Published in Nucleic Acids Res on July 24, 2013
Astrocytic abnormalities and global DNA methylation patterns in depression and suicide. Mol Psychiatry (2014) 0.99
Genome-wide DNA methylation analysis predicts an epigenetic switch for GATA factor expression in endometriosis. PLoS Genet (2014) 0.98
Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genomics (2015) 0.95
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res (2015) 0.90
Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Nat Commun (2016) 0.87
Hypomethylation of the IL17RC promoter in peripheral blood leukocytes is not a hallmark of age-related macular degeneration. Cell Rep (2013) 0.86
Cross-tissue comparisons of leptin and adiponectin: DNA methylation profiles. Adipocyte (2014) 0.84
Prediction of promoters and enhancers using multiple DNA methylation-associated features. BMC Genomics (2015) 0.83
A novel approach to the discovery of survival biomarkers in glioblastoma using a joint analysis of DNA methylation and gene expression. Epigenetics (2014) 0.82
Prioritizing protein complexes implicated in human diseases by network optimization. BMC Syst Biol (2014) 0.78
Transcription factors as readers and effectors of DNA methylation. Nat Rev Genet (2016) 0.78
Whole genome DNA methylation: beyond genes silencing. Oncotarget (2016) 0.78
Conserved and divergent patterns of DNA methylation in higher vertebrates. Genome Biol Evol (2014) 0.76
Epigenetic Mechanisms of the Aging Human Retina. J Exp Neurosci (2016) 0.76
DNA methylation in oligodendroglial cells during developmental myelination and in disease. Neurogenesis (Austin) (2017) 0.75
In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene. Cell Stress Chaperones (2016) 0.75
Genome Wide Methylome Alterations in Lung Cancer. PLoS One (2015) 0.75
Estimating the prevalence of functional exonic splice regulatory information. Hum Genet (2017) 0.75
Alternatively spliced MEFV transcript lacking exon 2 and its protein isoform pyrin-2d implies an epigenetic regulation of the gene in inflammatory cell culture models. Genet Mol Biol (2017) 0.75
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet (2009) 18.90
CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature (2000) 12.97
A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res (2010) 11.42
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet (2009) 10.54
Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81
Quantifying similarity between motifs. Genome Biol (2007) 9.27
The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res (2012) 9.02
Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62
Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science (2010) 8.46
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A (2010) 7.30
Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature (2010) 6.06
Chromatin organization marks exon-intron structure. Nat Struct Mol Biol (2009) 5.90
Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 5.50
Relationship between nucleosome positioning and DNA methylation. Nature (2010) 5.27
Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell (2013) 4.16
Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res (2009) 3.95
Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet (2010) 3.91
Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet (2010) 3.38
Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol (2012) 3.31
Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res (2011) 2.51
Co-transcriptional splicing of constitutive and alternative exons. RNA (2009) 2.29
Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics (2010) 2.11
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife (2013) 1.63
Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res (2011) 1.60
Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics (2011) 1.56
WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes Dev (1998) 1.50
DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res (2013) 1.44
Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol (2009) 1.33
Genome-wide association between DNA methylation and alternative splicing in an invertebrate. BMC Genomics (2012) 1.29
High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One (2012) 1.29
Human epigenome data reveal increased CpG methylation in alternatively spliced sites and putative exonic splicing enhancers. DNA Cell Biol (2011) 1.18
CpG island shore methylation regulates caveolin-1 expression in breast cancer. Oncogene (2012) 1.12
Epigenetic features are significantly associated with alternative splicing. BMC Genomics (2012) 1.11
Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res (2012) 1.04
