The UCSC Genome Browser Database: update 2009.

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

Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58

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

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics (2009) 8.69

The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87

Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature (2009) 7.39

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev (2010) 7.14

Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet (2010) 6.79

JBrowse: a next-generation genome browser. Genome Res (2009) 6.77

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

Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res (2009) 5.09

A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics (2010) 4.68

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

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res (2013) 4.33

ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol (2010) 3.39

The UCSC genome browser and associated tools. Brief Bioinform (2012) 3.29

Massively parallel sequencing and rare disease. Hum Mol Genet (2010) 3.28

Ensembl variation resources. BMC Genomics (2010) 3.17

The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res (2010) 3.15

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol (2011) 3.09

Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res (2010) 2.87

The Microbe browser for comparative genomics. Nucleic Acids Res (2009) 2.71

Large-scale discovery of enhancers from human heart tissue. Nat Genet (2011) 2.70

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res (2010) 2.61

Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. PLoS Biol (2012) 2.29

miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics (2009) 2.22

The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21

MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol (2011) 2.15

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res (2009) 2.11

Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res (2010) 2.08

Endoplasmic reticulum stress-induced transcription factor, CHOP, is crucial for dendritic cell IL-23 expression. Proc Natl Acad Sci U S A (2010) 1.97

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet (2011) 1.83

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res (2012) 1.80

The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics (2010) 1.79

Serum response factor-dependent MicroRNAs regulate gastrointestinal smooth muscle cell phenotypes. Gastroenterology (2011) 1.79

deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Res (2010) 1.77

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome. Hum Mol Genet (2011) 1.74

Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res (2010) 1.73

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol (2010) 1.69

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68

Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A (2011) 1.66

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res (2009) 1.60

Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res (2011) 1.60

The UCSC Genome Browser. Curr Protoc Bioinformatics (2009) 1.59

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One (2009) 1.57

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol (2009) 1.57

Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. BMC Med Genomics (2010) 1.57

Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics (2010) 1.56

Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser. Circ Cardiovasc Genet (2009) 1.53

Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions. Mol Biol Cell (2010) 1.51

Genome-wide analysis of histone modifications in human pancreatic islets. Genome Res (2010) 1.51

Whole-exome sequencing identifies OR2W3 mutation as a cause of autosomal dominant retinitis pigmentosa. Sci Rep (2015) 1.49

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res (2010) 1.48

Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification. PLoS One (2010) 1.42

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics (2012) 1.42

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. BMC Bioinformatics (2010) 1.36

ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res (2009) 1.36

SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res (2010) 1.33

Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells. PLoS Genet (2011) 1.33

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res (2010) 1.32

A multilevel data integration resource for breast cancer study. BMC Syst Biol (2010) 1.32

De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol (2009) 1.31

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation. BMC Genomics (2011) 1.28

Whole-genome SNP association in the horse: identification of a deletion in myosin Va responsible for Lavender Foal Syndrome. PLoS Genet (2010) 1.27

HHMD: the human histone modification database. Nucleic Acids Res (2009) 1.27

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Res (2009) 1.26

Variants affecting exon skipping contribute to complex traits. PLoS Genet (2012) 1.24

Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Res (2011) 1.23

Visualization of shared genomic regions and meiotic recombination in high-density SNP data. PLoS One (2009) 1.23

A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res (2010) 1.22

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. Database (Oxford) (2013) 1.21

Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol (2011) 1.21

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res (2013) 1.20

NGSView: an extensible open source editor for next-generation sequencing data. Bioinformatics (2009) 1.20

Exome sequencing and cis-regulatory mapping identify mutations in MAK, a gene encoding a regulator of ciliary length, as a cause of retinitis pigmentosa. Am J Hum Genet (2011) 1.16

Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21. PLoS One (2011) 1.15

Hematopoietic differentiation of induced pluripotent stem cells from patients with mucopolysaccharidosis type I (Hurler syndrome). Blood (2010) 1.15

Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. PLoS One (2009) 1.15

Alternative translation start sites are conserved in eukaryotic genomes. Nucleic Acids Res (2010) 1.15

Linking genes to diseases: it's all in the data. Genome Med (2009) 1.14

RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Res (2010) 1.13

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PLoS One (2009) 1.13

The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. Philos Trans R Soc Lond B Biol Sci (2013) 1.13

Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics (2011) 1.13

Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A (2009) 1.12

Inferring causative variants in microRNA target sites. Nucleic Acids Res (2011) 1.12

Statistics and truth in phylogenomics. Mol Biol Evol (2011) 1.12

Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues. Nucleic Acids Res (2013) 1.12

Evolution of genomic sequence inhomogeneity at mid-range scales. BMC Genomics (2009) 1.11

Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease. J Clin Invest (2009) 1.10

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. Nucleic Acids Res (2011) 1.08

Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. PLoS One (2011) 1.07

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation. BMC Genomics (2010) 1.06

Expression patterns of intronic microRNAs in Caenorhabditis elegans. Silence (2010) 1.06

Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics (2009) 1.04

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

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

The International HapMap Project. Nature (2003) 73.65

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

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10

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

miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61

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

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 Genome Browser Database. Nucleic Acids Res (2003) 32.84

Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28

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

The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53

Ensembl 2008. Nucleic Acids Res (2007) 20.67

GenBank. Nucleic Acids Res (2007) 16.92

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

The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33

The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04

The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05

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

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

Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03

The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics (2004) 8.40

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

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21

FlyBase: integration and improvements to query tools. Nucleic Acids Res (2007) 5.14

A navigator for human genome epidemiology. Nat Genet (2008) 5.07

The Rat Genome Database, update 2007--easing the path from disease to data and back again. Nucleic Acids Res (2006) 4.80

Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res (2007) 4.30

ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80

WormBase 2007. Nucleic Acids Res (2007) 3.69

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

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res (2006) 3.40

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

Database development in toxicogenomics: issues and efforts. Environ Health Perspect (2004) 2.26

Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol (2007) 2.07

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

The UCSC Genome Browser Database. Nucleic Acids Res (2003) 32.84

Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57

The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci (1996) 19.74

Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A (2000) 19.39

Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics (2000) 13.33

Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31

The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04

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

Improved splice site detection in Genie. J Comput Biol (1997) 11.57

A generalized hidden Markov model for the recognition of human genes in DNA. Proc Int Conf Intell Syst Mol Biol (1996) 11.45

The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05

Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature (2001) 10.96

Using Dirichlet mixture priors to derive hidden Markov models for protein families. Proc Int Conf Intell Syst Mol Biol (1993) 10.73

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

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09

Six widespread bacterial clones among Escherichia coli K1 isolates. Infect Immun (1983) 8.35

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

Genie--gene finding in Drosophila melanogaster. Genome Res (2000) 7.47

Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res (1994) 6.29

Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol (2001) 6.07

Integrating database homology in a probabilistic gene structure model. Pac Symp Biocomput (1997) 5.96

A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res (1994) 5.50

Epidemiology and clonality of community-acquired methicillin-resistant Staphylococcus aureus in Minnesota, 1996-1998. Clin Infect Dis (2001) 5.07

GABA(B) receptors function as a heteromeric assembly of the subunits GABA(B)R1 and GABA(B)R2. Nature (1998) 5.03

Sexual problems among women and men aged 40-80 y: prevalence and correlates identified in the Global Study of Sexual Attitudes and Behaviors. Int J Impot Res (2005) 4.61

Regulation of synaptic responses to high-frequency stimulation and LTP by neurotrophins in the hippocampus. Nature (1996) 4.41

RNA modeling using Gibbs sampling and stochastic context free grammars. Proc Int Conf Intell Syst Mol Biol (1994) 4.32

Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput (2004) 4.25

Strong association between malnutrition, inflammation, and atherosclerosis in chronic renal failure. Kidney Int (1999) 4.25

Acute and subacute stent occlusion; risk-reduction by ionic contrast media. Eur Heart J (2001) 4.02

Renal and intestinal absorptive defects in mice lacking the NHE3 Na+/H+ exchanger. Nat Genet (1998) 3.96

Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA (1999) 3.40

A motivational interviewing intervention to increase fruit and vegetable intake through Black churches: results of the Eat for Life trial. Am J Public Health (2001) 3.37

Comparison of radiation side-effects of conformal and conventional radiotherapy in prostate cancer: a randomised trial. Lancet (1999) 3.16

Aerobic glycolysis during lymphocyte proliferation. Nature (1976) 2.94

The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol (2003) 2.83

Optimally parsing a sequence into different classes based on multiple types of evidence. Proc Int Conf Intell Syst Mol Biol (1994) 2.73

Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol (2004) 2.47

Molecular basis of phenotypic heterogeneity in phenylketonuria. N Engl J Med (1991) 2.40

A let-7 microRNA-binding site polymorphism in 3'-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy. Ann Oncol (2010) 2.39

TLR engagement prevents transplantation tolerance. Am J Transplant (2006) 2.36

Does early responsive parenting have a special importance for children's development or is consistency across early childhood necessary? Dev Psychol (2001) 2.34

Induction of bacteremia in newborn rats by Escherichia coli K1 is correlated with only certain O (lipopolysaccharide) antigen types. Infect Immun (1983) 2.33

Activation of ZAP-70 kinase activity by phosphorylation of tyrosine 493 is required for lymphocyte antigen receptor function. EMBO J (1995) 2.31

A discriminative framework for detecting remote protein homologies. J Comput Biol (2000) 2.30