Published in Proc Natl Acad Sci U S A on July 22, 2013
The proteome of human cytomegalovirus virions and dense bodies is conserved across different strains. Med Microbiol Immunol (2015) 0.87
An epistatic relationship between the viral protein kinase UL97 and the UL133-UL138 latency locus during the human cytomegalovirus lytic cycle. J Virol (2014) 0.84
Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surface. J Virol (2013) 0.81
Functional annotation of human cytomegalovirus gene products: an update. Front Microbiol (2014) 0.79
Cytomegalovirus latency and reactivation: recent insights into an age old problem. Rev Med Virol (2015) 0.78
Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection. PLoS One (2015) 0.78
Human Cytomegalovirus Immediate-Early 1 Protein Rewires Upstream STAT3 to Downstream STAT1 Signaling Switching an IL6-Type to an IFNγ-Like Response. PLoS Pathog (2016) 0.77
Analysis of the functional interchange between the IE1 and pp71 proteins of human cytomegalovirus and ICP0 of herpes simplex virus 1. J Virol (2014) 0.77
Multiple Transcripts Encode Full-Length Human Cytomegalovirus IE1 and IE2 Proteins during Lytic Infection. J Virol (2016) 0.76
Epigenetically repressing human cytomegalovirus lytic infection and reactivation from latency in THP-1 model by targeting H3K9 and H3K27 histone demethylases. PLoS One (2017) 0.75
An Essential Viral Transcription Activator Modulates Chromatin Dynamics. PLoS Pathog (2016) 0.75
Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature (1997) 44.55
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 15.60
A genomic code for nucleosome positioning. Nature (2006) 15.38
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Subunit structure of chromatin. Nature (1974) 8.45
Regulation of chromatin by histone modifications. Cell Res (2011) 8.44
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J Mol Biol (2002) 8.42
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell (2005) 6.17
Determinants of nucleosome organization in primary human cells. Nature (2011) 5.50
High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol (2007) 5.24
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
Histone variants--ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol (2010) 4.45
Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J Cell Biol (1999) 3.79
Determinants and dynamics of genome accessibility. Nat Rev Genet (2011) 3.15
What controls nucleosome positions? Trends Genet (2009) 3.15
A deletion mutant in the human cytomegalovirus gene encoding IE1(491aa) is replication defective due to a failure in autoregulation. Proc Natl Acad Sci U S A (1996) 3.14
G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics (2009) 3.05
Chromatin control of herpes simplex virus lytic and latent infection. Nat Rev Microbiol (2008) 2.86
Defective growth correlates with reduced accumulation of a viral DNA replication protein after low-multiplicity infection by a human cytomegalovirus ie1 mutant. J Virol (1998) 2.86
High nucleosome occupancy is encoded at human regulatory sequences. PLoS One (2010) 2.43
Control of cytomegalovirus lytic gene expression by histone acetylation. EMBO J (2002) 2.06
Expression of the acidic nuclear immediate-early protein (IE1) of human cytomegalovirus in stable cell lines and its preferential association with metaphase chromosomes. Virology (1989) 1.97
Human cytomegalovirus immediate-early 1 protein facilitates viral replication by antagonizing histone deacetylation. Proc Natl Acad Sci U S A (2004) 1.90
VP16-dependent association of chromatin-modifying coactivators and underrepresentation of histones at immediate-early gene promoters during herpes simplex virus infection. J Virol (2004) 1.89
Herpes simplex virus ICP0 promotes both histone removal and acetylation on viral DNA during lytic infection. J Virol (2008) 1.88
Cytomegalovirus: pathogen, paradigm, and puzzle. J Clin Invest (2011) 1.82
Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol (2010) 1.72
DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc Natl Acad Sci U S A (2007) 1.53
Antisense transcription in the human cytomegalovirus transcriptome. J Virol (2007) 1.40
Chromatin structure regulates human cytomegalovirus gene expression during latency, reactivation and lytic infection. Biochim Biophys Acta (2009) 1.36