Hypermethylation of CpG islands and shores around specific microRNAs and mirtrons is associated with the phenotype and presence of bladder cancer. Clin Cancer Res (2010) 1.02
Cell-specific DNA methylation patterns of retina-specific genes. PLoS One (2012) 1.00
Dynamic usage of alternative splicing exons during mouse retina development. Nucleic Acids Res (2011) 0.97
DNA hypermethylation of alternatively spliced and repeat sequences in humans. Mol Genet Genomics (2012) 0.91
Use of laser capture microdissection for analysis of retinal mRNA/miRNA expression and DNA methylation. Methods Mol Biol (2012) 0.88
A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples. Epigenetics Chromatin (2013) 0.87
Adaptation of the CHARM DNA methylation platform for the rat genome reveals novel brain region-specific differences. Epigenetics (2011) 0.84
Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. RNA (2007) 0.82
Tissue-specific expression of IL-15RA alternative splicing transcripts and its regulation by DNA methylation. Eur Cytokine Netw (2010) 0.80
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Toll-like receptor 3 and geographic atrophy in age-related macular degeneration. N Engl J Med (2008) 4.46
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics (2008) 4.36
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Proc Natl Acad Sci U S A (2010) 4.30
Seven new loci associated with age-related macular degeneration. Nat Genet (2013) 3.81
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell (2009) 3.69
A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet (2011) 3.55
TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics (2008) 3.37
Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Proc Natl Acad Sci U S A (2010) 3.33
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Protein analysis on a proteomic scale. Nature (2003) 3.12
Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell (2009) 2.99
Phase 3, randomized, controlled trial of atrasentan in patients with nonmetastatic, hormone-refractory prostate cancer. Cancer (2008) 2.86
Clinical and pathological continuum of multisystem TDP-43 proteinopathies. Arch Neurol (2009) 2.68
Enhancement of cardiac function and suppression of heart failure progression by inhibition of protein phosphatase 1. Circ Res (2005) 2.52
Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res (2006) 2.26
A genomic atlas of mouse hypothalamic development. Nat Neurosci (2010) 2.25
Regulation of gene expression by a metabolic enzyme. Science (2004) 2.15
Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell (2011) 2.10
Pigment epithelium-derived factor suppresses ischemia-induced retinal neovascularization and VEGF-induced migration and growth. Invest Ophthalmol Vis Sci (2002) 2.03
Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration. Hum Mol Genet (2011) 1.98
Gene therapy with brain-derived neurotrophic factor as a protection: retinal ganglion cells in a rat glaucoma model. Invest Ophthalmol Vis Sci (2003) 1.83
Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration. PLoS Genet (2010) 1.83
Caspase activation and amyloid precursor protein cleavage in rat ocular hypertension. Invest Ophthalmol Vis Sci (2002) 1.82
Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A (2004) 1.75
Changes in gene expression in experimental glaucoma and optic nerve transection: the equilibrium between protective and detrimental mechanisms. Invest Ophthalmol Vis Sci (2007) 1.74
Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics (2012) 1.65
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.65
DNA methylation presents distinct binding sites for human transcription factors. Elife (2013) 1.63
Hsp20-engineered mesenchymal stem cells are resistant to oxidative stress via enhanced activation of Akt and increased secretion of growth factors. Stem Cells (2009) 1.60
Novel cardioprotective role of a small heat-shock protein, Hsp20, against ischemia/reperfusion injury. Circulation (2005) 1.60
Construction of human activity-based phosphorylation networks. Mol Syst Biol (2013) 1.59
Inducible expression of vascular endothelial growth factor in adult mice causes severe proliferative retinopathy and retinal detachment. Am J Pathol (2002) 1.59
Fine mapping of chromosome 3 in uveal melanoma: identification of a minimal region of deletion on chromosomal arm 3p25.1-p25.2. Cancer Res (2003) 1.59
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol (2002) 1.59
Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics (2002) 1.58
AAV-mediated gene transfer of pigment epithelium-derived factor inhibits choroidal neovascularization. Invest Ophthalmol Vis Sci (2002) 1.58
