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Ensembl 2014. Nucleic Acids Res (2013) 12.62

The UCSC Genome Browser database: 2014 update. Nucleic Acids Res (2013) 6.54

The UCSC Genome Browser database: 2015 update. Nucleic Acids Res (2014) 4.87

The landscape of long noncoding RNAs in the human transcriptome. Nat Genet (2015) 3.58

Retracted RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet (2013) 2.91

Innate immunity pathways regulate the nephropathy gene Apolipoprotein L1. Kidney Int (2014) 2.83

CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res (2014) 2.59

Emerging patterns of somatic mutations in cancer. Nat Rev Genet (2013) 2.50

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet (2014) 2.38

The UCSC Genome Browser database: 2016 update. Nucleic Acids Res (2015) 2.18

Nuclear lamin stiffness is a barrier to 3D migration, but softness can limit survival. J Cell Biol (2014) 2.01

Gene regulation by the act of long non-coding RNA transcription. BMC Biol (2013) 1.97

Widespread and extensive lengthening of 3' UTRs in the mammalian brain. Genome Res (2013) 1.72

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins. Cell (2015) 1.68

The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res (2012) 1.66

circBase: a database for circular RNAs. RNA (2014) 1.66

Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development. Circulation (2015) 1.60

Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition. Genome Res (2014) 1.49

Natural selection and infectious disease in human populations. Nat Rev Genet (2014) 1.48

RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PLoS Genet (2016) 1.42

HIV latency and integration site placement in five cell-based models. Retrovirology (2013) 1.42

Pathway, in silico and tissue-specific expression quantitative analyses of oesophageal squamous cell carcinoma genome-wide association studies data. Int J Epidemiol (2015) 1.41

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics (2015) 1.40

R-loops induce repressive chromatin marks over mammalian gene terminators. Nature (2014) 1.34

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data. Nucleic Acids Res (2013) 1.33

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res (2014) 1.28

GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics (2013) 1.27

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility. Nat Commun (2015) 1.27

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res (2013) 1.23

C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD. Acta Neuropathol (2014) 1.22

Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. Nat Commun (2015) 1.18

Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet (2015) 1.16

Age-related variations in the methylome associated with gene expression in human monocytes and T cells. Nat Commun (2014) 1.13

Genetic interactions affecting human gene expression identified by variance association mapping. Elife (2014) 1.12

rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res (2013) 1.11

MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells. Proc Natl Acad Sci U S A (2015) 1.11

Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev (2014) 1.09

Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun (2016) 1.08

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events. PLoS Comput Biol (2015) 1.07

Peppy: proteogenomic search software. J Proteome Res (2013) 1.07

Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken. PLoS One (2013) 1.06

Retracted Mutation pattern is an influential factor on functional mutation rates in cancer. Cancer Cell Int (2016) 1.06

Transcriptional divergence and conservation of human and mouse erythropoiesis. Proc Natl Acad Sci U S A (2014) 1.05

Lean Big Data integration in systems biology and systems pharmacology. Trends Pharmacol Sci (2014) 1.05

A chromatin structure-based model accurately predicts DNA replication timing in human cells. Mol Syst Biol (2014) 1.04

Transcriptional regulation by STAT1 and STAT2 in the interferon JAK-STAT pathway. JAKSTAT (2013) 1.04

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature (2014) 1.03

Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci (2013) 1.03

PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res (2013) 1.01

Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. Nat Commun (2015) 1.01

ENCODE data at the ENCODE portal. Nucleic Acids Res (2015) 1.00

Long noncoding RNA PANDA and scaffold-attachment-factor SAFA control senescence entry and exit. Nat Commun (2014) 0.99

Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells. Methods Mol Biol (2014) 0.99

Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network. Cell Rep (2014) 0.99

Genotype to phenotype via network analysis. Curr Opin Genet Dev (2013) 0.99

Genome-wide DNA methylation analysis predicts an epigenetic switch for GATA factor expression in endometriosis. PLoS Genet (2014) 0.98

Methylomics of gene expression in human monocytes. Hum Mol Genet (2013) 0.97

Genome-wide diet-gene interaction analyses for risk of colorectal cancer. PLoS Genet (2014) 0.96

Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels. Nat Genet (2015) 0.95

Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics (2014) 0.94

Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. Diabetes (2015) 0.93

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. Genome Biol (2014) 0.93

Characterization of T gene sequence variants and germline duplications in familial and sporadic chordoma. Hum Genet (2014) 0.92

LKB1 Loss induces characteristic patterns of gene expression in human tumors associated with NRF2 activation and attenuation of PI3K-AKT. J Thorac Oncol (2014) 0.92

