Sequencing technologies - the next generation.

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05

A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One (2011) 15.19

Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet (2011) 14.29

Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44

Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol (2010) 10.05

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol (2011) 9.60

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res (2010) 9.55

Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet (2010) 9.53

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics (2010) 9.47

Charting a course for genomic medicine from base pairs to bedside. Nature (2011) 9.39

Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol (2012) 8.99

RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96

Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38

Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One (2013) 7.23

Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88

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

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol (2011) 6.54

Statistical analysis of rare sequence variants: an overview of collapsing methods. Genet Epidemiol (2011) 6.18

Next-generation transcriptome assembly. Nat Rev Genet (2011) 5.89

Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Brief Bioinform (2013) 5.67

A decade's perspective on DNA sequencing technology. Nature (2011) 5.61

Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science (2012) 5.50

Adaptive seeds tame genomic sequence comparison. Genome Res (2011) 4.96

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A (2011) 4.68

Haplotype phasing: existing methods and new developments. Nat Rev Genet (2011) 4.66

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics (2011) 4.39

MicroRNA profiling: approaches and considerations. Nat Rev Genet (2012) 4.39

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31

Nanopore sensors for nucleic acid analysis. Nat Nanotechnol (2011) 4.19

FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res (2010) 4.16

Exome sequencing and the genetic basis of complex traits. Nat Genet (2012) 4.11

Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. Leukemia (2013) 3.93

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open (2012) 3.93

The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods (2012) 3.89

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci U S A (2010) 3.85

Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One (2011) 3.74

A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60

Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58

Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet (2010) 3.47

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One (2014) 3.45

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics (2011) 3.42

Effects of the absence of apolipoprotein e on lipoproteins, neurocognitive function, and retinal function. JAMA Neurol (2014) 3.39

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics (2010) 3.32

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res (2010) 3.31

A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol (2012) 3.29

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

A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet (2011) 3.13

Origins, evolution, and phenotypic impact of new genes. Genome Res (2010) 2.98

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics (2014) 2.81

Human-specific transcriptional networks in the brain. Neuron (2012) 2.80

ConDeTri--a content dependent read trimmer for Illumina data. PLoS One (2011) 2.78

Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol (2011) 2.78

Crop genomics: advances and applications. Nat Rev Genet (2011) 2.72

Single cell analysis: the new frontier in 'omics'. Trends Biotechnol (2010) 2.71

Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol (2011) 2.64

Landscape of next-generation sequencing technologies. Anal Chem (2011) 2.58

Revisiting Mendelian disorders through exome sequencing. Hum Genet (2011) 2.57

The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57

Sequencing technologies and genome sequencing. J Appl Genet (2011) 2.52

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet (2012) 2.50

Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet (2016) 2.48

Genome-wide copy number analysis of single cells. Nat Protoc (2012) 2.47

Loss-of-function variants in the genomes of healthy humans. Hum Mol Genet (2010) 2.45

Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell (2010) 2.45

The genetics of asthma and allergic disease: a 21st century perspective. Immunol Rev (2011) 2.44

Metagenomics - a guide from sampling to data analysis. Microb Inform Exp (2012) 2.42

The impact of next-generation sequencing on genomics. J Genet Genomics (2011) 2.41

Cohort Profile: TwinsUK and healthy ageing twin study. Int J Epidemiol (2012) 2.37

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics (2014) 2.37

Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J Clin Endocrinol Metab (2013) 2.34

Viral population analysis and minority-variant detection using short read next-generation sequencing. Philos Trans R Soc Lond B Biol Sci (2013) 2.33

Dual RNA-seq of pathogen and host. Nat Rev Microbiol (2012) 2.32

Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32

Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol (2011) 2.32

Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev (2011) 2.31

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One (2012) 2.31

Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection. PLoS Pathog (2012) 2.30

Efficiency and power as a function of sequence coverage, SNP array density, and imputation. PLoS Comput Biol (2012) 2.29

SDM--a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res (2011) 2.28

The real cost of sequencing: higher than you think! Genome Biol (2011) 2.22

GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics (2012) 2.21

Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces. J Virol (2012) 2.21

Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet (2010) 2.19

Picking up speed: advances in the genetics of primary ciliary dyskinesia. Pediatr Res (2013) 2.17

Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science (2012) 2.14

Molecular spandrels: tests of adaptation at the genetic level. Nat Rev Genet (2011) 2.07

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics (2013) 2.07

Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol (2011) 2.06

Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res (2014) 2.06

Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat Commun (2012) 2.06

Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases. PLoS One (2015) 2.05

Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res (2012) 2.04

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol (2012) 2.04

Molecular genetic testing and the future of clinical genomics. Nat Rev Genet (2013) 2.03