A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods (2007) 1.54
Inducible expression of active protein phosphatase-1 inhibitor-1 enhances basal cardiac function and protects against ischemia/reperfusion injury. Circ Res (2009) 1.52
Severe subcortical TDP-43 pathology in sporadic frontotemporal lobar degeneration with motor neuron disease. Acta Neuropathol (2007) 1.51
Oncomodulin links inflammation to optic nerve regeneration. Proc Natl Acad Sci U S A (2009) 1.50
Myelination transition zone astrocytes are constitutively phagocytic and have synuclein dependent reactivity in glaucoma. Proc Natl Acad Sci U S A (2011) 1.47
A model to study differences between primary and secondary degeneration of retinal ganglion cells in rats by partial optic nerve transection. Invest Ophthalmol Vis Sci (2003) 1.46
A splice-site mutation in a retina-specific exon of BBS8 causes nonsyndromic retinitis pigmentosa. Am J Hum Genet (2010) 1.46
Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I. Genes Dev (2003) 1.46
Increased expression of brain-derived neurotrophic factor preserves retinal function and slows cell death from rhodopsin mutation or oxidative damage. J Neurosci (2003) 1.44
Definitions and standardization of a new grading scheme for eyelid contour abnormalities after trichiasis surgery. PLoS Negl Trop Dis (2012) 1.44
Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS One (2010) 1.44
Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe (2011) 1.43
Inducible expression of cre recombinase in the retinal pigmented epithelium. Invest Ophthalmol Vis Sci (2008) 1.41
Analysis of the VMD2 promoter and implication of E-box binding factors in its regulation. J Biol Chem (2004) 1.41
Heat shock protein 20 interacting with phosphorylated Akt reduces doxorubicin-triggered oxidative stress and cardiotoxicity. Circ Res (2008) 1.40
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol (2011) 1.39
The dorsal root ganglion in Friedreich's ataxia. Acta Neuropathol (2009) 1.38
Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species. Proc Natl Acad Sci U S A (2011) 1.38
Functional analysis of cone-rod homeobox (CRX) mutations associated with retinal dystrophy. Hum Mol Genet (2002) 1.37
hPDI: a database of experimental human protein-DNA interactions. Bioinformatics (2009) 1.37
Functional genomic screening identifies dual leucine zipper kinase as a key mediator of retinal ganglion cell death. Proc Natl Acad Sci U S A (2013) 1.36
Analysis of regulatory network topology reveals functionally distinct classes of microRNAs. Nucleic Acids Res (2008) 1.36
Small heat-shock protein Hsp20 attenuates beta-agonist-mediated cardiac remodeling through apoptosis signal-regulating kinase 1. Circ Res (2006) 1.35
RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci U S A (2007) 1.35
The pathology of superficial siderosis of the central nervous system. Acta Neuropathol (2008) 1.34
Identification of gene expression changes associated with the progression of retinal degeneration in the rd1 mouse. Invest Ophthalmol Vis Sci (2004) 1.33
Nonredundant role of Akt2 for neuroprotection of rod photoreceptor cells from light-induced cell death. J Neurosci (2007) 1.33
Effect of CNTF on retinal ganglion cell survival in experimental glaucoma. Invest Ophthalmol Vis Sci (2008) 1.31
Inactivation of the microRNA-183/96/182 cluster results in syndromic retinal degeneration. Proc Natl Acad Sci U S A (2013) 1.31
The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev (2011) 1.30
A functional variant in the CFI gene confers a high risk of age-related macular degeneration. Nat Genet (2013) 1.29
Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology (2008) 1.28
Iron and iron-responsive proteins in the cardiomyopathy of Friedreich's ataxia. Cerebellum (2006) 1.28
The dentate nucleus in Friedreich's ataxia: the role of iron-responsive proteins. Acta Neuropathol (2007) 1.27
Lack of BRAF mutation in primary uveal melanoma. Invest Ophthalmol Vis Sci (2003) 1.26
Vitreous levels of pigment epithelium-derived factor and vascular endothelial growth factor: implications for ocular angiogenesis. Am J Ophthalmol (2004) 1.26
Phase 2 trial of linifanib (ABT-869) in patients with advanced renal cell cancer after sunitinib failure. Eur J Cancer (2011) 1.26
Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat Chem Biol (2012) 1.24
Protein array identification of substrates of the Epstein-Barr virus protein kinase BGLF4. J Virol (2009) 1.21
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors. BMC Bioinformatics (2007) 1.20
Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL. Blood (2010) 1.19
Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol (2009) 1.19