Published in Science on October 09, 2009
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Integrative analysis of 111 reference human epigenomes. Nature (2015) 10.32
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
The long-range interaction landscape of gene promoters. Nature (2012) 9.20
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell (2014) 8.79
A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74
Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73
Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39
A three-dimensional model of the yeast genome. Nature (2010) 7.01
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell (2013) 6.37
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet (2011) 5.97
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70
Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature (2014) 5.61
Functional and mechanistic diversity of distal transcription enhancers. Cell (2011) 5.22
A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature (2013) 5.18
Chromosome territories. Cold Spring Harb Perspect Biol (2010) 5.00
Transcription factors: from enhancer binding to developmental control. Nat Rev Genet (2012) 5.00
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res (2010) 4.67
Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol (2011) 4.56
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet (2013) 4.48
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature (2013) 4.47
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet (2013) 4.38
Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods (2012) 4.26
A decade of 3C technologies: insights into nuclear organization. Genes Dev (2012) 4.25
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (2013) 4.12
Chromothripsis from DNA damage in micronuclei. Nature (2015) 4.04
Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet (2013) 4.03
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell (2012) 4.02
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature (2013) 3.93
Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature (2012) 3.92
A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res (2010) 3.89
Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell (2013) 3.83
Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell (2011) 3.81
Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell (2011) 3.65
Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature (2015) 3.64
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57
The hierarchy of the 3D genome. Mol Cell (2013) 3.54
Organization of the mitotic chromosome. Science (2013) 3.50
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol (2010) 3.39
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat Rev Genet (2012) 3.29
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
The nuclear pore complex: bridging nuclear transport and gene regulation. Nat Rev Mol Cell Biol (2010) 3.19
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell (2015) 3.10
Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell (2012) 3.08
Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol (2012) 3.01
Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res (2010) 2.96
Origin of chromosomal translocations in lymphoid cancer. Cell (2010) 2.94
Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol (2010) 2.80
Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J (2009) 2.78
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res (2013) 2.77
Chromatin architecture reorganization during stem cell differentiation. Nature (2015) 2.71
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Genomics tools for unraveling chromosome architecture. Nat Biotechnol (2010) 2.63
High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat Biotechnol (2011) 2.63
DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat Biotechnol (2011) 2.62
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell (2015) 2.59
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus. Nat Genet (2011) 2.54
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev (2011) 2.53
Enhancers: the abundance and function of regulatory sequences beyond promoters. Dev Biol (2009) 2.50
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
The fractal globule as a model of chromatin architecture in the cell. Chromosome Res (2011) 2.48
DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature (2012) 2.44
Mapping human epigenomes. Cell (2013) 2.44
Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods (2012) 2.42
Polymorphic cis- and trans-regulation of human gene expression. PLoS Biol (2010) 2.42
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet (2014) 2.42
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A (2015) 2.34
Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription. Nat Rev Genet (2012) 2.29
Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol (2012) 2.25
The real cost of sequencing: higher than you think! Genome Biol (2011) 2.22
Single-cell chromatin accessibility reveals principles of regulatory variation. Nature (2015) 2.22
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature (2016) 2.21
Harnessing cloud computing with Galaxy Cloud. Nat Biotechnol (2011) 2.19
Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. EMBO J (2012) 2.17
High-resolution mapping of the spatial organization of a bacterial chromosome. Science (2013) 2.17
Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature (2017) 2.16
Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol (2012) 2.16
Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature (2015) 2.15
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell (2015) 2.11
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res (2012) 2.09
Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity. Annu Rev Immunol (2012) 2.06
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res (2013) 2.05
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol (2013) 2.05
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol (2013) 2.05
Complex multi-enhancer contacts captured by genome architecture mapping. Nature (2017) 2.04
Tackling the epigenome: challenges and opportunities for collaboration. Nat Biotechnol (2010) 2.04
Topology of mammalian developmental enhancers and their regulatory landscapes. Nature (2013) 2.02
Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02
Hi-C: a comprehensive technique to capture the conformation of genomes. Methods (2012) 2.00
Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet (2013) 1.98
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
Capturing chromosome conformation. Science (2002) 23.93
CTCF: master weaver of the genome. Cell (2009) 15.09
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet (2001) 11.70
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet (2006) 11.02
Beyond the sequence: cellular organization of genome function. Cell (2007) 10.32
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet (2004) 9.57
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet (2006) 8.99
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods (2006) 8.52
Nuclear organization of the genome and the potential for gene regulation. Nature (2007) 8.22
In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods (1999) 6.76
Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol (1999) 6.35
Going the distance: a current view of enhancer action. Science (1998) 5.83
Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science (2001) 5.37
Gene regulation in the third dimension. Science (2008) 4.91
The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet (2001) 4.79
Perturbation of nuclear architecture by long-distance chromosome interactions. Cell (1996) 4.73
Gene regulation through nuclear organization. Nat Struct Mol Biol (2007) 3.44
Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus. J Cell Biol (1995) 3.42
Form follows function: The genomic organization of cellular differentiation. Genes Dev (2004) 3.20
Spatially confined folding of chromatin in the interphase nucleus. Proc Natl Acad Sci U S A (2009) 3.19
Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol (2008) 3.13
Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J Cell Biol (2006) 2.63
Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J Biol Chem (2008) 2.40
Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutat Res (2002) 2.24
Protein knot server: detection of knots in protein structures. Nucleic Acids Res (2007) 2.15
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The mammalian epigenome. Cell (2007) 18.13
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Genetic mapping in human disease. Science (2008) 15.12
Systematic localization of common disease-associated variation in regulatory DNA. Science (2012) 14.47
Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 14.34
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature (2011) 11.59
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A (2012) 11.23
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87
Genetic screens in human cells using the CRISPR-Cas9 system. Science (2013) 10.75
Detecting novel associations in large data sets. Science (2011) 10.60
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Reactive oxygen species have a causal role in multiple forms of insulin resistance. Nature (2006) 10.07
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell (2013) 9.24
The long-range interaction landscape of gene promoters. Nature (2012) 9.20
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18