Zebrafish as a model to study cardiac development and human cardiac disease. Cardiovasc Res (2011) 2.03

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology (2012) 1.99

Homozygosity mapping in patients with cone-rod dystrophy: novel mutations and clinical characterizations. Invest Ophthalmol Vis Sci (2010) 1.98

Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21

Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81

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

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

Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13

Large-scale copy number polymorphism in the human genome. Science (2004) 34.64

Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med (2009) 33.09

Whole-genome sequencing and variant discovery in C. elegans. Nat Methods (2008) 31.92

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

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

Real-time DNA sequencing from single polymerase molecules. Science (2008) 29.53

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36

Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31

Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (2007) 23.38

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24

A sequencing method based on real-time pyrophosphate. Science (1998) 21.21

Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91

Origins and Mechanisms of miRNAs and siRNAs. Cell (2009) 20.77

ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97

Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97

Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2006) 18.71

Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73

Evolution and functions of long noncoding RNAs. Cell (2009) 17.54

Short read fragment assembly of bacterial genomes. Genome Res (2007) 15.40

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

Genetic mapping in human disease. Science (2008) 15.12

Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res (2008) 14.90

Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem (1996) 12.94

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A (2003) 12.91

Human genetic variation and its contribution to complex traits. Nat Rev Genet (2009) 12.11

Single-molecule DNA sequencing of a viral genome. Science (2008) 11.66

Emerging technologies in DNA sequencing. Genome Res (2005) 10.64

Microarray-based genomic selection for high-throughput resequencing. Nat Methods (2007) 9.62

Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59

Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol (1999) 9.35

Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44

Single-molecule sequencing of an individual human genome. Nat Biotechnol (2009) 8.35

A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis (2003) 8.29

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

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res (2008) 7.77

Zero-mode waveguides for single-molecule analysis at high concentrations. Science (2003) 7.69

De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res (2008) 7.66

A ligase-mediated gene detection technique. Science (1988) 7.61

Sequence census methods for functional genomics. Nat Methods (2007) 7.38

A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91

How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59

Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods (2009) 6.36

Analysis of one million base pairs of Neanderthal DNA. Nature (2006) 6.17

Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (2009) 5.79

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods (2008) 5.70

Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34

Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci U S A (2003) 5.24

Unique features of a highly pathogenic Campylobacter jejuni strain. Infect Immun (2006) 5.21

Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science (2007) 5.19

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res (2006) 4.93

High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet (2008) 4.86

Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol (2009) 4.80

Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods (2008) 4.71

Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am (2007) 4.66

Direct RNA sequencing. Nature (2009) 4.37

The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science (2009) 4.25

Highly parallel genomic assays. Nat Rev Genet (2006) 4.24

Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol (2009) 3.86

A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc Natl Acad Sci U S A (2008) 3.48

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res (2008) 3.41

Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods (2009) 2.83

Fluorescent in situ sequencing on polymerase colonies. Anal Biochem (2003) 2.70

Enrichment of super-sized resequencing targets from the human genome. Nat Methods (2007) 2.68

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods (2008) 2.61

Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A (2006) 2.58

DNA ligases: structure, reaction mechanism, and function. Chem Rev (2006) 2.57

How to get genomes at one ten-thousandth the cost. Nat Biotechnol (2008) 2.29

DNA sequencing: bench to bedside and beyond. Nucleic Acids Res (2007) 2.25

Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One (2008) 2.24

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics (2008) 2.21

Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates. Nucleic Acids Res (1994) 1.95

A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res (2008) 1.82

Fixing the front end. Nat Biotechnol (2008) 1.70

Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci U S A (2008) 1.64

Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates. Nucleic Acids Res (2007) 1.64

Identification of concomitant infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and biological characterizations. Infect Immun (2008) 1.48

Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum Mol Genet (2008) 1.41

Terminal phosphate labeled nucleotides: synthesis, applications, and linker effect on incorporation by DNA polymerases. Nucleosides Nucleotides Nucleic Acids (2005) 1.38

Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. J Biol Chem (1979) 1.36

A-beta-subtype of ketosis-prone diabetes is not predominantly a monogenic diabetic syndrome. Diabetes Care (2009) 1.34

DNA polymerase fluorescent substrates with reversible 3'-tags. Gene (1994) 1.25

Personal genomes: Standard and pores. Nature (2008) 1.17

Sequencing by Cyclic Ligation and Cleavage (CycLiC) directly on a microarray captured template. Nucleic Acids Res (2008) 1.16

Sequencing in real time. Nat Biotechnol (2009) 1.11