Published in Genome Biol on March 27, 2009
Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57
VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (2009) 16.04
Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet (2011) 9.26
Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34
Computational methods for discovering structural variation with next-generation sequencing. Nat Methods (2009) 7.20
Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol (2010) 5.79
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol (2009) 4.80
A primer on metagenomics. PLoS Comput Biol (2010) 4.40
Characterizing and measuring bias in sequence data. Genome Biol (2013) 4.39
Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci U S A (2010) 3.85
Taxonomizing, sizing, and overcoming the incidentalome. Genet Med (2012) 3.82
The theory of discovering rare variants via DNA sequencing. BMC Genomics (2009) 3.12
Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet (2010) 2.98
Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res (2010) 2.84
Towards a comprehensive structural variation map of an individual human genome. Genome Biol (2010) 2.79
Detecting copy number variation with mated short reads. Genome Res (2010) 2.75
Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res (2011) 2.48
RADSeq: next-generation population genetics. Brief Funct Genomics (2010) 2.48
Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet (2016) 2.48
The impact of next-generation sequencing on genomics. J Genet Genomics (2011) 2.41
Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet (2010) 2.39
SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One (2012) 2.37
Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics (2014) 2.37
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev (2011) 2.31
A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol (2010) 1.98
Photosystem I gene cassettes are present in marine virus genomes. Nature (2009) 1.95
Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics (2011) 1.93
Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics (2011) 1.93
Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet (2012) 1.92
EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol (2013) 1.90
Association studies for next-generation sequencing. Genome Res (2011) 1.89
Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front Microbiol (2012) 1.89
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics (2011) 1.88
Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet (2012) 1.75
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ (2015) 1.75
Quantifying adaptive evolution in the Drosophila immune system. PLoS Genet (2009) 1.74
Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences? Nucleic Acids Res (2009) 1.66
Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci (2011) 1.64
A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PLoS Pathog (2011) 1.63
Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One (2011) 1.63
Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics (2011) 1.63
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics (2012) 1.59
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res (2013) 1.56
Modeling read counts for CNV detection in exome sequencing data. Stat Appl Genet Mol Biol (2011) 1.55
Comparison of three targeted enrichment strategies on the SOLiD sequencing platform. PLoS One (2011) 1.55
The next-generation sequencing technology and application. Protein Cell (2010) 1.52
Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet (2013) 1.51
Replication strategies for rare variant complex trait association studies via next-generation sequencing. Am J Hum Genet (2010) 1.51
Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One (2012) 1.51
The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nat Commun (2013) 1.50
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. J Math Biol (2012) 1.49
Graph accordance of next-generation sequence assemblies. Bioinformatics (2011) 1.47
Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One (2014) 1.47
Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res (2011) 1.44
High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A (2011) 1.41
New virologic tools for management of chronic hepatitis B and C. Gastroenterology (2012) 1.41
Improved lower bounds of DNA tags based on a modified genetic algorithm. PLoS One (2015) 1.39
Genome-wide association studies in cancer--current and future directions. Carcinogenesis (2009) 1.39
Reducing the exome search space for mendelian diseases using genetic linkage analysis of exome genotypes. Genome Biol (2011) 1.38
Mapping rare and common causal alleles for complex human diseases. Cell (2011) 1.38
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A (2010) 1.37
Protocol matters: which methylome are you actually studying? Epigenomics (2010) 1.37
Efficient study design for next generation sequencing. Genet Epidemiol (2011) 1.36
A new approach for detecting low-level mutations in next-generation sequence data. Genome Biol (2012) 1.35
Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment. Genome Res (2011) 1.33
Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons. Neuron (2011) 1.32
Finishing bacterial genome assemblies with Mix. BMC Bioinformatics (2013) 1.29
Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS One (2013) 1.28
Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res (2012) 1.27
Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response Signaling asymmetry and an extension of chemical neuroanatomy. Pharmacol Ther (2010) 1.27
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25
An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia. Hum Mutat (2012) 1.25
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol (2010) 1.25
Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing. PLoS One (2010) 1.25
Going deeper: metagenome of a hadopelagic microbial community. PLoS One (2011) 1.23
RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles. BMC Bioinformatics (2011) 1.23
Semi-automated library preparation for high-throughput DNA sequencing platforms. J Biomed Biotechnol (2010) 1.22
Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PLoS One (2010) 1.21
The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process. Nucleic Acids Res (2011) 1.18
Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerström test for nicotine dependence. Neuropsychopharmacology (2010) 1.17
A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics (2010) 1.17
Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol (2015) 1.17
Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol Biol Evol (2011) 1.17
Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males. Am J Med Genet A (2010) 1.16
Read length versus depth of coverage for viral quasispecies reconstruction. PLoS One (2012) 1.16
Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci (2014) 1.15
Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet Med (2011) 1.15
Reference-free validation of short read data. PLoS One (2010) 1.13
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights (2015) 1.13
Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol (2010) 1.12
Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol (2011) 1.11
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics (2013) 1.10
Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics (2011) 1.09
Comparison of the Illumina Genome Analyzer and Roche 454 GS FLX for resequencing of hypertrophic cardiomyopathy-associated genes. J Biomol Tech (2010) 1.09
Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol (2010) 1.08
DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A (1977) 790.54
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
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
Whole-genome sequencing and variant discovery in C. elegans. Nat Methods (2008) 31.92
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73
Repbase update: a database and an electronic journal of repetitive elements. Trends Genet (2000) 16.94
Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11
Next-generation sequencing transforms today's biology. Nat Methods (2007) 11.93
Microarray-based genomic selection for high-throughput resequencing. Nat Methods (2007) 9.62
Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet (2006) 9.04
Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res (2008) 8.01
Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods (2008) 7.50
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res (2008) 5.00
Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet (2004) 3.73
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res (2007) 2.96
Next-generation sequencing: the race is on. Cell (2008) 2.86
Estimating coverage and power for genetic association studies using near-complete variation data. Nat Genet (2008) 2.80
Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet (2006) 2.61
Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat (2005) 2.55
Primer-site SNPs mask mutations. Nat Methods (2007) 1.83
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc (2009) 38.62
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Whole-genome patterns of common DNA variation in three human populations. Science (2005) 21.22
Clopidogrel and aspirin versus aspirin alone for the prevention of atherothrombotic events. N Engl J Med (2006) 18.25
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Human genetic variation and its contribution to complex traits. Nat Rev Genet (2009) 12.11
Early and sustained dual oral antiplatelet therapy following percutaneous coronary intervention: a randomized controlled trial. JAMA (2002) 11.06
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science (2008) 10.90
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet (2005) 9.61
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02
Identification of ALK as a major familial neuroblastoma predisposition gene. Nature (2008) 7.38
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One (2008) 7.16
Mobile elements create structural variation: analysis of a complete human genome. Genome Res (2009) 7.06
Effect of direct-to-consumer genomewide profiling to assess disease risk. N Engl J Med (2011) 6.90
High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet (2005) 6.86
Effect of stromal-cell-derived factor 1 on stem-cell homing and tissue regeneration in ischaemic cardiomyopathy. Lancet (2003) 6.85
Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev (2009) 6.85
Prevalence of conventional risk factors in patients with coronary heart disease. JAMA (2003) 6.84
Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet (2010) 6.79
Genetic variation in an individual human exome. PLoS Genet (2008) 6.68
Standard- vs high-dose clopidogrel based on platelet function testing after percutaneous coronary intervention: the GRAVITAS randomized trial. JAMA (2011) 6.39
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat Genet (2008) 6.06
Prognostic value of myeloperoxidase in patients with chest pain. N Engl J Med (2003) 5.89
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
A prospective, blinded determination of the natural history of aspirin resistance among stable patients with cardiovascular disease. J Am Coll Cardiol (2003) 5.51
Use of antioxidant vitamins for the prevention of cardiovascular disease: meta-analysis of randomised trials. Lancet (2003) 5.34
The gene encoding 5-lipoxygenase activating protein confers risk of myocardial infarction and stroke. Nat Genet (2004) 5.31
Relationship of blood transfusion and clinical outcomes in patients with acute coronary syndromes. JAMA (2004) 5.11
Platelet glycoprotein IIb/IIIa inhibitors in acute coronary syndromes: a meta-analysis of all major randomised clinical trials. Lancet (2002) 5.04
Fine-scale recombination patterns differ between chimpanzees and humans. Nat Genet (2005) 5.00
Implementing genomic medicine in the clinic: the future is here. Genet Med (2013) 4.89
Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol (2009) 4.80
Can mobile health technologies transform health care? JAMA (2013) 4.75
The cardiac mechanical stretch sensor machinery involves a Z disc complex that is defective in a subset of human dilated cardiomyopathy. Cell (2002) 4.72
Critical issues in peripheral arterial disease detection and management: a call to action. Arch Intern Med (2003) 4.72
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
Genetic structure, self-identified race/ethnicity, and confounding in case-control association studies. Am J Hum Genet (2004) 4.51
A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction. Nat Genet (2005) 4.45
SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res (2012) 4.45
An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A (2002) 4.45
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A (2003) 4.36
Protein carbamylation links inflammation, smoking, uremia and atherogenesis. Nat Med (2007) 4.30
Effect of muraglitazar on death and major adverse cardiovascular events in patients with type 2 diabetes mellitus. JAMA (2005) 4.23
Histopathology of pediatric nonalcoholic fatty liver disease. Hepatology (2005) 4.21
An agenda for personalized medicine. Nature (2009) 4.14
Pathway analysis of seven common diseases assessed by genome-wide association. Genomics (2008) 4.11
The dynamic genome of Hydra. Nature (2010) 4.00
Common variants in KCNN3 are associated with lone atrial fibrillation. Nat Genet (2010) 3.97
Mutation of GATA3 in human breast tumors. Oncogene (2004) 3.92
Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91
Accommodating linkage disequilibrium in genetic-association analyses via ridge regression. Am J Hum Genet (2008) 3.86
Generalized genomic distance-based regression methodology for multilocus association analysis. Am J Hum Genet (2006) 3.79
Transgenerational epigenetic instability is a source of novel methylation variants. Science (2011) 3.66
Relationship of paraoxonase 1 (PON1) gene polymorphisms and functional activity with systemic oxidative stress and cardiovascular risk. JAMA (2008) 3.64
A second-generation combined linkage physical map of the human genome. Genome Res (2007) 3.60
Lack of adverse clopidogrel-atorvastatin clinical interaction from secondary analysis of a randomized, placebo-controlled clopidogrel trial. Circulation (2003) 3.38
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. Nat Genet (2010) 3.37
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36
Mutation of MEF2A in an inherited disorder with features of coronary artery disease. Science (2003) 3.34
Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet (2007) 3.29
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
Multicenter validation of the diagnostic accuracy of a blood-based gene expression test for assessing obstructive coronary artery disease in nondiabetic patients. Ann Intern Med (2010) 3.17
Heritability of nonalcoholic fatty liver disease. Gastroenterology (2009) 3.17