Published in Proc Natl Acad Sci U S A on December 10, 2004
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Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts. BMC Genomics (2006) 1.39
Shifts in replication timing actively affect histone acetylation during nucleosome reassembly. Mol Cell (2009) 1.27
Genome-wide analysis of the replication program in mammals. Chromosome Res (2010) 1.23
Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels. J Cell Biol (2010) 1.20
Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genet (2010) 1.16
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Domain-wide regulation of DNA replication timing during mammalian development. Chromosome Res (2010) 1.06
H3 k36 methylation helps determine the timing of cdc45 association with replication origins. PLoS One (2009) 1.05
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Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei. J Cell Sci (2008) 0.99
3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res (2012) 0.98
DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts. Nucleic Acids Res (2008) 0.96
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A mechanistic role for DNA methylation in endothelial cell (EC)-enriched gene expression: relationship with DNA replication timing. Blood (2013) 0.90
USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator. PLoS Biol (2012) 0.89
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm. Nat Protoc (2012) 0.89
Drosophila functional elements are embedded in structurally constrained sequences. PLoS Genet (2013) 0.87
The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture. J Mol Biol (2013) 0.86
Epigenetic landscape for initiation of DNA replication. Chromosoma (2013) 0.86
Regulation of DNA replication by chromatin structures: accessibility and recruitment. Chromosoma (2010) 0.85
Timeless-dependent DNA replication-coupled recombination promotes Kaposi's Sarcoma-associated herpesvirus episome maintenance and terminal repeat stability. J Virol (2013) 0.84
DNA replication origins-where do we begin? Genes Dev (2016) 0.83
Cdc6: a multi-functional molecular switch with critical role in carcinogenesis. Transcription (2012) 0.82
Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays. Nucleic Acids Res (2007) 0.81
Cell cycle reentry from the late S phase: implications from stem cell formation in the moss Physcomitrella patens. J Plant Res (2015) 0.80
Impaired replication dynamics at the FRA3B common fragile site. Hum Mol Genet (2010) 0.80
Sororin actively maintains sister chromatid cohesion. EMBO J (2016) 0.80
Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin. Nucleic Acids Res (2007) 0.80
Conservation of domain structure in a fast-evolving heterochromatic SUUR protein in drosophilids. Genetics (2009) 0.79
Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin. Chromosoma (2012) 0.78
Organization of the amplified type I interferon gene cluster and associated chromosome regions in the interphase nucleus of human osteosarcoma cells. Chromosome Res (2009) 0.77
Initiation of DNA Replication in the Human Genome. Hereditary Genet (2012) 0.77
Repliscan: a tool for classifying replication timing regions. BMC Bioinformatics (2017) 0.76
Microarray data normalization and transformation. Nat Genet (2002) 15.04
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
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Multicolor spectral karyotyping of human chromosomes. Science (1996) 7.65
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev (2004) 7.57
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet (2002) 4.68
Eucaryotic DNA: organization of the genome for replication. Cell (1978) 4.53
Replication timing of the human genome. Hum Mol Genet (2003) 4.10
Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet (2001) 4.09
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Replication program of active and inactive multigene families in mammalian cells. Mol Cell Biol (1988) 3.55
Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell (1993) 2.52
Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication. Nat Cell Biol (2003) 2.21
The control of mammalian DNA replication: a brief history of space and timing. Cell (2001) 2.15
Control of collagen production by human diploid lung fibroblasts. J Biol Chem (1980) 1.72
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The timing of XIST replication: dominance of the domain. Hum Mol Genet (1999) 1.54
Long-distance control of origin choice and replication timing in the human beta-globin locus are independent of the locus control region. Mol Cell Biol (2000) 1.53
Sequence of DNA replication in 277 R- and Q-bands of human chromosomes using a BrdU treatment. Chromosoma (1976) 1.36
The pattern of replication at a human telomeric region (16p13.3): its relationship to chromosome structure and gene expression. Hum Mol Genet (1999) 1.29
High-resolution replication bands compared with morphologic G- and R-bands. Adv Hum Genet (1994) 1.21
The gene-richest bands of human chromosomes replicate at the onset of the S-phase. Cytogenet Cell Genet (1998) 0.98
Human chromosomal banding by in situ hybridization of isochores. Methods Cell Sci (2001) 0.84
Effects of adenine arabinoside and coformycin on the kinetics of G2 chromatid aberrations in X-irradiated human lymphocytes. Mutagenesis (1992) 0.82
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet (2005) 15.37
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Unlocking the secrets of the genome. Nature (2009) 11.80
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature (2011) 8.75
Controlling the double helix. Nature (2003) 8.61
Interferon signaling and treatment outcome in chronic hepatitis C. Proc Natl Acad Sci U S A (2008) 8.56
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation. Mol Cell Biol (2007) 7.97
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Bacterial disease resistance in Arabidopsis through flagellin perception. Nature (2004) 7.74
Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell (2008) 7.68
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev (2004) 7.57
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (2012) 7.27
HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (2006) 7.12
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell (2005) 5.77
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Chemokine receptor CXCR4 downregulated by von Hippel-Lindau tumour suppressor pVHL. Nature (2003) 5.57
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
Functional and mechanistic diversity of distal transcription enhancers. Cell (2011) 5.22
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
What is a gene, post-ENCODE? History and updated definition. Genome Res (2007) 4.96
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet (2002) 4.68
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol (2008) 4.50
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Targets and dynamics of promoter DNA methylation during early mouse development. Nat Genet (2010) 4.27
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15