The UCSC genome browser and associated tools.

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

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84

RCircos: an R package for Circos 2D track plots. BMC Bioinformatics (2013) 1.95

DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res (2013) 1.83

Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol (2013) 1.81

Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69

Lagging-strand replication shapes the mutational landscape of the genome. Nature (2015) 1.63

Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL. Nat Cell Biol (2016) 1.51

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nat Biotechnol (2014) 1.48

Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science (2016) 1.41

CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics (2013) 1.33

Human promoters are intrinsically directional. Mol Cell (2015) 1.31

The ensembl regulatory build. Genome Biol (2015) 1.21

miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun (2015) 1.18

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res (2012) 1.17

MOF-associated complexes ensure stem cell identity and Xist repression. Elife (2014) 1.06

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome Res (2014) 1.03

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis. PLoS One (2014) 1.02

dbSUPER: a database of super-enhancers in mouse and human genome. Nucleic Acids Res (2015) 1.02

De novo mutations in the genome organizer CTCF cause intellectual disability. Am J Hum Genet (2013) 1.01

bwtool: a tool for bigWig files. Bioinformatics (2014) 1.01

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells. Genome Biol (2013) 1.00

Kinase-independent role of cyclin D1 in chromosomal instability and mammary tumorigenesis. Oncotarget (2015) 0.96

The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. Front Genet (2013) 0.96

A tour through the transcriptional landscape of platelets. Blood (2014) 0.94

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

CGAT: computational genomics analysis toolkit. Bioinformatics (2014) 0.92

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

HiCPlotter integrates genomic data with interaction matrices. Genome Biol (2015) 0.89

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

HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes. Epigenetics (2015) 0.89

Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell (2015) 0.88

Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. BMC Bioinformatics (2014) 0.88

5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy. J Clin Invest (2014) 0.88

Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. Hum Mol Genet (2013) 0.87

Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia. PLoS Biol (2013) 0.87

Research resource: progesterone receptor targetome underlying mammary gland branching morphogenesis. Mol Endocrinol (2013) 0.87

metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res (2014) 0.86

Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain. Transl Psychiatry (2015) 0.85

Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Res (2014) 0.85

The UCSC Genome Browser: What Every Molecular Biologist Should Know. Curr Protoc Mol Biol (2014) 0.84

High-frequency aberrantly methylated targets in pancreatic adenocarcinoma identified via global DNA methylation analysis using methylCap-seq. Clin Epigenetics (2014) 0.84

Analysis of unannotated equine transcripts identified by mRNA sequencing. PLoS One (2013) 0.84

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nat Genet (2016) 0.84

Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition. Sci Rep (2016) 0.83

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. BMC Genomics (2014) 0.83

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation. Elife (2017) 0.83

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica. BMC Genomics (2015) 0.82

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics (2013) 0.82

Insights into the miRNA regulations in human disease genes. BMC Genomics (2014) 0.82

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants. Am J Hum Genet (2015) 0.81

Estrogen and progesterone together expand murine endometrial epithelial progenitor cells. Stem Cells (2013) 0.81

An integrated analysis of the effects of microRNA and mRNA on esophageal squamous cell carcinoma. Mol Med Rep (2015) 0.81

Nonparametric Bayesian clustering to detect bipolar methylated genomic loci. BMC Bioinformatics (2015) 0.81

Cell-Type Specific Determinants of NRAMP1 Expression in Professional Phagocytes. Biology (Basel) (2013) 0.79

Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma. Clin Epigenetics (2014) 0.79

Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium. Proc Natl Acad Sci U S A (2016) 0.79

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons. BMC Genomics (2014) 0.79

Extensive allele-specific translational regulation in hybrid mice. Mol Syst Biol (2015) 0.79

The vertebrate RCAN gene family: novel insights into evolution, structure and regulation. PLoS One (2014) 0.79

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinformatics (2015) 0.79

GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data. Mol Ther Nucleic Acids (2016) 0.78

Vials: Visualizing Alternative Splicing of Genes. IEEE Trans Vis Comput Graph (2016) 0.78

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. G3 (Bethesda) (2016) 0.78

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data. Genomics Proteomics Bioinformatics (2014) 0.78

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res (2015) 0.78

A polymorphism affecting MYB binding within the promoter of the PDCD4 gene is associated with severe asthma in children. Hum Mutat (2013) 0.78

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research. J Clin Bioinforma (2014) 0.78

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). G3 (Bethesda) (2016) 0.77

Genetic variation of TBX21 gene increases risk of asthma and its severity in Indian children. J Hum Genet (2014) 0.77

Patterns of gene expression and DNA methylation in human fetal and adult liver. BMC Genomics (2015) 0.77

Reassessing ecdysteroidogenic cells from the cell membrane receptors' perspective. Sci Rep (2016) 0.77

Epidaurus: aggregation and integration analysis of prostate cancer epigenome. Nucleic Acids Res (2014) 0.77

Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS One (2016) 0.77

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole Genome Shotgun Sequencing Data. G3 (Bethesda) (2017) 0.76

The human olfactory transcriptome. BMC Genomics (2016) 0.76

Global and disease-associated genetic variation in the human Fanconi anemia gene family. Hum Mol Genet (2014) 0.76

PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. Elife (2016) 0.76

Nicotinic receptors in non-human primates: Analysis of genetic and functional conservation with humans. Neuropharmacology (2015) 0.76

