Published in Genome Res on June 01, 2002
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A (2009) 54.68
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
RNA-guided human genome engineering via Cas9. Science (2013) 48.29
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
Strong association of de novo copy number mutations with autism. Science (2007) 27.84
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76
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
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A (2003) 16.58
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics (2010) 13.54
VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52
The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res (2006) 11.60
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res (2011) 11.03
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity (2009) 9.73
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature (2009) 9.47
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (2010) 9.11
The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res (2012) 9.02
Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol (2010) 8.69
Circular RNAs are a large class of animal RNAs with regulatory potency. Nature (2013) 8.54
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
ChromHMM: automating chromatin-state discovery and characterization. Nat Methods (2012) 7.66
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res (2005) 7.09
The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res (2005) 7.06
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93
The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res (2011) 6.88
JBrowse: a next-generation genome browser. Genome Res (2009) 6.77
Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol (2004) 6.67
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
The UCSC Genome Browser database: 2014 update. Nucleic Acids Res (2013) 6.54
Savant: genome browser for high-throughput sequencing data. Bioinformatics (2010) 6.51
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
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res (2005) 6.08
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res (2006) 5.99
ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res (2009) 5.98
The International HapMap Project Web site. Genome Res (2005) 5.96
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
The Ensembl analysis pipeline. Genome Res (2004) 5.90
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics (2011) 5.86
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78
Distinguishing regulatory DNA from neutral sites. Genome Res (2003) 5.63
Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature (2014) 5.61
Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53
Natural mutagenesis of human genomes by endogenous retrotransposons. Cell (2010) 5.50
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Runs of homozygosity in European populations. Am J Hum Genet (2008) 5.34
Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet (2010) 5.26
An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol (2002) 5.24
Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol (2005) 5.19
Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol (2009) 5.14
Identification of conserved regulatory elements by comparative genome analysis. J Biol (2003) 5.11
Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res (2007) 4.89
The UCSC Genome Browser database: 2015 update. Nucleic Acids Res (2014) 4.87
Strategies and tools for whole-genome alignments. Genome Res (2003) 4.86
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83
Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res (2005) 4.81
Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol (2007) 4.80
Clustering and conservation patterns of human microRNAs. Nucleic Acids Res (2005) 4.79
Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science (2012) 4.77
F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (2008) 4.77
Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev (2010) 4.75
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res (2007) 4.73
LINE-1 retrotransposition activity in human genomes. Cell (2010) 4.60
Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat Genet (2007) 4.59
NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma. Cancer Cell (2008) 4.57
Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Nat Genet (2009) 4.56
Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res (2007) 4.52
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
RTCGD: retroviral tagged cancer gene database. Nucleic Acids Res (2004) 4.41
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Nat Genet (2012) 4.37
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Genome sequence of the nematode C. elegans: a platform for investigating biology. Science (1998) 61.48
Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76
Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21
RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res (2001) 45.29
The distributed annotation system. BMC Bioinformatics (2001) 42.98
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature (2001) 42.18
The DNA sequence of human chromosome 22. Nature (1999) 30.88
A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature (1996) 27.61
GenBank. Nucleic Acids Res (1999) 21.47
SGD: Saccharomyces Genome Database. Nucleic Acids Res (1998) 20.26
Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet (1998) 19.35
Ab initio gene finding in Drosophila genomic DNA. Genome Res (2000) 19.23
WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res (2001) 18.52
An STS-based map of the human genome. Science (1995) 17.72
Repbase update: a database and an electronic journal of repetitive elements. Trends Genet (2000) 16.94
The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Res (2000) 14.77
Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev (1999) 14.64
Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet (2000) 14.51
A physical map of 30,000 human genes. Science (1998) 12.43
A physical map of the human genome. Nature (2001) 12.39
Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. Proc Int Conf Intell Syst Mol Biol (1997) 11.52
A generalized hidden Markov model for the recognition of human genes in DNA. Proc Int Conf Intell Syst Mol Biol (1996) 11.45
Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature (2001) 10.96
ACeDB and macace. Methods Cell Biol (1995) 10.64
SAGEmap: a public gene expression resource. Genome Res (2000) 10.41
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res (2000) 10.40
Experimental annotation of the human genome using microarray technology. Nature (2001) 10.39
A public database for gene expression in human cancers. Cancer Res (1999) 8.81
NCBI's LocusLink and RefSeq. Nucleic Acids Res (2000) 8.63
Assembly of the working draft of the human genome with GigAssembler. Genome Res (2001) 8.23
Chemical differentiation along metaphase chromosomes. Exp Cell Res (1968) 6.82
Integrating database homology in a probabilistic gene structure model. Pac Symp Biocomput (1997) 5.96
Mining the draft human genome. Nature (2001) 5.81
Electronic PCR: bridging the gap between genome mapping and genome sequencing. Trends Biotechnol (1998) 5.64
A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome. Nat Genet (2000) 4.78
Getting started with Acedb. Brief Bioinform (2000) 4.65
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
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 accessible chromatin landscape of the human genome. Nature (2012) 16.86
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
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
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
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
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Complete Khoisan and Bantu genomes from southern Africa. Nature (2010) 9.06
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
Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science (2002) 6.52
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
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
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
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature (2013) 5.35
F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (2008) 4.77
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
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
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
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
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 UCSC genome browser and associated tools. Brief Bioinform (2012) 3.29
Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods (2005) 3.21
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
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods (2010) 2.71
The Human Epigenome Browser at Washington University. Nat Methods (2011) 2.62
Classifying G-protein coupled receptors with support vector machines. Bioinformatics (2002) 2.54
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
Human genome ultraconserved elements are ultraselected. Science (2007) 2.34
The DNA sequence and biology of human chromosome 19. Nature (2004) 2.29
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature (2005) 2.27
The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21