr Biol (2004) 1.36
Efficient degradation and expression prioritization with small RNAs. Phys Biol (2007) 1.33
Single-cell analysis of lambda immunity regulation. J Mol Biol (2003) 1.28
Role of the fission yeast SUMO E3 ligase Pli1p in centromere and telomere maintenance. EMBO J (2004) 1.25
Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucleic Acids Res (2006) 1.25
Signal integration in the galactose network of Escherichia coli. Mol Microbiol (2007) 1.25
Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1. Nucleic Acids Res (2006) 1.23
Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. J Mol Biol (2008) 1.15
Coexistence of phage and bacteria on the boundary of self-organized refuges. Proc Natl Acad Sci U S A (2012) 1.14
Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A (2007) 1.11
Computational architecture of the yeast regulatory network. Phys Biol (2005) 1.10
Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res (2012) 1.06
Protein interaction networks beyond artifacts. FEBS Lett (2002) 1.04
Why do phage play dice? J Virol (2009) 1.03
Localization of denaturation bubbles in random DNA sequences. Proc Natl Acad Sci U S A (2003) 1.01
Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus. MBio (2012) 0.99
The generation of promoter-mediated transcriptional noise in bacteria. PLoS Comput Biol (2008) 0.99
Targeted bacterial immunity buffers phage diversity. J Virol (2011) 0.98
Ultrasensitive gene regulation by positive feedback loops in nucleosome modification. Mol Syst Biol (2008) 0.96
Sustainability of virulence in a phage-bacterial ecosystem. J Virol (2010) 0.95
Sensitivity of OR in phage lambda. Biophys J (2004) 0.95
DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch. Proc Natl Acad Sci U S A (2013) 0.95
Modelling transcriptional interference and DNA looping in gene regulation. J Mol Biol (2007) 0.93
Structure and function of negative feedback loops at the interface of genetic and metabolic networks. Nucleic Acids Res (2006) 0.93
Quorum sensing regulation in Aeromonas hydrophila. J Mol Biol (2010) 0.92
Theory for the stability and regulation of epigenetic landscapes. Phys Biol (2010) 0.92
Modeling the two-hybrid detector: experimental bias on protein interaction networks. Biophys J (2007) 0.92
Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res (2011) 0.91
Dominant negative autoregulation limits steady-state repression levels in gene networks. J Bacteriol (2009) 0.91
Functional alignment of regulatory networks: a study of temperate phages. PLoS Comput Biol (2005) 0.91
Relation of intracellular signal levels and promoter activities in the gal regulon of Escherichia coli. J Mol Biol (2009) 0.90
UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model. PLoS Comput Biol (2007) 0.89
The fission yeast ubiquitin-conjugating enzymes UbcP3, Ubc15, and Rhp6 affect transcriptional silencing of the mating-type region. Eukaryot Cell (2002) 0.89
Network models of phage-bacteria coevolution. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.88
Labyrinthine clustering in a spatial rock-paper-scissors ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.88
Competition between diffusion and fragmentation: an important evolutionary process of nature. Phys Rev Lett (2003) 0.88
Ecosystems with mutually exclusive interactions self-organize to a state of high diversity. Phys Rev Lett (2011) 0.87
Variability-based sequence alignment identifies residues responsible for functional differences in alpha and beta tubulin. Protein Sci (2004) 0.86
The functional half-life of an mRNA depends on the ribosome spacing in an early coding region. J Mol Biol (2011) 0.86
Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states. J Mol Biol (2011) 0.84
Modeling of the genetic switch of bacteriophage TP901-1: A heteromer of CI and MOR ensures robust bistability. J Mol Biol (2009) 0.84
Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. Biophys J (2008) 0.83
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states. Nucleic Acids Res (2013) 0.83
A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res (2004) 0.83
Quantifying the benefits of translation regulation in the unfolded protein response. Phys Biol (2004) 0.82
Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes. Nucleic Acids Res (2013) 0.82
Degree landscapes in scale-free networks. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.82
Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy. PLoS Comput Biol (2013) 0.81
Concerted action of the ubiquitin-fusion degradation protein 1 (Ufd1) and Sumo-targeted ubiquitin ligases (STUbLs) in the DNA-damage response. PLoS One (2013) 0.81
Detection of topological patterns in protein networks. Genet Eng (N Y) (2004) 0.81
Minimal gene regulatory circuits for a lysis-lysogeny choice in the presence of noise. PLoS One (2010) 0.81
Clonal selection prevents tragedy of the commons when neighbors compete in a rock-paper-scissors game. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.81
Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One (2009) 0.80
H3K9me-independent gene silencing in fission yeast heterochromatin by Clr5 and histone deacetylases. PLoS Genet (2011) 0.80
Spreading out of perturbations in reversible reaction networks. New J Phys (2007) 0.80
Longevity of orders is related to the longevity of their constituent genera rather than genus richness. Theory Biosci (2008) 0.80
Spreading of multiple epidemics with cross immunization. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.80
Subnuclear relocalization and silencing of a chromosomal region by an ectopic ribosomal DNA repeat. Proc Natl Acad Sci U S A (2013) 0.79
Two portable recombination enhancers direct donor choice in fission yeast heterochromatin. PLoS Genet (2013) 0.79
Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.79
Emergence of diversity in a model ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.78
Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression. Nucleic Acids Res (2012) 0.77
Information spreading and development of cultural centers. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.77
Genetic regulatory networks that count to 3. J Theor Biol (2013) 0.76
Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas. Phys Biol (2016) 0.76
New romance between RNA degradation pathways: Mmi1 and RNAi meet on heterochromatic islands. EMBO J (2012) 0.76
Protein localization with flexible DNA or RNA. PLoS One (2012) 0.75
Key players in the genetic switch of bacteriophage TP901-1. Biophys J (2011) 0.75
Competing to destroy: a fight between two RNA-degradation systems. Nat Struct Mol Biol (2008) 0.75
One hub-one process: a tool based view on regulatory network topology. BMC Syst Biol (2008) 0.75
Modeling dynamics of information networks. Phys Rev Lett (2003) 0.75
Quality control system response to stochastic growth of amyloid fibrils. FEBS Lett (2013) 0.75
Locally self-organized quasicritical percolation in a multiple-disease model. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75
Dynamics of the recovery from sRNA-mediated gene silencing. Cell Cycle (2009) 0.75
Organizational structure and communication networks in a university environment. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75
Visualization of large-scale correlations in gene expressions. Funct Integr Genomics (2004) 0.75