Published in Nature on October 28, 2010
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
An integrated map of genetic variation from 1,092 human genomes. Nature (2012) 59.82
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
The variant call format and VCFtools. Bioinformatics (2011) 25.88
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet (2011) 18.88
Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci U S A (2013) 16.74
Biological insights from 108 schizophrenia-associated genetic loci. Nature (2014) 16.13
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med (2013) 15.85
Ensembl 2012. Nucleic Acids Res (2011) 14.55
Systematic localization of common disease-associated variation in regulatory DNA. Science (2012) 14.47
A global reference for human genetic variation. Nature (2015) 12.85
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet (2011) 11.94
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
Widespread RNA and DNA sequence differences in the human transcriptome. Science (2011) 11.45
Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet (2012) 11.29
Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet (2012) 11.09
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res (2011) 11.03
The life history of 21 breast cancers. Cell (2012) 10.59
Architecture of the human regulatory network derived from ENCODE data. Nature (2012) 10.28
Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res (2010) 9.55
Charting a course for genomic medicine from base pairs to bedside. Nature (2011) 9.39
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
Genetic Analysis Workshop 17 mini-exome simulation. BMC Proc (2011) 9.16
Accurate and comprehensive sequencing of personal genomes. Genome Res (2011) 8.99
Variation in genome-wide mutation rates within and between human families. Nat Genet (2011) 8.84
From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics (2013) 8.79
Genotype imputation with thousands of genomes. G3 (Bethesda) (2011) 8.77
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Dindel: accurate indel calls from short-read data. Genome Res (2010) 8.62
Predicting the functional effect of amino acid substitutions and indels. PLoS One (2012) 8.61
Genome partitioning of genetic variation for complex traits using common SNPs. Nat Genet (2011) 8.57
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet (2011) 8.53
Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34
A mosaic activating mutation in AKT1 associated with the Proteus syndrome. N Engl J Med (2011) 8.26
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 8.19
Inference of human population history from individual whole-genome sequences. Nature (2011) 8.05
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
Discovery and refinement of loci associated with lipid levels. Nat Genet (2013) 7.86
Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A (2011) 7.36
Genome structural variation discovery and genotyping. Nat Rev Genet (2011) 7.34
Guidelines for investigating causality of sequence variants in human disease. Nature (2014) 7.30
An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (2012) 7.27
Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet (2013) 7.13
Differential expression in RNA-seq: a matter of depth. Genome Res (2011) 7.13
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res (2011) 6.88
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet (2014) 6.69
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet (2011) 6.67
Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet (2011) 6.59
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet (2011) 6.36
A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry (2012) 6.34
Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A (2011) 6.29
A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet (2013) 6.19
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. PLoS Genet (2012) 6.15
The complete genome sequence of a Neanderthal from the Altai Mountains. Nature (2013) 6.10
Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat Rev Genet (2012) 5.99
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
A decade's perspective on DNA sequencing technology. Nature (2011) 5.61
De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet (2012) 5.61
Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res (2011) 5.60
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet (2011) 5.58
Recent explosive human population growth has resulted in an excess of rare genetic variants. Science (2012) 5.58
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat Genet (2012) 5.55
Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science (2012) 5.50
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Low-coverage sequencing: implications for design of complex trait association studies. Genome Res (2011) 5.34
Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol (2010) 5.32
Differential confounding of rare and common variants in spatially structured populations. Nat Genet (2012) 5.28
Modernizing reference genome assemblies. PLoS Biol (2011) 5.23
Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med (2012) 5.16
ART: a next-generation sequencing read simulator. Bioinformatics (2011) 5.13
A public genome-scale lentiviral expression library of human ORFs. Nat Methods (2011) 4.98
Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells. Nature (2011) 4.92
Inference of population structure using dense haplotype data. PLoS Genet (2012) 4.87
APOL1 genetic variants in focal segmental glomerulosclerosis and HIV-associated nephropathy. J Am Soc Nephrol (2011) 4.80
DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics (2012) 4.79
Allele-specific FKBP5 DNA demethylation mediates gene-childhood trauma interactions. Nat Neurosci (2012) 4.71
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet (2011) 4.67
IFITM3 restricts the morbidity and mortality associated with influenza. Nature (2012) 4.66
Haplotype phasing: existing methods and new developments. Nat Rev Genet (2011) 4.66
Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics (2013) 4.61
Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease. Nat Genet (2014) 4.60
Clan genomics and the complex architecture of human disease. Cell (2011) 4.53
Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One (2012) 4.52