Human RECQ Helicase Pathogenic Variants, Population Variation and "Missing" Diseases. Hum Mutat (2016) 0.76

Flexible approaches for teaching computational genomics in a health information management program. Perspect Health Inf Manag (2013) 0.76

cgmisc: enhanced genome-wide association analyses and visualization. Bioinformatics (2015) 0.76

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. BMC Bioinformatics (2015) 0.76

Regulation of alternative splicing at the single-cell level. Mol Syst Biol (2015) 0.75

DNAism: exploring genomic datasets on the web with Horizon Charts. BMC Bioinformatics (2016) 0.75

Genome Wide Mapping of NR4A Binding Reveals Cooperativity with ETS Factors to Promote Epigenetic Activation of Distal Enhancers in Acute Myeloid Leukemia Cells. PLoS One (2016) 0.75

Identification of Tox chromatin binding properties and downstream targets by DamID-Seq. Genom Data (2016) 0.75

Improved definition of the mouse transcriptome via targeted RNA sequencing. Genome Res (2016) 0.75

GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets. Bioinformatics (2016) 0.75

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. Nucleic Acids Res (2017) 0.75

MPD: multiplex primer design for next-generation targeted sequencing. BMC Bioinformatics (2017) 0.75

Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection. Sci Rep (2016) 0.75

KIF13B establishes a CAV1-enriched microdomain at the ciliary transition zone to promote Sonic hedgehog signalling. Nat Commun (2017) 0.75

NECTAR: a database of codon-centric missense variant annotations. Nucleic Acids Res (2013) 0.75

Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo. PLoS Genet (2016) 0.75

Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. Sci Rep (2016) 0.75

A novel retroviral mutagenesis screen identifies prognostic genes in RUNX1 mediated myeloid leukemogenesis. Oncotarget (2015) 0.75

ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression. Oncotarget (2016) 0.75

Immunodominance of Antibody Recognition of the HIV Envelope V2 Region in Ig-Humanized Mice. J Immunol (2016) 0.75

BLAT-based comparative analysis for transposable elements: BLATCAT. Biomed Res Int (2014) 0.75

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39

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

BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78

dbSNP: the NCBI database of genetic variation. Nucleic Acids Res (2001) 76.97

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Detection of large-scale variation in the human genome. Nat Genet (2004) 49.18

A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81

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

Integrative genomics viewer. Nat Biotechnol (2011) 42.83

The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64

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

The variant call format and VCFtools. Bioinformatics (2011) 25.88

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

Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41

Structural variation in the human genome. Nat Rev Genet (2006) 21.40

Recent segmental duplications in the human genome. Science (2002) 21.30

The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res (2009) 19.70

Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet (2000) 19.33

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

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics (2010) 15.90

The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Res (2000) 14.77

Ensembl 2011. Nucleic Acids Res (2010) 14.68

The UCSC Known Genes. Bioinformatics (2006) 14.67

Ensembl 2012. Nucleic Acids Res (2011) 14.55

The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99

DNA sequencing. A plan to capture human diversity in 1000 genomes. Science (2008) 13.17

McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res (2008) 12.83

A physical map of the human genome. Nature (2001) 12.39

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

The UCSC Genome Browser Database: update 2009. Nucleic Acids Res (2008) 10.31

The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res (2007) 9.75

A copy number variation morbidity map of developmental delay. Nat Genet (2011) 9.58

BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (2010) 9.11

GenBank. Nucleic Acids Res (2010) 8.63

Assembly of the working draft of the human genome with GigAssembler. Genome Res (2001) 8.23

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet (2009) 7.61

The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res (2007) 7.29

Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered (2009) 7.18

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

TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63

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

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res (2003) 4.29

Public data archives for genomic structural variation. Nat Genet (2010) 3.92

GeneTests-GeneClinics: genetic testing information for a growing audience. Hum Mutat (2002) 2.97

Using multiple alignments to improve gene prediction. J Comput Biol (2006) 2.48

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

The UCSC Known Genes. Bioinformatics (2006) 14.67

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

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

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

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

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00

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

Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73

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

28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42

ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol (2003) 6.04

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

A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature (2006) 5.98

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics (2008) 5.46

Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol (2006) 4.63

Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A (2011) 4.55

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

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11

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

Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol (2004) 3.95

Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83

Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68

Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res (2005) 3.59

The ENCODE Project at UC Santa Cruz. Nucleic Acids Res (2006) 3.57

Posttranscriptional crossregulation between Drosha and DGCR8. Cell (2009) 3.54

Comparative recombination rates in the rat, mouse, and human genomes. Genome Res (2004) 3.50

Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res (2004) 3.45

The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Res (2010) 3.37

Forces shaping the fastest evolving regions in the human genome. PLoS Genet (2006) 3.32

The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature (2011) 3.32

The DNA sequence of human chromosome 7. Nature (2003) 3.18

Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proc Natl Acad Sci U S A (2011) 3.10

The UCSC Cancer Genomics Browser. Nat Methods (2009) 3.08

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics (2005) 3.05

The UCSC Proteome Browser. Nucleic Acids Res (2005) 3.03

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A (2007) 3.00

Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics (2003) 2.97

Hotspots of mammalian chromosomal evolution. Genome Biol (2004) 2.92

The structure and evolution of centromeric transition regions within the human genome. Nature (2004) 2.78