Temporal dynamics of cytomegalovirus chromatin assembly in productively infected human cells. J Virol (2008) 1.35
Dynamic histone H3 acetylation and methylation at human cytomegalovirus promoters during replication in fibroblasts. J Virol (2008) 1.31
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol (2010) 1.25
Control of human cytomegalovirus gene expression by differential histone modifications during lytic and latent infection of a monocytic cell line. Gene (2006) 1.22
Lytic infection of permissive cells with human cytomegalovirus is regulated by an intrinsic 'pre-immediate-early' repression of viral gene expression mediated by histone post-translational modification. J Gen Virol (2009) 1.11
Regulation of histone deposition on the herpes simplex virus type 1 genome during lytic infection. J Virol (2009) 1.00
How to control an infectious bead string: nucleosome-based regulation and targeting of herpesvirus chromatin. Rev Med Virol (2011) 1.00
Histone H3 lysine 4 methylation marks postreplicative human cytomegalovirus chromatin. J Virol (2012) 0.92
Human cytomegalovirus IE72 protein interacts with the transcriptional repressor hDaxx to regulate LUNA gene expression during lytic infection. J Virol (2010) 0.90
An acidic region of the 89K murine cytomegalovirus immediate early protein interacts with DNA. J Gen Virol (1992) 0.89
The replication defect of ICP0-null mutant herpes simplex virus 1 can be largely complemented by the combined activities of human cytomegalovirus proteins IE1 and pp71. J Virol (2012) 0.86
Relating periodicity of nucleosome organization and gene regulation. Bioinformatics (2009) 0.80
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
The role of site accessibility in microRNA target recognition. Nat Genet (2007) 18.52
Long noncoding RNA as modular scaffold of histone modification complexes. Science (2010) 15.23
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell (2008) 7.69
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol (2008) 5.71
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35
A transcriptional profile of aging in the human kidney. PLoS Biol (2004) 3.69
Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes Dev (2007) 3.16
Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nat Cell Biol (2008) 3.08
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A (2004) 2.99
Genome-wide measurement of RNA folding energies. Mol Cell (2012) 2.85
Accuracy of transpulmonary thermodilution versus gravimetric measurement of extravascular lung water. Crit Care Med (2004) 2.68
Genomics: ENCODE explained. Nature (2012) 2.62
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol (2012) 2.49
Determinants of nucleosome positioning. Nat Struct Mol Biol (2013) 2.47
Understanding the transcriptome through RNA structure. Nat Rev Genet (2011) 2.46
High nucleosome occupancy is encoded at human regulatory sequences. PLoS One (2010) 2.43
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol (2008) 2.27
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet (2009) 2.22
EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Sci Signal (2010) 2.16
A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol (2008) 2.12
Overlapping codes within protein-coding sequences. Genome Res (2010) 2.02
Human cytomegalovirus immediate-early 1 protein facilitates viral replication by antagonizing histone deacetylation. Proc Natl Acad Sci U S A (2004) 1.90
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet (2012) 1.89
Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res (2008) 1.83
Proteome-wide prediction of acetylation substrates. Proc Natl Acad Sci U S A (2009) 1.81
Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res (2009) 1.72
Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol (2010) 1.72
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A (2008) 1.51
Reconstruction of cell lineage trees in mice. PLoS One (2008) 1.46
A human cytomegalovirus antagonist of type I IFN-dependent signal transducer and activator of transcription signaling. Proc Natl Acad Sci U S A (2006) 1.43
Snapshots: chromatin control of viral infection. Virology (2013) 1.39
Reversal of aging by NFkappaB blockade. Cell Cycle (2007) 1.36
Temporal dynamics of cytomegalovirus chromatin assembly in productively infected human cells. J Virol (2008) 1.35
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Comput Biol (2008) 1.34
