Advanced sequencing technologies: methods and goals.

De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91

The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04

SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96

The colorectal microRNAome. Proc Natl Acad Sci U S A (2006) 11.59

Circulating mutant DNA to assess tumor dynamics. Nat Med (2007) 10.33

The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19

Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res (2009) 6.42

An analysis of the feasibility of short read sequencing. Nucleic Acids Res (2005) 6.10

Challenges and standards in integrating surveys of structural variation. Nat Genet (2007) 6.05

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res (2007) 5.95

Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet (2007) 5.64

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

Genetic design and statistical power of nested association mapping in maize. Genetics (2008) 4.92

Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol (2006) 4.85

Genome engineering. Nat Biotechnol (2009) 4.60

Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res (2005) 3.59

A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J Am Chem Soc (2008) 3.04

Fast DNA sequencing via transverse electronic transport. Nano Lett (2006) 2.90

Crystallizing short-read assemblies around seeds. BMC Bioinformatics (2009) 2.89

Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Res (2007) 2.70

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

Understanding incidental findings in the context of genetics and genomics. J Law Med Ethics (2008) 2.50

Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagn (2008) 2.24

Mass spectrometry tools for the classification and identification of bacteria. Nat Rev Microbiol (2010) 2.18

Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome Res (2006) 2.17

Mayday--integrative analytics for expression data. BMC Bioinformatics (2010) 1.91

Serial analysis of chromatin occupancy identifies beta-catenin target genes in colorectal carcinoma cells. Proc Natl Acad Sci U S A (2007) 1.89

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res (2008) 1.82

Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics (2007) 1.78

Population genetic inference from resequencing data. Genetics (2008) 1.77

Single-molecule, motion-based DNA sequencing using RNA polymerase. Science (2006) 1.69

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

Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett (2010) 1.58

Beyond the Gene Chip. Bell Labs Tech J (2005) 1.57

Inheritance analysis of congenital left ventricular outflow tract obstruction malformations: Segregation, multiplex relative risk, and heritability. Am J Med Genet A (2005) 1.57

Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing. Genome Res (2009) 1.55

The next-generation sequencing technology and application. Protein Cell (2010) 1.52

Targeted massive parallel sequencing: the effective detection of novel causative mutations associated with hearing loss in small families. Orphanet J Rare Dis (2012) 1.49

PieceMaker: selection of DNA fragments for selector-guided multiplex amplification. Nucleic Acids Res (2005) 1.46

Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer. Clin Cancer Res (2015) 1.46

Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res (2006) 1.40

SeqAnt: a web service to rapidly identify and annotate DNA sequence variations. BMC Bioinformatics (2010) 1.36

Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics (2013) 1.36

Microbial shift and periodontitis. Periodontol 2000 (2011) 1.33

Systems biology approaches for the study of multiple sclerosis. J Cell Mol Med (2008) 1.33

Combining microarray-based genomic selection (MGS) with the Illumina Genome Analyzer platform to sequence diploid target regions. Ann Hum Genet (2009) 1.32

Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics (2006) 1.32

Personal genomes in progress: from the human genome project to the personal genome project. Dialogues Clin Neurosci (2010) 1.29

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics (2009) 1.29

An improved allele-specific PCR primer design method for SNP marker analysis and its application. Plant Methods (2012) 1.26

MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics (2009) 1.24

Analyzing schizophrenia by DNA microarrays. Biol Psychiatry (2011) 1.16

Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics (2007) 1.16

Intraspecies sequence comparisons for annotating genomes. Genome Res (2004) 1.15

A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. Nucleic Acids Res (2007) 1.14

Retracted DNA sequencing using electrical conductance measurements of a DNA polymerase. Nat Nanotechnol (2013) 1.12

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

GenePING: secure, scalable management of personal genomic data. BMC Genomics (2006) 1.10

The detection of microRNA associated with Alzheimer's disease in biological fluids using next-generation sequencing technologies. Front Genet (2013) 1.08

Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics (2006) 1.07

Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. J Phys Chem C Nanomater Interfaces (2012) 1.02

