Published in Cell Cycle on February 15, 2012
Mapping of Replication Origins in the X Inactivation Center of Vole Microtus levis Reveals Extended Replication Initiation Zone. PLoS One (2015) 1.39
DNA replication origins. Cold Spring Harb Perspect Biol (2013) 1.37
The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells. PLoS Genet (2014) 1.20
G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J (2014) 1.14
Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of Origin Recognition Complex-binding sites in the Drosophila genome. Nucleic Acids Res (2013) 1.10
Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization. PLoS Genet (2014) 1.05
Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins. Genome Res (2013) 1.05
Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells. EMBO J (2014) 1.04
Human origin recognition complex binds preferentially to G-quadruplex-preferable RNA and single-stranded DNA. J Biol Chem (2013) 1.02
Human genome replication proceeds through four chromatin states. PLoS Comput Biol (2013) 1.01
Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol (2015) 0.98
Rif1 binds to G quadruplexes and suppresses replication over long distances. Nat Struct Mol Biol (2015) 0.96
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Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res (2015) 0.94
Activation of a human chromosomal replication origin by protein tethering. Nucleic Acids Res (2013) 0.92
Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program. Mol Cell (2015) 0.91
G-quadruplexes significantly stimulate Pif1 helicase-catalyzed duplex DNA unwinding. J Biol Chem (2015) 0.91
High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep (2015) 0.90
Replication origins run (ultra) deep. Nat Struct Mol Biol (2012) 0.89
Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res (2016) 0.89
High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins. EMBO J (2013) 0.88
Epigenetic landscape for initiation of DNA replication. Chromosoma (2013) 0.86
Cdc45 is limiting for replication initiation in humans. Cell Cycle (2016) 0.86
The hunt for origins of DNA replication in multicellular eukaryotes. F1000Prime Rep (2015) 0.86
The chromatin environment shapes DNA replication origin organization and defines origin classes. Genome Res (2015) 0.85
The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding. Nucleic Acids Res (2014) 0.84
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Age at cancer onset in germline TP53 mutation carriers: association with polymorphisms in predicted G-quadruplex structures. Carcinogenesis (2013) 0.83
Allele-specific analysis of DNA replication origins in mammalian cells. Nat Commun (2015) 0.81
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Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency. PLoS Comput Biol (2015) 0.80
The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics (2014) 0.80
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Evidence of selection for an accessible nucleosomal array in human. BMC Genomics (2016) 0.79
Distinct epigenetic features of differentiation-regulated replication origins. Epigenetics Chromatin (2016) 0.78
Noncoding RNAs in the regulation of DNA replication. Trends Biochem Sci (2014) 0.77
DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Res (2015) 0.77
Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics (2014) 0.76
Evidence for the kinetic partitioning of polymerase activity on G-quadruplex DNA. Biochemistry (2015) 0.76
G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction. Nucleic Acids Res (2016) 0.76
Quadruplex formation by both G-rich and C-rich DNA strands of the C9orf72 (GGGGCC)8•(GGCCCC)8 repeat: effect of CpG methylation. Nucleic Acids Res (2015) 0.76
Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Res (2015) 0.75
DNA Replication Origins and Fork Progression at Mammalian Telomeres. Genes (Basel) (2017) 0.75
Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq). Nucleic Acids Res (2016) 0.75
RNA G-quadruplexes and their potential regulatory roles in translation. Translation (Austin) (2016) 0.75
The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation. G3 (Bethesda) (2016) 0.75
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res (2009) 23.27
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci U S A (2002) 9.60
Prevalence of quadruplexes in the human genome. Nucleic Acids Res (2005) 7.79
G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res (2006) 5.84
Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication. Cell (2009) 5.74
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol (2008) 4.50
In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc Natl Acad Sci U S A (2001) 3.97
DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell (2011) 3.70
Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell (2004) 3.63
Beginning to understand the end of the chromosome. Cell (2004) 3.46
Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat Struct Mol Biol (2006) 3.35
G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics (2009) 3.05
Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A (2008) 2.77
Conserved nucleosome positioning defines replication origins. Genes Dev (2010) 2.74
Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science (2000) 2.72
High nucleosome occupancy is encoded at human regulatory sequences. PLoS One (2010) 2.43
Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc Natl Acad Sci U S A (2004) 2.35
DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J (2004) 2.29
Sequence analysis of ARS elements in fission yeast. EMBO J (1988) 2.17
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Epigenetic instability due to defective replication of structured DNA. Mol Cell (2010) 1.86
Prediction of Saccharomyces cerevisiae replication origins. Genome Biol (2004) 1.81
The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites. Mol Cell Biol (1995) 1.79
G-quadruplex-induced instability during leading-strand replication. EMBO J (2011) 1.77
Clustered adenine/thymine stretches are essential for function of a fission yeast replication origin. Mol Cell Biol (1999) 1.65
In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc Natl Acad Sci U S A (2001) 1.60
Protein kinase C phosphorylates topoisomerase II: topoisomerase activation and its possible role in phorbol ester-induced differentiation of HL-60 cells. Proc Natl Acad Sci U S A (1986) 1.56
FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA. Nucleic Acids Res (2011) 1.45
Replication and partitioning of papillomavirus genomes. Adv Virus Res (2008) 1.21
Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix. J Mol Biol (2006) 1.16
