Published in BMC Bioinformatics on December 10, 2008
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res (2010) 4.67
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res (2009) 3.36
Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02
G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc Natl Acad Sci U S A (2009) 1.91
Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells. Cell (2016) 1.88
A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res (2012) 1.37
DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nat Commun (2013) 1.30
Replication timing: a fingerprint for cell identity and pluripotency. PLoS Comput Biol (2011) 1.21
Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol (2012) 1.18
Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Proc Natl Acad Sci U S A (2012) 1.17
Clusters, factories and domains: The complex structure of S-phase comes into focus. Cell Cycle (2010) 1.15
Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res (2012) 1.11
Domain-wide regulation of DNA replication timing during mammalian development. Chromosome Res (2010) 1.06
G2 phase chromatin lacks determinants of replication timing. J Cell Biol (2010) 1.01
DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy. PLoS One (2011) 1.01
Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Hum Mol Genet (2012) 0.92
Complex correlations: replication timing and mutational landscapes during cancer and genome evolution. Curr Opin Genet Dev (2014) 0.92
A mechanistic role for DNA methylation in endothelial cell (EC)-enriched gene expression: relationship with DNA replication timing. Blood (2013) 0.90
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm. Nat Protoc (2012) 0.89
Cyclin E deregulation promotes loss of specific genomic regions. Curr Biol (2015) 0.88
Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells. Genome Res (2015) 0.87
Characterization and dynamics of pericentromere-associated domains in mice. Genome Res (2015) 0.85
Replication stress in Mammalian cells and its consequences for mitosis. Genes (Basel) (2015) 0.85
Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding. Nucleus (2012) 0.83
Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells. Proc Natl Acad Sci U S A (2016) 0.82
Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization. Genome Biol (2015) 0.81
Shape-based alignment of genomic landscapes in multi-scale resolution. Nucleic Acids Res (2012) 0.81
Recent advances in the genome-wide study of DNA replication origins in yeast. Front Microbiol (2015) 0.79
Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains. Epigenetics Chromatin (2013) 0.79
Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution. PLoS One (2011) 0.78
Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating. PLoS One (2015) 0.76
Databases and bioinformatics tools for the study of DNA repair. Mol Biol Int (2011) 0.76
CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis. Hum Mol Genet (2014) 0.76
Fetal de novo mutations and preterm birth. PLoS Genet (2017) 0.75
Genome-wide analysis of replication timing in mammalian cells: troubleshooting problems encountered when comparing different cell types. Methods (2012) 0.75
Cell line differences in replication timing of human glutamate receptor genes and other large genes associated with neural disease. Epigenetics (2014) 0.75
FOXO3 longevity interactome on chromosome 6. Aging Cell (2017) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J Embryol Exp Morphol (1985) 12.74
Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science (2007) 12.41
Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat Biotechnol (2003) 9.41
Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet (2002) 4.68
Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol (2008) 4.50
Coordination of replication and transcription along a Drosophila chromosome. Genes Dev (2004) 4.13
Replication timing of the human genome. Hum Mol Genet (2003) 4.10
A novel ES cell line, TT2, with high germline-differentiating potency. Anal Biochem (1993) 3.79
Replication timing and transcriptional control: beyond cause and effect. Curr Opin Cell Biol (2002) 3.68
Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. Mol Cell (2005) 3.22
Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res (2007) 2.82
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
A genomic view of eukaryotic DNA replication. Chromosome Res (2005) 2.30
Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum Mol Genet (2002) 2.12