Competitive science: is competition ruining science? Infect Immun (2015) 1.01

Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res (2007) 1.01

Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies. Infect Immun (2008) 1.00

Value of a newly sequenced bacterial genome. World J Biol Chem (2014) 0.99

Finding the needles in the metagenome haystack. Microb Ecol (2007) 0.98

Phylogenetics of modern birds in the era of genomics. Proc Biol Sci (2005) 0.98

Estimating RNA editing efficiency of five editing sites in the serotonin 2C receptor by pyrosequencing. RNA (2005) 0.96

Ancient DNA studies: new perspectives on old samples. Genet Sel Evol (2012) 0.95

miRNA profiling for biomarker discovery in multiple sclerosis: from microarray to deep sequencing. J Neuroimmunol (2011) 0.95

A technological update of molecular diagnostics for infectious diseases. Infect Disord Drug Targets (2008) 0.95

Comparison of mating designs for establishing nested association mapping populations in maize and Arabidopsis thaliana. Genetics (2009) 0.91

Disperse--a software system for design of selector probes for exon resequencing applications. Bioinformatics (2009) 0.90

Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. Stat Biosci (2013) 0.89

Multiplex Chromosomal Exome Sequencing Accelerates Identification of ENU-Induced Mutations in the Mouse. G3 (Bethesda) (2012) 0.88

Surface immobilizable chelator for label-free electrical detection of pyrophosphate. Chem Commun (Camb) (2011) 0.87

Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize. Theor Appl Genet (2009) 0.87

Genotyping of Bacillus cereus strains by microarray-based resequencing. PLoS One (2008) 0.87

A fast and accurate SNP detection algorithm for next-generation sequencing data. Nat Commun (2012) 0.86

Determination of primary structure and microheterogeneity of a beta-amyloid plaque-specific antibody using high-performance LC-tandem mass spectrometry. Anal Bioanal Chem (2008) 0.85

Specificity and overlap in gene segment-defined antibody repertoires. BMC Genomics (2005) 0.85

DNA sequencing by denaturation: principle and thermodynamic simulations. Anal Biochem (2008) 0.85

The genetic pleiotropy of musculoskeletal aging. Front Physiol (2012) 0.85

'Finitics'. A plea for biological realism. EMBO Rep (2008) 0.84

Better estimation of protein-DNA interaction parameters improve prediction of functional sites. BMC Biotechnol (2008) 0.84

Dilute-'N'-Go dideoxy sequencing of all DNA strands generated in multiplex LATE-PCR assays. Nucleic Acids Res (2010) 0.83

On the Feasibility of Using the Intrinsic Fluorescence of Nucleotides for DNA Sequencing. J Phys Chem C Nanomater Interfaces (2010) 0.83

Perspectives on an education in computational biology and medicine. Yale J Biol Med (2012) 0.82

Signal transduction: From the atomic age to the post-genomic era. Cold Spring Harb Perspect Biol (2014) 0.82

The future of human cerebral cartography: a novel approach. Philos Trans R Soc Lond B Biol Sci (2015) 0.82

The Metabolic Interplay between Plants and Phytopathogens. Metabolites (2013) 0.82

The positive role of the ecological community in the genomic revolution. Microb Ecol (2007) 0.81

Targeted resequencing of HIV variants by microarray thermodynamics. Nucleic Acids Res (2013) 0.80

Next-generation sequencing for mitochondrial disorders. Br J Pharmacol (2014) 0.80

Transcriptome annotation using tandem SAGE tags. Nucleic Acids Res (2007) 0.80

Applying rapid genome sequencing technologies to characterize pathogen genomes. Anal Chem (2008) 0.80

Enzymatic synthesis of structure-free DNA with pseudo-complementary properties. Nucleic Acids Res (2008) 0.79

DNA sequencing and bar-coding using solid-state nanopores. Electrophoresis (2012) 0.79

