Direct detection of DNA methylation during single-molecule, real-time sequencing

scientific article

Direct detection of DNA methylation during single-molecule, real-time sequencing is …
instance of (P31):
scholarly articleQ13442814

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P6179Dimensions Publication ID1032824809
P356DOI10.1038/NMETH.1459
P932PMC publication ID2879396
P698PubMed publication ID20453866
P5875ResearchGate publication ID44583899

P2093author name stringTyson A Clark
Jonas Korlach
Stephen W Turner
Dale R Webster
Eric C Olivares
Benjamin A Flusberg
Jessica H Lee
Kevin J Travers
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A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promotersQ24537436
Genome-scale DNA methylation maps of pluripotent and differentiated cellsQ24621431
Human DNA methylomes at base resolution show widespread epigenomic differencesQ24633677
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Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerasesQ24684192
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CpG islands in vertebrate genomesQ27861045
Targeted mutation of the DNA methyltransferase gene results in embryonic lethalityQ28131773
Real-time DNA sequencing from single polymerase moleculesQ28301519
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencingQ28749183
Zero-Mode Waveguides for Single-Molecule Analysis at High ConcentrationsQ29038289
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DNA methylation and human diseaseQ29615417
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Highly integrated single-base resolution maps of the epigenome in ArabidopsisQ29616098
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Genome-wide high throughput analysis of DNA methylation in eukaryotesQ33379320
X inactivation, differentiation, and DNA methylationQ33999850
Continuous base identification for single-molecule nanopore DNA sequencingQ34016957
Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.Q34135626
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymeraseQ34342518
Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosineQ34625289
Long, processive enzymatic DNA synthesis using 100% dye-labeled terminal phosphate-linked nucleotidesQ34810379
Finding the fifth base: genome-wide sequencing of cytosine methylation.Q37253268
An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kineticsQ38337035
DNA methylation in early developmentQ40934961
Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAsQ41439427
The fundamental role of epigenetic events in cancerQ56421597
DNA methylation: Bisulphite modification and analysisQ61283947
DNA modification mechanisms and gene activity during developmentQ66907977
Chemistry. How are alkynes scrambled?Q95780598
P433issue6
P921main subjectDNA methylationQ874745
P304page(s)461-465
P577publication date2010-05-09
P1433published inNature MethodsQ680640
P1476titleDirect detection of DNA methylation during single-molecule, real-time sequencing
P478volume7