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell (2004) 1.32
A novel human cytomegalovirus locus modulates cell type-specific outcomes of infection. PLoS Pathog (2011) 1.30
New insights into replication origin characteristics in metazoans. Cell Cycle (2012) 1.29
Characterization of a novel Golgi apparatus-localized latency determinant encoded by human cytomegalovirus. J Virol (2009) 1.29
Revealing targeted therapy for human cancer by gene module maps. Cancer Res (2008) 1.29
Stress-inducible alternative translation initiation of human cytomegalovirus latency protein pUL138. J Virol (2010) 1.29
Murine cytomegalovirus m41 open reading frame encodes a Golgi-localized antiapoptotic protein. J Virol (2003) 1.28
Promoter sequence determines the relationship between expression level and noise. PLoS Biol (2013) 1.28
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol (2010) 1.25
Minimally cultured or selected autologous tumor-infiltrating lymphocytes after a lympho-depleting chemotherapy regimen in metastatic melanoma patients. J Immunother (2009) 1.25
A transcriptional program mediating entry into cellular quiescence. PLoS Genet (2007) 1.23
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res (2011) 1.19
p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res (2010) 1.19
Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci U S A (2013) 1.18
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol (2007) 1.18
Perianesthetic dental injuries: analysis of incident reports. J Clin Anesth (2004) 1.17
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics (2012) 1.16
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res (2010) 1.15
Cell lineage analysis of the mammalian female germline. PLoS Genet (2012) 1.13
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Res (2013) 1.08
Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol (2010) 1.07
Estimating cell depth from somatic mutations. PLoS Comput Biol (2008) 1.06
Stemness, cancer and cancer stem cells. Cell Cycle (2008) 1.02
Chromatinisation of herpesvirus genomes. Rev Med Virol (2010) 1.01
Sequence features of yeast and human core promoters that are predictive of maximal promoter activity. Nucleic Acids Res (2013) 1.00
An endothelial cell-specific requirement for the UL133-UL138 locus of human cytomegalovirus for efficient virus maturation. J Virol (2013) 1.00
How to control an infectious bead string: nucleosome-based regulation and targeting of herpesvirus chromatin. Rev Med Virol (2011) 1.00
Physical requirements and functional consequences of complex formation between the cytomegalovirus IE1 protein and human STAT2. J Virol (2009) 0.95
The grammar of transcriptional regulation. Hum Genet (2014) 0.95
Human cytomegalovirus IE1 protein elicits a type II interferon-like host cell response that depends on activated STAT1 but not interferon-γ. PLoS Pathog (2011) 0.95
Predicting disease risk using bootstrap ranking and classification algorithms. PLoS Comput Biol (2013) 0.94
Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy. Bioinformatics (2009) 0.94
Possible role of recombinant activated factor VII (rFVIIa) in the control of hemorrhage associated with massive trauma. Can J Anaesth (2002) 0.93
Histone H3 lysine 4 methylation marks postreplicative human cytomegalovirus chromatin. J Virol (2012) 0.92
Probabilistic discovery of overlapping cellular processes and their regulation. J Comput Biol (2005) 0.90
Outcome of patients with cystic fibrosis admitted to the intensive care unit: is invasive mechanical ventilation a risk factor for death in patients waiting lung transplantation? Heart Lung (2009) 0.90
The multi-targeted kinase inhibitor sorafenib inhibits human cytomegalovirus replication. Cell Mol Life Sci (2010) 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
Human cytomegalovirus IE1 protein disrupts interleukin-6 signaling by sequestering STAT3 in the nucleus. J Virol (2013) 0.89
Interactions between proteins encoded within the human cytomegalovirus UL133-UL138 locus. J Virol (2012) 0.89
Codep: maximizing co-evolutionary interdependencies to discover interacting proteins. Proteins (2006) 0.89
A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host. Gut Microbes (2015) 0.88
Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivity. PLoS Comput Biol (2008) 0.88