Sequence-based linkage analysis. Am J Hum Genet (2004) 0.78

RNA-guided human genome engineering via Cas9. Science (2013) 48.29

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

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

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

Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol (2011) 12.86

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol (2013) 11.35

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18

Clinical assessment incorporating a personal genome. Lancet (2010) 10.18

Modular epistasis in yeast metabolism. Nat Genet (2004) 8.64

Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32

Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A (2003) 7.95

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res (2013) 7.77

Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol (2006) 7.64

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science (2009) 6.96

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

Cas9 as a versatile tool for engineering biology. Nat Methods (2013) 6.87

Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67

From genetic privacy to open consent. Nat Rev Genet (2008) 5.95

Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods (2013) 5.93

The brain activity map project and the challenge of functional connectomics. Neuron (2012) 5.52

Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22

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

A logic-gated nanorobot for targeted transport of molecular payloads. Science (2012) 4.96

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods (2013) 4.61

Genome engineering. Nat Biotechnol (2009) 4.60

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51

Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A (2002) 4.44

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38

Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25

Tuberculosis drug resistance mutation database. PLoS Med (2009) 4.13

Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol (2002) 4.00

Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol (2013) 3.84

Highly multiplexed subcellular RNA sequencing in situ. Science (2014) 3.77

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74

A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A (2012) 3.72

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol (2006) 3.68

Quantification of rare allelic variants from pooled genomic DNA. Nat Methods (2009) 3.66

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61

Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics (2009) 3.50

Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science (2011) 3.49

Bacteria subsisting on antibiotics. Science (2008) 3.47

Information access. Raw personal data: providing access. Science (2014) 3.41

Neuroscience. The brain activity map. Science (2013) 3.36

Generation of functional human hepatic endoderm from human induced pluripotent stem cells. Hepatology (2010) 3.36

The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36

Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol (2002) 3.28

Gene synthesis by circular assembly amplification. Nat Methods (2007) 3.21

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol (2010) 3.14

Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families. PLoS One (2012) 3.11

Photosynthesis genes in marine viruses yield proteins during host infection. Nature (2005) 2.99

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell (2006) 2.99

Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res (2003) 2.97

Reprogramming of T cells from human peripheral blood. Cell Stem Cell (2010) 2.93

Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res (2009) 2.91

The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop. Genet Med (2009) 2.91

The challenges of sequencing by synthesis. Nat Biotechnol (2009) 2.89

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet (2009) 2.78

Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci U S A (2003) 2.77

Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics (2004) 2.76

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res (2002) 2.74

Nanotools for neuroscience and brain activity mapping. ACS Nano (2013) 2.74

Genomically recoded organisms expand biological functions. Science (2013) 2.73

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

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol (2010) 2.68

The amino-acid mutational spectrum of human genetic disease. Genome Biol (2003) 2.55

Towards synthesis of a minimal cell. Mol Syst Biol (2006) 2.55

Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet (2002) 2.52

Regulatory network of acid resistance genes in Escherichia coli. Mol Microbiol (2003) 2.42

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res (2009) 2.38

Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature (2007) 2.27

The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell (2008) 2.19

Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res (2011) 2.12

A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res (2003) 2.10

Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res (2012) 2.09

Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev (2005) 2.06

From systems biology to synthetic biology. Mol Syst Biol (2005) 2.05

Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res (2002) 2.04

Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol (2009) 1.99

An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci (2007) 1.98

Causes and effects of N-terminal codon bias in bacterial genes. Science (2013) 1.95

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat Genet (2006) 1.92

Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol (2011) 1.90

PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics (2006) 1.90

Expression dynamics of a cellular metabolic network. Mol Syst Biol (2005) 1.85

High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res (2010) 1.83

A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PLoS Genet (2010) 1.81

Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods (2008) 1.77

Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics (2008) 1.76

Escherichia coli gene expression responsive to levels of the response regulator EvgA. J Bacteriol (2002) 1.74

Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol (2002) 1.73

Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics (2013) 1.72

Localization to the proteasome is sufficient for degradation. J Biol Chem (2004) 1.72

Long-range polony haplotyping of individual human chromosome molecules. Nat Genet (2006) 1.69