Global organization of replication time zones of the mouse genome. Genome Res (2008) 2.11
A question of timing: emerging links between transcription and replication. Curr Opin Genet Dev (2006) 2.00
Orc mutants arrest in metaphase with abnormally condensed chromosomes. Development (2001) 1.84
Replicating by the clock. Nat Rev Mol Cell Biol (2003) 1.79
Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant. Hum Mol Genet (2000) 1.61
Aberrant replication timing induces defective chromosome condensation in Drosophila ORC2 mutants. Curr Biol (2001) 1.57
Replication timing of human chromosome 6. Cell Cycle (2005) 1.52
Replication delay along FRA7H, a common fragile site on human chromosome 7, leads to chromosomal instability. Mol Cell Biol (2000) 1.27
Delayed replication timing leads to delayed mitotic chromosome condensation and chromosomal instability of chromosome translocations. Proc Natl Acad Sci U S A (2001) 1.26
Directed differentiation of pluripotent cells to neural lineages: homogeneous formation and differentiation of a neurectoderm population. Development (2002) 1.15
Engineering translocations with delayed replication: evidence for cis control of chromosome replication timing. Hum Mol Genet (2005) 1.14
Amplicons on human chromosome 11q are located in the early/late-switch regions of replication timing. Genomics (2004) 0.99
Chromosomes with delayed replication timing lead to checkpoint activation, delayed recruitment of Aurora B and chromosome instability. Oncogene (2006) 0.98
Replication timing of homologous alpha-satellite DNA in Roberts syndrome. Chromosome Res (2000) 0.92
Allele-specific replication associated with aneuploidy in blood cells of patients with hematologic malignancies. Cancer Genet Cytogenet (2002) 0.92
Expression and replication timing patterns of wildtype and translocated BCL2 genes. Genomics (2001) 0.86
Asynchronous replication of biallelically expressed loci: a new phenomenon in Turner syndrome. Genet Med (2003) 0.84
Replication status in leukocytes of treated and untreated patients with polycythemia vera and essential thrombocytosis. Cancer Genet Cytogenet (2002) 0.83
The influence of cytogenetic aberrations on gene replication in chronic lymphocytic leukemia patients. Cancer Genet Cytogenet (2001) 0.83
Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science (2003) 4.74
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res (2010) 4.67
Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol (2008) 4.50
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res (2009) 3.36
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Actin up in the nucleus. Nat Rev Mol Cell Biol (2004) 2.13
Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma (2002) 2.03
Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02
Functional contribution of Pds5 to cohesin-mediated cohesion in human cells and Xenopus egg extracts. J Cell Sci (2005) 2.00
Heterochromatin and tri-methylated lysine 20 of histone H4 in animals. J Cell Sci (2004) 1.98
G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc Natl Acad Sci U S A (2009) 1.91
Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells. EMBO J (2012) 1.85
Replication timing and transcriptional control: beyond cause and effect--part II. Curr Opin Genet Dev (2009) 1.84
Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol Biol Cell (2005) 1.77
Epigenomic replication: linking epigenetics to DNA replication. Bioessays (2003) 1.66
The Xenopus receptor tyrosine kinase Xror2 modulates morphogenetic movements of the axial mesoderm and neuroectoderm via Wnt signaling. Development (2002) 1.60
Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. J Cell Biol (2007) 1.59
The many faces of the origin recognition complex. Curr Opin Cell Biol (2007) 1.58
Replication timing as an epigenetic mark. Epigenetics (2009) 1.53
Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores. Proc Natl Acad Sci U S A (2004) 1.53
Mammalian nuclei become licensed for DNA replication during late telophase. J Cell Sci (2002) 1.51
Genome-scale analysis of replication timing: from bench to bioinformatics. Nat Protoc (2011) 1.49
Uncoupling global and fine-tuning replication timing determinants for mouse pericentric heterochromatin. J Cell Biol (2006) 1.41
DNA replication timing. Cold Spring Harb Perspect Biol (2013) 1.38
Chromosome engineering allows the efficient isolation of vertebrate neocentromeres. Dev Cell (2013) 1.30
Productive hepatitis C virus infection of stem cell-derived hepatocytes reveals a critical transition to viral permissiveness during differentiation. PLoS Pathog (2012) 1.29