Evidence of the formation of G-quadruplex structures in the promoter region of the human vascular endothelial growth factor gene. Nucleic Acids Res (2010) 1.04
AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev (2011) 1.02
Differential binding of replication proteins across the human c-myc replicator. Mol Cell Biol (2006) 1.02
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Replication and recombination of herpes simplex virus DNA. J Biol Chem (2011) 0.98
Molecular determinants of origin discrimination by Orc1 initiators in archaea. Nucleic Acids Res (2011) 0.98
A toolbox for predicting g-quadruplex formation and stability. J Nucleic Acids (2010) 0.94
Atomic force microscopic analysis of the binding of the Schizosaccharomyces pombe origin recognition complex and the spOrc4 protein with origin DNA. Proc Natl Acad Sci U S A (2004) 0.89
Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe. EMBO J (2010) 0.88
A sequence within the varicella-zoster virus (VZV) OriS is a negative regulator of DNA replication and is bound by a protein complex containing the VZV ORF29 protein. J Virol (2011) 0.84
Site-specific interaction of the murine pre-replicative complex with origin DNA: assembly and disassembly during cell cycle transit and differentiation. Nucleic Acids Res (2007) 0.83
Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site. Biochemistry (2010) 0.79
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
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 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
Mitotic remodeling of the replicon and chromosome structure. Cell (2005) 2.44
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
Specification of a DNA replication origin by a transcription complex. Nat Cell Biol (2004) 2.16
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
Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res (2011) 1.94
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
MCM proteins and DNA replication. Curr Opin Cell Biol (2006) 1.81
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
MCM8- and MCM9-deficient mice reveal gametogenesis defects and genome instability due to impaired homologous recombination. Mol Cell (2012) 1.64
Phosphorylation of Skp2 regulated by CDK2 and Cdc14B protects it from degradation by APC(Cdh1) in G1 phase. EMBO J (2008) 1.53
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
MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation. Cell (2005) 1.40
A Cdt1-geminin complex licenses chromatin for DNA replication and prevents rereplication during S phase in Xenopus. EMBO J (2006) 1.40
DNA replication origins. Cold Spring Harb Perspect Biol (2013) 1.37
Reversal of aging by NFkappaB blockade. Cell Cycle (2007) 1.36
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
Revealing targeted therapy for human cancer by gene module maps. Cancer Res (2008) 1.29
HoxB domain induction silences DNA replication origins in the locus and specifies a single origin at its boundary. EMBO Rep (2006) 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
Rho family GTPases are required for activation of Jak/STAT signaling by G protein-coupled receptors. Mol Cell Biol (2003) 1.22
MCM9 binds Cdt1 and is required for the assembly of prereplication complexes. Mol Cell (2008) 1.21
Activation loop phosphorylation of the atypical MAP kinases ERK3 and ERK4 is required for binding, activation and cytoplasmic relocalization of MK5. J Cell Physiol (2008) 1.20
Nuclear export of ERK3 by a CRM1-dependent mechanism regulates its inhibitory action on cell cycle progression. J Biol Chem (2003) 1.19
Involvement of the IkappaB kinase (IKK)-related kinases tank-binding kinase 1/IKKi and cullin-based ubiquitin ligases in IFN regulatory factor-3 degradation. J Immunol (2006) 1.19
p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res (2010) 1.19
Vertebrate HoxB gene expression requires DNA replication. EMBO J (2003) 1.19
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res (2011) 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
Functional annotation prediction: all for one and one for all. Protein Sci (2006) 1.17
Genetic and epigenetic determinants of DNA replication origins, position and activation. Curr Opin Genet Dev (2013) 1.17
Cdk1 and Cdk2 activity levels determine the efficiency of replication origin firing in Xenopus. EMBO J (2008) 1.16
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res (2010) 1.15
Structural organization of the inactive X chromosome in the mouse. Nature (2016) 1.15
Phosphorylation of Ser72 does not regulate the ubiquitin ligase activity and subcellular localization of Skp2. Cell Cycle (2010) 1.13
Cell lineage analysis of the mammalian female germline. PLoS Genet (2012) 1.13
DNA replication initiates at domains overlapping with nuclear matrix attachment regions in the xenopus and mouse c-myc promoter. Gene (2004) 1.08
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
Programming DNA replication origins and chromosome organization. Chromosome Res (2010) 1.05
E4F1: a novel candidate factor for mediating BMI1 function in primitive hematopoietic cells. Genes Dev (2006) 1.04
MCM-BP regulates unloading of the MCM2-7 helicase in late S phase. Genes Dev (2010) 1.04
p107 inhibits G1 to S phase progression by down-regulating expression of the F-box protein Skp2. J Cell Biol (2005) 1.03
Stemness, cancer and cancer stem cells. Cell Cycle (2008) 1.02
Crystal structure of the coiled-coil dimerization motif of geminin: structural and functional insights on DNA replication regulation. J Mol Biol (2004) 1.01
Sequence features of yeast and human core promoters that are predictive of maximal promoter activity. Nucleic Acids Res (2013) 1.00
Synergic reprogramming of mammalian cells by combined exposure to mitotic Xenopus egg extracts and transcription factors. Proc Natl Acad Sci U S A (2011) 1.00
Formation of extrachromosomal circles from telomeric DNA in Xenopus laevis. EMBO Rep (2002) 0.99
Genome-scale identification of active DNA replication origins. Methods (2012) 0.95
The grammar of transcriptional regulation. Hum Genet (2014) 0.95
Cell cycle regulation of the licensing activity of Cdt1 in Xenopus laevis. Exp Cell Res (2004) 0.95
Competence to replicate in the unfertilized egg is conferred by Cdc6 during meiotic maturation. Nature (2002) 0.95
How to load a replicative helicase onto chromatin: a more and more complex matter during evolution. Cell Cycle (2009) 0.95
Identification of full genes and proteins of MCM9, a novel, vertebrate-specific member of the MCM2-8 protein family. Gene (2005) 0.95
Predicting disease risk using bootstrap ranking and classification algorithms. PLoS Comput Biol (2013) 0.94