Published in Nat Methods on May 09, 2010
STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2012) 25.21
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97
Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol (2010) 9.35
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol (2010) 9.01
Epigenome-wide association studies for common human diseases. Nat Rev Genet (2011) 7.96
Computational solutions to large-scale data management and analysis. Nat Rev Genet (2010) 6.58
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics (2012) 6.16
Comparison of next-generation sequencing systems. J Biomed Biotechnol (2012) 4.56
Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet (2011) 4.25
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev (2011) 4.09
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol (2012) 3.44
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39
SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res (2010) 3.34
The advantages of SMRT sequencing. Genome Biol (2013) 3.33
The methylomes of six bacteria. Nucleic Acids Res (2012) 3.19
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res (2011) 3.18
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res (2014) 2.84
Landscape of next-generation sequencing technologies. Anal Chem (2011) 2.58
Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet (2016) 2.48
Mapping human epigenomes. Cell (2013) 2.44
A twin approach to unraveling epigenetics. Trends Genet (2011) 2.38
The Epigenomic Landscape of Prokaryotes. PLoS Genet (2016) 2.28
Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc Natl Acad Sci U S A (2013) 2.09
Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res (2012) 2.04
The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol (2012) 1.96
Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun (Camb) (2010) 1.93
Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods (2011) 1.90
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res (2010) 1.77
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proc Natl Acad Sci U S A (2013) 1.75
Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships. Microb Genom (2015) 1.72
Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel. Proc Natl Acad Sci U S A (2012) 1.70
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc (2012) 1.66
DNA Methylation on N6-Adenine in C. elegans. Cell (2015) 1.65
Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules. J Am Chem Soc (2010) 1.59
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res (2012) 1.59
Taking the measure of the methylome. Nat Biotechnol (2010) 1.57
PacBio Sequencing and Its Applications. Genomics Proteomics Bioinformatics (2015) 1.57
Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle (2011) 1.55
Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc (2013) 1.54
Type I restriction enzymes and their relatives. Nucleic Acids Res (2013) 1.54
Existing and emerging technologies for tumor genomic profiling. J Clin Oncol (2013) 1.52
Mapping recently identified nucleotide variants in the genome and transcriptome. Nat Biotechnol (2012) 1.51
Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells. Cell Cycle (2011) 1.51
The Landscape of long noncoding RNA classification. Trends Genet (2015) 1.47
Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania. Cell (2012) 1.46
High-throughput sequencing technologies. Mol Cell (2015) 1.42
The dynamics of DNA methylation in schizophrenia and related psychiatric disorders. Neuropsychopharmacology (2012) 1.40
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
The DNA methylome. FEBS Lett (2010) 1.38
Allele-specific methylation in the human genome: implications for genetic studies of complex disease. Epigenetics (2010) 1.37
Protocol matters: which methylome are you actually studying? Epigenomics (2010) 1.37
Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics (2011) 1.35
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32
A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res (2011) 1.32
Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data (2014) 1.30
Entering the era of bacterial epigenomics with single molecule real time DNA sequencing. Curr Opin Microbiol (2013) 1.29
Cellular dynamics of RNA modification. Acc Chem Res (2011) 1.28
Cytidine deaminases: AIDing DNA demethylation? Genes Dev (2010) 1.28
Comparative genomics of the Campylobacter lari group. Genome Biol Evol (2014) 1.26
A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem (2011) 1.26
The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic Acids Res (2013) 1.25
Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC Biol (2013) 1.24
Epigenetics of host-pathogen interactions: the road ahead and the road behind. PLoS Pathog (2012) 1.24
O(6)-methylguanine-DNA methyltransferase in glioma therapy: promise and problems. Biochim Biophys Acta (2012) 1.22
Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases. Inflamm Bowel Dis (2012) 1.22
Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol (2013) 1.21
Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes. Mol Cell (2011) 1.21
Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars. PLoS One (2015) 1.20
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology (2013) 1.19
Human papillomavirus DNA methylation as a potential biomarker for cervical cancer. Cancer Epidemiol Biomarkers Prev (2012) 1.19
Nanopores discriminate among five C5-cytosine variants in DNA. J Am Chem Soc (2014) 1.17
A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling. PLoS One (2012) 1.16
DNA methylation profiling in nanochannels. Biomicrofluidics (2011) 1.14