Structure of a palindromic amplicon junction implicates microhomology-mediated end joining as a mechanism of sister chromatid fusion during gene amplification. Nucleic Acids Res (2004) 1.23
Replication timing: a fingerprint for cell identity and pluripotency. PLoS Comput Biol (2011) 1.21
FISH Finder: a high-throughput tool for analyzing FISH images. Bioinformatics (2011) 1.20
Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Proc Natl Acad Sci U S A (2012) 1.17
Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res (2010) 1.13
Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res (2012) 1.11
Identification of novel candidate compounds targeting TrkB to induce apoptosis in neuroblastoma. Cancer Med (2014) 1.10
Spatial distribution and specification of mammalian replication origins during G1 phase. J Cell Biol (2003) 1.09
Spatio-temporal organization of DNA replication in murine embryonic stem, primary, and immortalized cells. J Cell Biochem (2005) 1.08
The Chinese hamster dihydrofolate reductase replication origin decision point follows activation of transcription and suppresses initiation of replication within transcription units. Mol Cell Biol (2006) 1.07
Domain-wide regulation of DNA replication timing during mammalian development. Chromosome Res (2010) 1.06
DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy. PLoS One (2011) 1.01
G2 phase chromatin lacks determinants of replication timing. J Cell Biol (2010) 1.01
RB reversibly inhibits DNA replication via two temporally distinct mechanisms. Mol Cell Biol (2004) 1.01
Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload. J Cell Biol (2011) 1.00
Chinese hamster ORC subunits dynamically associate with chromatin throughout the cell-cycle. Exp Cell Res (2005) 0.95
Replication labeling with halogenated thymidine analogs. Curr Protoc Cell Biol (2007) 0.95
LMO3 interacts with p53 and inhibits its transcriptional activity. Biochem Biophys Res Commun (2009) 0.93
Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Hum Mol Genet (2012) 0.92
DNA Replication Timing. Cold Spring Harb Perspect Med (2013) 0.90
Replication origins run (ultra) deep. Nat Struct Mol Biol (2012) 0.89
Electrolytic transformation of ordinance related compounds (ORCs) in groundwater: laboratory mass balance studies. Chemosphere (2005) 0.88
Observing S-phase dynamics of histone modifications with fluorescently labeled antibodies. Methods Mol Biol (2006) 0.88
The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture. J Mol Biol (2013) 0.86
Overexpression of ORC subunits and increased ORC-chromatin association in transformed mammalian cells. J Cell Biochem (2005) 0.86
Sensitivity of the origin decision point to specific inhibitors of cellular signaling and metabolism. Exp Cell Res (2002) 0.85
SnapShot: Replication timing. Cell (2013) 0.85
Cell cycle regulated transcription of heterochromatin in mammals vs. fission yeast: functional conservation or coincidence? Cell Cycle (2008) 0.84
Evidence for a pre-restriction point Cdk3 activity. J Cell Biochem (2002) 0.84
Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding. Nucleus (2012) 0.83
Microfluidic extraction and stretching of chromosomal DNA from single cell nuclei for DNA fluorescence in situ hybridization. Biomed Microdevices (2012) 0.80
Replication timing and metazoan evolution. Nat Genet (2002) 0.79
Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains. Epigenetics Chromatin (2013) 0.79
Novel adaptor protein Shf interacts with ALK receptor and negatively regulates its downstream signals in neuroblastoma. Cancer Sci (2013) 0.78
Tracking the Clonal Evolution of Adenosquamous Carcinoma, a Rare Variant of Intraductal Papillary Mucinous Neoplasm of the Pancreas. Pancreas (2016) 0.78
Development of a single-cell array for large-scale DNA fluorescence in situ hybridization. Lab Chip (2013) 0.77
Nucleus and gene expression: the structure and function conundrum. Curr Opin Cell Biol (2010) 0.77
Evidence for a mammalian late-G1 phase inhibitor of replication licensing distinct from geminin or Cdk activity. Nucleus (2011) 0.77
Autosomal lyonization of replication domains during early Mammalian development. Adv Exp Med Biol (2010) 0.76
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A (2014) 0.76
Low-cost fabrication of centimetre-scale periodic arrays of single plasmid DNA molecules. Lab Chip (2013) 0.75
Genome-wide analysis of replication timing in mammalian cells: troubleshooting problems encountered when comparing different cell types. Methods (2012) 0.75