Published in Nucleic Acids Res on October 29, 2013
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Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet (2006) 8.99
Nuclear organization of the genome and the potential for gene regulation. Nature (2007) 8.22
CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science (2006) 7.68
Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer (2005) 7.53
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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Chromatin compaction by a polycomb group protein complex. Science (2004) 4.95
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PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol (2008) 2.85
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol (2007) 2.72
Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc (2007) 2.69
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev (2011) 2.53
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Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus. Proc Natl Acad Sci U S A (2011) 2.15
Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res (2006) 2.13
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CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Res (2007) 1.89
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The role of HOX genes in malignant myeloid disease. Curr Opin Hematol (2007) 1.39
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Aberrant expression of HOX genes in human invasive breast carcinoma. Oncol Rep (2005) 1.18
Altered expressions of HOX genes in human cutaneous malignant melanoma. Int J Cancer (2005) 1.12
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From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (2012) 0.89
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics (2004) 3.63
Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab (2007) 3.00
Associations with early-life socio-economic position in adult DNA methylation. Int J Epidemiol (2011) 2.67
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A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
Gene expression during acute and prolonged hypoxia is regulated by distinct mechanisms of translational control. EMBO J (2006) 2.41
Promoter-wide hypermethylation of the ribosomal RNA gene promoter in the suicide brain. PLoS One (2008) 2.40
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. Proc Natl Acad Sci U S A (2004) 2.21
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol (2014) 2.01
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Broad epigenetic signature of maternal care in the brain of adult rats. PLoS One (2011) 1.86
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics (2011) 1.78
Complexity of chromatin folding is captured by the strings and binders switch model. Proc Natl Acad Sci U S A (2012) 1.73
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
The Gemin6-Gemin7 heterodimer from the survival of motor neurons complex has an Sm protein-like structure. Structure (2005) 1.64
Definition of the landscape of promoter DNA hypomethylation in liver cancer. Cancer Res (2011) 1.58
Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Res (2006) 1.50
BH3-ligand regulates access of MCL-1 to its E3 ligase. FEBS Lett (2005) 1.49
Gemins modulate the expression and activity of the SMN complex. Hum Mol Genet (2005) 1.42
Repurposing CRISPR/Cas9 for in situ functional assays. Genes Dev (2013) 1.41
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res (2010) 1.36
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem. J Comput Biol (2007) 1.35
Molecular characterization of pandemic H1N1 influenza viruses isolated from turkeys and pathogenicity of a human pH1N1 isolate in turkeys. Avian Dis (2010) 1.35
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet (2009) 1.32
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods (2009) 1.24
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation. Genome Biol (2009) 1.14
On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol (2006) 1.14
Seeder: discriminative seeding DNA motif discovery. Bioinformatics (2008) 1.10
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment. Genome Biol (2013) 1.06
Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Nucleic Acids Res (2009) 1.06
The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Mol Immunol (2010) 1.05
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 1.03
Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics (2009) 1.01
Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol (2010) 0.99
Detecting non-coding selective pressure in coding regions. BMC Evol Biol (2007) 0.98
Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. Nucleic Acids Res (2004) 0.98
Childhood abuse is associated with methylation of multiple loci in adult DNA. BMC Med Genomics (2014) 0.95
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
Discovering genome regulation with 3C and 3C-related technologies. Biochim Biophys Acta (2011) 0.93
Chromatin conformation signatures: ideal human disease biomarkers? Biomark Med (2010) 0.92
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
Epigenomic socioeconomic studies more similar than different. Proc Natl Acad Sci U S A (2013) 0.92
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Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS One (2011) 0.90
Shaping the Genome with Non-Coding RNAs. Curr Genomics (2011) 0.90
From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (2012) 0.89
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis. Genome Biol (2009) 0.89
p53 inhibits angiogenesis by inducing the production of Arresten. Cancer Res (2012) 0.89
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Transcription onset of genes critical in liver carcinogenesis is epigenetically regulated by methylated DNA-binding protein MBD2. Carcinogenesis (2013) 0.86
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Glucocorticoid programming of the fetal male hippocampal epigenome. Endocrinology (2013) 0.85
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 0.85
Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells. Nucleic Acids Res (2008) 0.85
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2. Nucleic Acids Res (2013) 0.84
A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing. Methods Enzymol (2012) 0.84
Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth. Epigenetics (2014) 0.84
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 0.83
An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria. PLoS One (2012) 0.83
A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses. J Comput Biol (2009) 0.82
A polymer model explains the complexity of large-scale chromatin folding. Nucleus (2013) 0.82
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). Biochem Cell Biol (2008) 0.81
Pre-exposing Canada Geese (Branta canadensis) to a low-pathogenic H1N1 avian influenza virus protects them against H5N1 HPAI virus challenge. J Wildl Dis (2013) 0.81
Methylated DNA binding domain protein 2 (MBD2) coordinately silences gene expression through activation of the microRNA hsa-mir-496 promoter in breast cancer cell line. PLoS One (2013) 0.81
Gestational Diabetes Alters Offspring DNA Methylation Profiles in Human and Rat: Identification of Key Pathways Involved in Endocrine System Disorders, Insulin Signaling, Diabetes Signaling, and ILK Signaling. Endocrinology (2014) 0.80
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res (2012) 0.80
Effects of antenatal synthetic glucocorticoid on glucocorticoid receptor binding, DNA methylation, and genome-wide mRNA levels in the fetal male hippocampus. Endocrinology (2013) 0.80
Genetic map refinement using a comparative genomic approach. J Comput Biol (2009) 0.79
Discovery and validation of DNA hypomethylation biomarkers for liver cancer using HRM-specific probes. PLoS One (2013) 0.79
A model of the large-scale organization of chromatin. Biochem Soc Trans (2013) 0.78
Searching for signaling balance through the identification of genetic interactors of the Rab guanine-nucleotide dissociation inhibitor gdi-1. PLoS One (2010) 0.78
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77