Replication of a GWAS signal in a Caucasian population implicates ADD3 in susceptibility to biliary atresia. Hum Genet (2013) 0.92

Germline variants in MRE11/RAD50/NBN complex genes in childhood leukemia. BMC Cancer (2013) 0.91

Morphological and population genomic evidence that human faces have evolved to signal individual identity. Nat Commun (2014) 0.91

Ontology application and use at the ENCODE DCC. Database (Oxford) (2015) 0.91

MYC regulation of cell growth through control of transcription by RNA polymerases I and III. Cold Spring Harb Perspect Med (2014) 0.91

Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition. Epigenetics Chromatin (2013) 0.91

Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A (2014) 0.91

Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis (2014) 0.90

Distinct and separable roles for EZH2 in neurogenic astroglia. Elife (2014) 0.90

Genetic Factors of the Disease Course after Sepsis: A Genome-Wide Study for 28Day Mortality. EBioMedicine (2016) 0.90

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

microRNA-29 negatively regulates EMT regulator N-myc interactor in breast cancer. Mol Cancer (2014) 0.90

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models. PLoS Comput Biol (2015) 0.90

PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. Nucleic Acids Res (2013) 0.89

DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical Atherosclerosis. Circ Cardiovasc Genet (2015) 0.89

Ankylosing spondylitis is associated with the anthrax toxin receptor 2 gene (ANTXR2). Ann Rheum Dis (2014) 0.88

Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res (2015) 0.88

Meta-analysis of loci associated with age at natural menopause in African-American women. Hum Mol Genet (2014) 0.88

Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk. Sci Rep (2016) 0.88

Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes. Epigenetics (2013) 0.88

Vitamin D and the RNA transcriptome: more than mRNA regulation. Front Physiol (2014) 0.88

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. Nucleic Acids Res (2015) 0.87

Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. Nucleic Acids Res (2013) 0.87

Genetics of PICALM expression and Alzheimer's disease. PLoS One (2014) 0.87

Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity. PLoS Genet (2015) 0.87

Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate. Transl Psychiatry (2014) 0.87

Engineered zinc-finger transcription factors activate OCT4 (POU5F1), SOX2, KLF4, c-MYC (MYC) and miR302/367. Nucleic Acids Res (2014) 0.87

The UCSC Genome Browser database: 2017 update. Nucleic Acids Res (2016) 0.87

In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. Cell Rep (2016) 0.86

DCLK1 is a broadly dysregulated target against epithelial-mesenchymal transition, focal adhesion, and stemness in clear cell renal carcinoma. Oncotarget (2015) 0.86

Genetic associations of the interleukin locus at 1q32.1 with clinical outcomes of cutaneous melanoma. J Med Genet (2015) 0.85

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biol (2015) 0.85

Defining the identity of mouse embryonic dermal fibroblasts. Genesis (2016) 0.85

Gender-specific postnatal demethylation and establishment of epigenetic memory. Genes Dev (2015) 0.85

Four Promoters of IRF5 Respond Distinctly to Stimuli and are Affected by Autoimmune-Risk Polymorphisms. Front Immunol (2013) 0.85

Inherited variation in the PARP1 gene and survival from melanoma. Int J Cancer (2014) 0.85

The human genome browser at UCSC. Genome Res (2002) 168.23

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24

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

Ensembl 2012. Nucleic Acids Res (2011) 14.55

NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28

Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

ChromHMM: automating chromatin-state discovery and characterization. Nat Methods (2012) 7.66

The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res (2011) 6.88

ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res (2009) 5.98

Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80

ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res (2010) 4.50

An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15

ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res (2011) 4.00

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol (2010) 3.24

PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85

Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc (2007) 2.69

Retrocopy contributions to the evolution of the human genome. BMC Genomics (2008) 1.95

The human genome browser at UCSC. Genome Res (2002) 168.23

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

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08

Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75

Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49

The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12

Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

International network of cancer genome projects. Nature (2010) 20.35

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

Ultraconserved elements in the human genome. Science (2004) 17.14

The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A (2003) 16.58

The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90

Ensembl 2011. Nucleic Acids Res (2010) 14.68

The UCSC Known Genes. Bioinformatics (2006) 14.67

Ensembl 2012. Nucleic Acids Res (2011) 14.55

Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet (2010) 13.70

Ensembl 2014. Nucleic Acids Res (2013) 12.62

The somatic genomic landscape of glioblastoma. Cell (2013) 11.73

Ensembl 2013. Nucleic Acids Res (2012) 11.70

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12

Ensembl's 10th year. Nucleic Acids Res (2009) 10.82

Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18

Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18

The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res (2012) 9.02

A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (2010) 8.44

Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38

An RNA gene expressed during cortical development evolved rapidly in humans. Nature (2006) 7.23

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05