Protein localization with flexible DNA or RNA.

PubWeight™: 0.75‹?›

🔗 View Article (PMC 3277508)

Published in PLoS One on February 10, 2012

Authors

Sebastian Bernhardsson1, Namiko Mitarai, Kim Sneppen

Author Affiliations

1: Niels Bohr institute, University of Copenhagen, Copenhagen, Denmark. sebbeb@nbi.dk

Articles cited by this

Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science (2008) 13.79

Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet (2001) 11.70

Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell (2008) 9.76

High mobility of proteins in the mammalian cell nucleus. Nature (2000) 9.39

A practical guide to single-molecule FRET. Nat Methods (2008) 8.62

The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science (2008) 8.45

Facilitated target location in biological systems. J Biol Chem (1989) 7.18

Probing transcription factor dynamics at the single-molecule level in a living cell. Science (2007) 6.85

Protein mobility in the cytoplasm of Escherichia coli. J Bacteriol (1999) 5.94

Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science (1998) 5.77

Protein dynamics: implications for nuclear architecture and gene expression. Science (2001) 4.38

A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell (2006) 3.67

Transcription factories: gene expression in unions? Nat Rev Genet (2009) 2.92

Making contacts on a nucleic acid polymer. Trends Biochem Sci (2001) 2.70

Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci (1995) 2.64

HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Nat Cell Biol (2009) 2.37

Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBF-alpha transcription factors. Proc Natl Acad Sci U S A (1997) 2.06

Tsix silences Xist through modification of chromatin structure. Dev Cell (2005) 1.97

Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation. Genes Dev (2005) 1.92

Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J (2000) 1.89

The DNA binding activity of p53 displays reaction-diffusion kinetics. Biophys J (2006) 1.61

The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb Perspect Biol (2010) 1.43

Identification of nuclear matrix protein alterations associated with human colon cancer. Cancer Res (2002) 1.08

Sp2 localizes to subnuclear foci associated with the nuclear matrix. Mol Biol Cell (2006) 0.87

The cis-specificity of the Q-gene product of bacteriophage lambda. Mol Gen Genet (1982) 0.87

Mechanogenomic control of DNA exposure and sequestration. Am J Pathol (2005) 0.79

Articles by these authors

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

Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell (2007) 3.17

Stability puzzles in phage lambda. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.25

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

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

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

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

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

Structure and function of negative feedback loops at the interface of genetic and metabolic networks. Nucleic Acids Res (2006) 0.93

Modelling transcriptional interference and DNA looping in gene regulation. J Mol Biol (2007) 0.93

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

Quorum sensing regulation in Aeromonas hydrophila. J Mol Biol (2010) 0.92

Functional alignment of regulatory networks: a study of temperate phages. PLoS Comput Biol (2005) 0.91

Dominant negative autoregulation limits steady-state repression levels in gene networks. J Bacteriol (2009) 0.91

Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res (2011) 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

Competition between diffusion and fragmentation: an important evolutionary process of nature. Phys Rev Lett (2003) 0.88

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

Ecosystems with mutually exclusive interactions self-organize to a state of high diversity. Phys Rev Lett (2011) 0.87

The functional half-life of an mRNA depends on the ribosome spacing in an early coding region. J Mol Biol (2011) 0.86

Variability-based sequence alignment identifies residues responsible for functional differences in alpha and beta tubulin. Protein Sci (2004) 0.86

Nonideal behavior of the intramolecular structure factor of dilute polymers in a theta solvent. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 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

Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states. Nucleic Acids Res (2013) 0.83

Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. Biophys J (2008) 0.83

Quantifying the benefits of translation regulation in the unfolded protein response. Phys Biol (2004) 0.82

Degree landscapes in scale-free networks. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.82

Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes. Nucleic Acids Res (2013) 0.82

Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy. PLoS Comput Biol (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

Spreading out of perturbations in reversible reaction networks. New J Phys (2007) 0.80

Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One (2009) 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

Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.79

Multistability with a metastable mixed state. Phys Rev Lett (2012) 0.78

Emergence of diversity in a model ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.78

Switching between oscillations and homeostasis in competing negative and positive feedback motifs. J Theor Biol (2012) 0.77

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

Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas. Phys Biol (2016) 0.76

Genetic regulatory networks that count to 3. J Theor Biol (2013) 0.76

One hub-one process: a tool based view on regulatory network topology. BMC Syst Biol (2008) 0.75

Key players in the genetic switch of bacteriophage TP901-1. Biophys J (2011) 0.75

Quality control system response to stochastic growth of amyloid fibrils. FEBS Lett (2013) 0.75

Dynamics of the recovery from sRNA-mediated gene silencing. Cell Cycle (2009) 0.75

Anomalous fluctuations in sliding motion of cytoskeletal filaments driven by molecular motors: model simulations. J Phys Chem B (2008) 0.75

Modeling dynamics of information networks. Phys Rev Lett (2003) 0.75

Locally self-organized quasicritical percolation in a multiple-disease model. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75

Fluid dynamics of dilatant fluids. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.75

Visualization of large-scale correlations in gene expressions. Funct Integr Genomics (2004) 0.75

Organizational structure and communication networks in a university environment. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75

Circuit architecture explains functional similarity of bacterial heat shock responses. Phys Biol (2012) 0.75

Loewner driving functions for off-critical percolation clusters. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.75