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Q37426790Methylome Analysis of Two Xanthomonas spp. Using Single-Molecule Real-Time Sequencing.
Q35144970Methylome diversification through changes in DNA methyltransferase sequence specificity.
Q34308957Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity.
Q33810504Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics
Q35611139Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection
Q35968766MinION nanopore sequencing of an influenza genome
Q24596678Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
Q26996463Molecular Technologies in the Clinical Diagnostic Laboratory
Q35439695Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition
Q40791674Mutagenesis as a tool in plant genetics, functional genomics, and breeding
Q93052477N 6-Methyladenine DNA Modification in the Woodland Strawberry (Fragaria vesca) Genome Reveals a Positive Relationship With Gene Transcription
Q35714187N(6) -Methyladenine: A Potential Epigenetic Mark in Eukaryotic Genomes
Q28817493N6-Methyladenine: A Conserved and Dynamic DNA Mark
Q58577532N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and Epigenetic Player Implicated in Determination of Stem Cell Fate
Q27022522N6-methyl-adenosine modification in messenger and long non-coding RNA
Q37973257NEW: network-enabled wisdom in biology, medicine, and health care
Q61799723NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
Q35185408Nanogel surface coatings for improved single-molecule imaging substrates.
Q53389437Nanopore sequencing meets epigenetics.
Q34778264Nanopores discriminate among five C5-cytosine variants in DNA
Q26782595New Technologies for Studying Biofilms
Q37651413Next generation DNA sequencing and the future of genomic medicine
Q33803561Next generation sequencing based approaches to epigenomics
Q26781271Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us?
Q89940347Next-Generation Sequencing Technologies in Blood Group Typing
Q26769919Next-generation sequencing as an approach to dairy starter selection
Q34225587Next-generation sequencing technologies for environmental DNA research
Q30712646Next-generation technologies and data analytical approaches for epigenomics
Q90613270No evidence for DNA N 6-methyladenine in mammals
Q92093980Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease
Q64262177Novel Iodine-induced Cleavage Real-time PCR Assay for Accurate Quantification of Phosphorothioate Modified Sites in Bacterial DNA
Q39151211Novel biotechnology approaches in colorectal cancer diagnosis and therapy
Q90185400Novel fluorescently labelled ATP analogues for direct monitoring of ubiquitin activation
Q64269386Novel genetic and epigenetic factors of importance for inter-individual differences in drug disposition, response and toxicity
Q42372152Novel m4C modification in type I restriction-modification systems
Q45323373Now you see it: genome methylation makes a comeback in Drosophila
Q26853112O(6)-methylguanine-DNA methyltransferase in glioma therapy: promise and problems
Q64967673Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria.
Q92876560Omics Analysis for Dinoflagellates Biology Research
Q89599627Opportunities and challenges in long-read sequencing data analysis
Q50506182Ordered genome change of plant and animal body cells revealed by the genome profiling method.
Q57135969Overcoming conservation in TALE-DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-methylcytosine
Q96303251Overcoming evanescent field decay using 3D-tapered nanocavities for on-chip targeted molecular analysis
Q64945578Overview of Next-Generation Sequencing Technologies.
Q41938716Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine
Q30383951OxyR-dependent formation of DNA methylation patterns in OpvABOFF and OpvABON cell lineages of Salmonella enterica.
Q26778958PacBio Sequencing and Its Applications
Q31157538Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine.
Q34341033Perspectives of international human epigenome consortium
Q49917740Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies
Q39157618Phosphate-Modified Nucleotides for Monitoring Enzyme Activity.
Q51164367Piercing the dark matter: bioinformatics of long-range sequencing and mapping.
Q35497720Plant exomics: concepts, applications and methodologies in crop improvement
Q90698448Plasmonic molecular assays: Recent advances and applications for mobile health
Q92653592Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input
Q93014310Population-level inferences from environmental DNA-Current status and future perspectives
Q36532705Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology
Q112755802Production and сharacterization of the exopolysaccharide from strain Paenibacillus polymyxa 2020
Q44849418Proteome variability among Helicobacter pylori isolates clustered according to genomic methylation
Q34955033Protocol matters: which methylome are you actually studying?
Q54343517Pull-down of 5-hydroxymethylcytosine DNA using JBP1-coated magnetic beads.
Q33740701Quality Control of the Traditional Patent Medicine Yimu Wan Based on SMRT Sequencing and DNA Barcoding
Q39195203Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine.
Q85156263Quantitative Trait Loci, Epigenetics, Sugars, and MicroRNAs: Quaternaries in Phosphate Acquisition and Use
Q30648439Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS).
Q43214917REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
Q92161127Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems
Q36001174Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel
Q90521869Realizing the potential of full-length transcriptome sequencing
Q90641525Recent advances in the detection of base modifications using the Nanopore sequencer
Q47282173Recognition of Oxidized 5-Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds
Q37647604Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production
Q35918832Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.
Q54944149Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing.
Q41995617Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.
Q34306123Reversible positioning of single molecules inside zero-mode waveguides
Q41140200SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis
Q29615052STAR: ultrafast universal RNA-seq aligner
Q33742951SUPERFAMILY 1.75 including a domain-centric gene ontology method
Q82313928Search for new genes involved in breast tumorigenesis by "Omics" analysis
Q37792988Selected technologies for measuring acquired genetic damage in humans
Q34154619Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
Q88446504Selective recognition of N4-methylcytosine in DNA by engineered transcription-activator-like effectors
Q34029463Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine.
Q36721299SeqEntropy: genome-wide assessment of repeats for short read sequencing
Q51293201Sequence-specific detection of cytosine methylation in DNA via the FRET mechanism between upconversion nanoparticles and gold nanorods.
Q38248556Sequencing technologies for animal cell culture research
Q24596776Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene
Q30606355Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea
Q36831563Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation
Q37172846Single DNA molecule patterning for high-throughput epigenetic mapping
Q27026725Single molecule and single cell epigenomics.
Q38148450Single molecule methods for the study of catalysis: from enzymes to heterogeneous catalysts.
Q50062948Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics
Q36857904Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships.
Q35813616Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes
Q38648727Single-Molecule Plasmon Sensing: Current Status and Future Prospects
Q30832049Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment
Q38716438Single-base resolution analysis of DNA epigenome via high-throughput sequencing.
Q38811466Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity
Q34497793Single-cell epigenomics: techniques and emerging applications
Q38220440Single-enzyme kinetics with fluorogenic substrates: lessons learnt and future directions.
Q38798182Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications.
Q49849302Single-molecule DNA sequencing: Getting to the bottom of the well
Q45391971Single-molecule detection of 5-hydroxymethylcytosine in DNA through chemical modification and nanopore analysis
Q61800366Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
Q37835470Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes
Q64982556Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA.
Q38256379Statistical methods for detecting differentially methylated loci and regions
Q27027577Stepping stones in DNA sequencing
Q37859094Strategies for DNA methylation analysis in developmental studies
Q36530688Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers
Q92268683Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å
Q61443084Study of the whole genome, methylome and transcriptome of Cordyceps militaris
Q43998243Synthetic polymers and their potential as genetic materials
Q49911969Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Q35096693Systematic genome sequence differences among leaf cells within individual trees
Q35021377TET proteins and the control of cytosine demethylation in cancer
Q53166129Taking the measure of the methylome.
Q84340287Technology: DNA methylation while you sequence
Q34034581Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.
Q38562645Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells.
Q37021634The Amaryllidaceae alkaloids: biosynthesis and methods for enzyme discovery
Q27325530The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius
Q50192087The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius
Q95933791The DNA methylation landscape of giant viruses
Q35085785The DNA methylome
Q40991392The Effects of Dithiothreitol on DNA.
Q28550136The Epigenomic Landscape of Prokaryotes
Q38998285The Helicobacter pylori Methylome: Roles in Gene Regulation and Virulence
Q28086829The Landscape of long noncoding RNA classification
Q92033437The Phylogenetic Relationships of a 4mC/6mA DNA Methyltransferase in Prokaryotes
Q28679295The advantages of SMRT sequencing
Q37651418The application of next generation sequencing in DNA methylation analysis
Q91287194The bacterial epigenome
Q21184012The birth of the Epitranscriptome: deciphering the function of RNA modifications
Q64259784The complete genome and methylome of hpNEAfrica strain HP14039
Q30652520The complete methylome of Helicobacter pylori UM032
Q58782985The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines
Q30572851The complex methylome of the human gastric pathogen Helicobacter pylori
Q64254964The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori
Q36465820The dynamics of DNA methylation in schizophrenia and related psychiatric disorders.
Q37808311The epigenomic interface between genome and environment in common complex diseases
Q37680400The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach
Q35352752The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.
Q36931989The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility
Q43096514The hunt for 5-hydroxymethylcytosine: the sixth base.
Q26774674The impact of next-generation sequencing on the DNA methylation-based translational cancer research
Q33914240The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei
Q24598577The methylomes of six bacteria
Q47307349The non-specific adenine DNA methyltransferase M.EcoGII.
Q35286123The properties and applications of single-molecule DNA sequencing.
Q26778223The sequence of sequencers: The history of sequencing DNA
Q41626758The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.
Q57267334Third generation sequencing: technology and its potential impact on evolutionary biodiversity research
Q35871069Third-generation sequencing techniques and applications to drug discovery
Q85116354Thirteenth AACR Special Conference on Cancer Epigenetics
Q64912239Tissue Culture of Oil Palm: Finding the Balance Between Mass Propagation and Somaclonal Variation.
Q38972400Towards DNA methylation detection using biosensors
Q50667159Tracking genomic hydroxymethylation by the base.
Q55711661Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium.
Q52680258Transposable elements and the multidimensional genome.
Q38143721Type I restriction enzymes and their relatives.
Q64102325Type II Restriction of Bacteriophage DNA With 5hmdU-Derived Base Modifications
Q57459967Type II restriction modification system in Ureaplasma parvum OMC-P162 strain
Q37956118Uncovering the role of 5-hydroxymethylcytosine in the epigenome
Q38167041Understanding posttraumatic stress disorder: insights from the methylome.
Q34253235Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity
Q36222658Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078.
Q64114114Using long-read sequencing to detect imprinted DNA methylation
Q38820366Using nanobiotechnology to increase the prevalence of epigenotyping assays in precision medicine.
Q28391825Validation of high throughput sequencing and microbial forensics applications
Q94545324Vitamin B and Vitamin C Affect DNA Methylation and Amino Acid Metabolism in Mycobacterium bovis BCG
Q36335257When Medicine Meets Engineering-Paradigm Shifts in Diagnostics and Therapeutics
Q41578925Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3
Q46058416Widespread adenine N6-methylation of active genes in fungi.
Q84318747Zeroing in on DNA methylomes with no BS
Q93165954i4mC-Mouse: Improved identification of DNA N4-methylcytosine sites in the mouse genome using multiple encoding schemes
Q100430126i6mA-stack: A stacking ensemble-based computational prediction of DNA N6-methyladenine (6mA) sites in the Rosaceae genome
Q46298862iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties.
Q47557569iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC.
Q36378100methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
Q30870320qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data
Q39057690tRNA biology in the omics era: Stress signalling dynamics and cancer progression

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