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
A haplotype map of the human genome. Nature (2005) 105.70
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Finding the missing heritability of complex diseases. Nature (2009) 67.95
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature (2001) 42.18
Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40
The hitch-hiking effect of a favourable gene. Genet Res (1974) 34.74
Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30
A map of recent positive selection in the human genome. PLoS Biol (2006) 29.19
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol (2010) 26.41
Population genomics of human gene expression. Nat Genet (2007) 24.49
Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med (2006) 23.83
Origins and functional impact of copy number variation in the human genome. Nature (2009) 23.63
A genome-wide association study of global gene expression. Nat Genet (2007) 22.98
The effect of deleterious mutations on neutral molecular variation. Genetics (1993) 20.07
Genotype imputation. Annu Rev Genomics Hum Genet (2009) 18.64
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science (2009) 16.35
Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science (2010) 16.00
Estimate of the mutation rate per nucleotide in humans. Genetics (2000) 15.08
Genotype imputation for genome-wide association studies. Nat Rev Genet (2010) 14.59
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature (2010) 12.27
SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science (2005) 12.02
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res (2006) 11.60
PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science (2009) 8.72
A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet (2008) 8.64
Dindel: accurate indel calls from short-read data. Genome Res (2010) 8.62
Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat Genet (2010) 8.55
Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Hum Mutat (2003) 8.35
Natural selection has driven population differentiation in modern humans. Nat Genet (2008) 7.48
Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science (2009) 7.35
Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat Genet (1995) 7.19
Mobile elements create structural variation: analysis of a complete human genome. Genome Res (2009) 7.06
Prdm9 controls activation of mammalian recombination hotspots. Science (2009) 7.02
Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med (2010) 6.84
High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res (2010) 5.38
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis. Nat Genet (2010) 4.69
A predominantly neolithic origin for European paternal lineages. PLoS Biol (2010) 4.39
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples. J Mol Evol (2009) 3.47
The theory of discovering rare variants via DNA sequencing. BMC Genomics (2009) 3.12
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
An integrated map of genetic variation from 1,092 human genomes. Nature (2012) 59.82
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science (2007) 51.70
The structure of haplotype blocks in the human genome. Science (2002) 50.88
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science (2007) 43.16
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet (2008) 35.06
Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30
Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet (2008) 30.94
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Biological, clinical and population relevance of 95 loci for blood lipids. Nature (2010) 28.21
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol (2010) 26.41
The variant call format and VCFtools. Bioinformatics (2011) 25.88
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet (2008) 25.83
Efficiency and power in genetic association studies. Nat Genet (2005) 25.56
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet (2010) 23.08
A genome-wide association study of global gene expression. Nat Genet (2007) 22.98
Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat Genet (2008) 22.35
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics (2010) 21.21
Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet (2008) 20.66
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature (2010) 20.01
Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med (2008) 19.71
Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet (2008) 19.55
A HapMap harvest of insights into the genetics of common disease. J Clin Invest (2008) 18.31
New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet (2010) 17.89
Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73
Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet (2006) 17.36
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (2012) 17.12
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet (2008) 16.25
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Replicating genotype-phenotype associations. Nature (2007) 16.11
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet (2008) 15.89
Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med (2013) 15.85
Calibrating a coalescent simulation of human genome sequence variation. Genome Res (2005) 15.04
Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet (2007) 14.99
Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet (2006) 14.76
Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature (2007) 14.43
Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet (2007) 14.37
Genes mirror geography within Europe. Nature (2008) 14.23
Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71
Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med (2010) 13.57
LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics (2010) 13.54
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet (2011) 13.25
Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature (2011) 13.25
A global reference for human genetic variation. Nature (2015) 12.85
Genome-wide association study identifies eight loci associated with blood pressure. Nat Genet (2009) 12.44
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature (2010) 12.27
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med (2007) 12.24
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet (2009) 12.19