N6-methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem Sci (2013) 1.13
TET proteins and the control of cytosine demethylation in cancer. Genome Med (2015) 1.13
Direct detection and sequencing of damaged DNA bases. Genome Integr (2011) 1.12
Pull-down of 5-hydroxymethylcytosine DNA using JBP1-coated magnetic beads. Nat Protoc (2012) 1.09
Application of ChIP-Seq and related techniques to the study of immune function. Immunity (2011) 1.09
DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature (2016) 1.08
Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics (2011) 1.08
Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle. Proc Natl Acad Sci U S A (2013) 1.06
Statistical methods for detecting differentially methylated loci and regions. Front Genet (2014) 1.06
Efficient and accurate whole genome assembly and methylome profiling of E. coli. BMC Genomics (2013) 1.05
Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. BMC Genomics (2014) 1.04
Advances in genome-wide DNA methylation analysis. Biotechniques (2010) 1.03
Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5. BMC Genomics (2015) 1.03
DNA sequencing: clinical applications of new DNA sequencing technologies. Circulation (2012) 1.03
Validation of high throughput sequencing and microbial forensics applications. Investig Genet (2014) 1.02
Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet (2015) 1.00
The properties and applications of single-molecule DNA sequencing. Genome Biol (2011) 1.00
Methylome diversification through changes in DNA methyltransferase sequence specificity. PLoS Genet (2014) 0.99
Identification of a selective polymerase enables detection of N(6)-methyladenosine in RNA. J Am Chem Soc (2013) 0.99
The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J (2012) 0.99
Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat Commun (2014) 0.99
The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. Nucleic Acids Res (2014) 0.98
Dissecting DNA hypermethylation in cancer. FEBS Lett (2010) 0.98
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS Comput Biol (2013) 0.97
Analyzing the cancer methylome through targeted bisulfite sequencing. Cancer Lett (2012) 0.96
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (2009) 32.97
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
The fundamental role of epigenetic events in cancer. Nat Rev Genet (2002) 30.05
Real-time DNA sequencing from single polymerase molecules. Science (2008) 29.53
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell (1992) 27.80
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet (2003) 25.57
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science (2009) 18.82
DNA modification mechanisms and gene activity during development. Science (1975) 13.72
Cancer epigenetics comes of age. Nat Genet (1999) 12.63
DNA methylation and human disease. Nat Rev Genet (2005) 12.00
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
X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet (1975) 8.74
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One (2010) 8.10
Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol (2009) 8.09
Zero-mode waveguides for single-molecule analysis at high concentrations. Science (2003) 7.69
Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res (2009) 4.16
Parallel confocal detection of single molecules in real time. Opt Lett (2008) 4.03
Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAs. Biochemistry (1979) 3.91
An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry (1991) 3.86
Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine. Nucleic Acids Res (1997) 3.54
DNA methylation: bisulphite modification and analysis. Nat Protoc (2006) 3.44
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature (2004) 2.68
DNA methylation in early development. Hum Mol Genet (1995) 2.45
Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev (2009) 2.41
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J (2007) 2.22
Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc Natl Acad Sci U S A (2008) 2.12
Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods (2008) 2.07
Long, processive enzymatic DNA synthesis using 100% dye-labeled terminal phosphate-linked nucleotides. Nucleosides Nucleotides Nucleic Acids (2008) 1.52
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods (2013) 31.15
Real-time DNA sequencing from single polymerase molecules. Science (2008) 29.53
HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
The origin of the Haitian cholera outbreak strain. N Engl J Med (2010) 9.85
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med (2011) 9.37
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics (2006) 5.59
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev (2007) 4.75
Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol (2006) 4.63
A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res (2010) 4.48
A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci U S A (2007) 4.35
Parallel confocal detection of single molecules in real time. Opt Lett (2008) 4.03
Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet (2008) 4.01
Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature (2012) 4.01
Real-time tRNA transit on single translating ribosomes at codon resolution. Nature (2010) 3.87
Maternal vitamin D intake during pregnancy and early childhood wheezing. Am J Clin Nutr (2007) 3.40
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39
Genetic architecture of transcript-level variation in humans. Am J Hum Genet (2008) 3.36
Real-time DNA sequencing from single polymerase molecules. Methods Enzymol (2010) 3.34
Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods (2005) 3.21
The methylomes of six bacteria. Nucleic Acids Res (2012) 3.19
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res (2011) 3.18
Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy. Nat Struct Mol Biol (2010) 3.07
Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach. Am J Hum Genet (2007) 3.05
Going beyond five bases in DNA sequencing. Curr Opin Struct Biol (2012) 2.80
Heritability of alternative splicing in the human genome. Genome Res (2007) 2.76
Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res (2014) 2.63
Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One (2008) 2.23
SEQanswers: an open access community for collaboratively decoding genomes. Bioinformatics (2012) 2.20
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J Am Chem Soc (2007) 2.20
Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat Struct Mol Biol (2010) 2.19
Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc Natl Acad Sci U S A (2008) 2.12
The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol (2012) 1.96
Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet (2008) 1.96
Integration specificity of phage phiC31 integrase in the human genome. J Mol Biol (2005) 1.95
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res (2007) 1.94
Genome-wide diversity and selective pressure in the human rhinovirus. Virol J (2007) 1.94
Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A (2010) 1.93
Heterogeneous pathways and timing of factor departure during translation initiation. Nature (2012) 1.91
Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods (2011) 1.90
ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics (2005) 1.88
Exploring functional relationships between components of the gene expression machinery. Nat Struct Mol Biol (2005) 1.87
Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res (2010) 1.84
DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels. Anal Chem (2002) 1.84
Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A (2011) 1.62
The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol (2006) 1.61
In vivo correction of murine hereditary tyrosinemia type I by phiC31 integrase-mediated gene delivery. Mol Ther (2005) 1.59
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res (2012) 1.59
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis. Nucleic Acids Res (2011) 1.56
Long, processive enzymatic DNA synthesis using 100% dye-labeled terminal phosphate-linked nucleotides. Nucleosides Nucleotides Nucleic Acids (2008) 1.52
Low maternal vitamin E intake during pregnancy is associated with asthma in 5-year-old children. Am J Respir Crit Care Med (2006) 1.51
Determining the Mg2+ stoichiometry for folding an RNA metal ion core. J Am Chem Soc (2005) 1.47
Achieving uniform mixing in a microfluidic device: hydrodynamic focusing prior to mixing. Anal Chem (2006) 1.44
Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae. Mol Cell Biol (2002) 1.36
Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res (2011) 1.35
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32
Lung function in infants with cystic fibrosis diagnosed by newborn screening. Am J Respir Crit Care Med (2008) 1.31
Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. J Allergy Clin Immunol (2013) 1.30
Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis. Blood (2009) 1.25
The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic Acids Res (2013) 1.25
Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC Biol (2013) 1.24
Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast. Genome Announc (2013) 1.23
Mutational derivatives of PhiC31 integrase with increased efficiency and specificity. Mol Ther (2008) 1.23
Focal volume confinement by submicrometer-sized fluidic channels. Anal Chem (2004) 1.23
Enhancement of plasmid-mediated gene therapy for muscular dystrophy by directed plasmid integration. Proc Natl Acad Sci U S A (2005) 1.22
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology (2013) 1.19
Nucleofection of muscle-derived stem cells and myoblasts with phiC31 integrase: stable expression of a full-length-dystrophin fusion gene by human myoblasts. Mol Ther (2004) 1.15
Conformational changes of calmodulin upon Ca2+ binding studied with a microfluidic mixer. Proc Natl Acad Sci U S A (2008) 1.13
Direct detection and sequencing of damaged DNA bases. Genome Integr (2011) 1.12
High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence. Proc Natl Acad Sci U S A (2013) 1.11
Measuring the folding transition time of single RNA molecules. Biophys J (2007) 1.09
Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle. Proc Natl Acad Sci U S A (2013) 1.06
First trimester maternal tobacco smoking habits and fetal growth. Thorax (2010) 1.05
Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. BMC Genomics (2014) 1.04
Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC). Opt Express (2013) 1.01
Measuring exhaled nitric oxide levels in adults: the importance of atopy and airway responsiveness. Chest (2004) 1.00
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS Comput Biol (2013) 0.97
Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J Bacteriol (2013) 0.95
The impact of aminoglycosides on the dynamics of translation elongation. Cell Rep (2013) 0.92
Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics (2009) 0.90
Live-cell imaging of single receptor composition using zero-mode waveguide nanostructures. Nano Lett (2012) 0.90
A survey of schoolchildren's exposure to secondhand smoke in Malaysia. BMC Public Health (2011) 0.89